diff --git a/pom.xml b/pom.xml
index ac467c9..c8590cb 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,14 +6,14 @@
org.publichealthbioinformatics
irida-plugin-snippy-phylogenomics
- 0.1.0
+ 0.1.1
snippy-phylogenomics
org.publichealthbioinformatics.irida.plugin.snippyphylogenomics.SnippyPhylogenomicsPlugin
- 0.1.0
+ 0.1.1
Dan Fornika
1.0.0
diff --git a/src/main/java/org/publichealthbioinformatics/irida/plugin/snippyphylogenomics/SnippyPhylogenomicsPlugin.java b/src/main/java/org/publichealthbioinformatics/irida/plugin/snippyphylogenomics/SnippyPhylogenomicsPlugin.java
index a3a1d52..b6e35c9 100644
--- a/src/main/java/org/publichealthbioinformatics/irida/plugin/snippyphylogenomics/SnippyPhylogenomicsPlugin.java
+++ b/src/main/java/org/publichealthbioinformatics/irida/plugin/snippyphylogenomics/SnippyPhylogenomicsPlugin.java
@@ -72,14 +72,14 @@ public AnalysisType getAnalysisType() {
* id entry in the irida_workflow.xml file.
*
*
- * {@code 0f42df8e-0e9f-4475-ac15-6e1b3c5ee475}
+ * {@code bd535929-cef1-4d03-9354-61e0d43945d9}
*
*
* @return A {@link UUID} defining the id of this pipeline.
*/
@Override
public UUID getDefaultWorkflowUUID() {
- return UUID.fromString("0f42df8e-0e9f-4475-ac15-6e1b3c5ee475");
+ return UUID.fromString("bd535929-cef1-4d03-9354-61e0d43945d9");
}
/*******************************************************************************
diff --git a/src/main/resources/workflows/0.1.1/irida_workflow.xml b/src/main/resources/workflows/0.1.1/irida_workflow.xml
new file mode 100644
index 0000000..d6d94d6
--- /dev/null
+++ b/src/main/resources/workflows/0.1.1/irida_workflow.xml
@@ -0,0 +1,79 @@
+
+
+ bd535929-cef1-4d03-9354-61e0d43945d9
+ snippy-phylogenomics
+ 0.1.1
+ SNIPPY_PHYLOGENOMICS
+
+ sequence_reads_paired
+ reference
+ false
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ snippy
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 3fe8ef358d66
+
+
+ gubbins
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 637ec5d5368c
+
+
+ snp_sites
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ 5804f786060d
+
+
+ iqtree
+ iuc
+ https://toolshed.g2.bx.psu.edu
+ f97743d52b87
+
+
+
diff --git a/src/main/resources/workflows/0.1.1/irida_workflow_structure.ga b/src/main/resources/workflows/0.1.1/irida_workflow_structure.ga
new file mode 100644
index 0000000..5c87278
--- /dev/null
+++ b/src/main/resources/workflows/0.1.1/irida_workflow_structure.ga
@@ -0,0 +1,507 @@
+{
+ "uuid": "6c4ad5b5-ef14-4ac0-bd9b-417eb637b0e0",
+ "tags": [],
+ "format-version": "0.1",
+ "name": "snippy-phylogenomics",
+ "version": 1,
+ "steps": {
+ "0": {
+ "tool_id": null,
+ "tool_version": null,
+ "outputs": [],
+ "workflow_outputs": [
+ {
+ "output_name": "output",
+ "uuid": "da8d1c51-751d-47fe-9a51-f1d1166f9873",
+ "label": null
+ }
+ ],
+ "input_connections": {},
+ "tool_state": "{\"collection_type\": \"list:paired\", \"name\": \"sequence_reads_paired\"}",
+ "id": 0,
+ "uuid": "06896898-839f-4bae-8388-9022ff53ef1e",
+ "errors": null,
+ "name": "Input dataset collection",
+ "label": "sequence_reads_paired",
+ "inputs": [
+ {
+ "name": "sequence_reads_paired",
+ "description": ""
+ }
+ ],
+ "position": {
+ "top": 336,
+ "left": 181
+ },
+ "annotation": "",
+ "content_id": null,
+ "type": "data_collection_input"
+ },
+ "1": {
+ "tool_id": null,
+ "tool_version": null,
+ "outputs": [],
+ "workflow_outputs": [
+ {
+ "output_name": "output",
+ "uuid": "6d46bf4c-af34-4cb1-ac95-9d1dc7667f5d",
+ "label": null
+ }
+ ],
+ "input_connections": {},
+ "tool_state": "{\"name\": \"reference\"}",
+ "id": 1,
+ "uuid": "9a9ab89c-c2db-46f3-9e02-2f86d603f7c8",
+ "errors": null,
+ "name": "Input dataset",
+ "label": "reference",
+ "inputs": [
+ {
+ "name": "reference",
+ "description": ""
+ }
+ ],
+ "position": {
+ "top": 221,
+ "left": 314.5
+ },
+ "annotation": "",
+ "content_id": null,
+ "type": "data_input"
+ },
+ "2": {
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.4.5+galaxy2",
+ "tool_version": "4.4.5+galaxy2",
+ "outputs": [
+ {
+ "type": "vcf",
+ "name": "snpvcf"
+ },
+ {
+ "type": "tabular",
+ "name": "snptab"
+ },
+ {
+ "type": "zip",
+ "name": "outdir"
+ }
+ ],
+ "workflow_outputs": [],
+ "input_connections": {
+ "reference_source|ref_file": {
+ "output_name": "output",
+ "id": 1
+ },
+ "fastq_input|fastq_input": {
+ "output_name": "output",
+ "id": 0
+ }
+ },
+ "tool_state": "{\"adv\": \"{\\\"bwaopt\\\": \\\"\\\", \\\"mapqual\\\": \\\"60\\\", \\\"mincov\\\": \\\"10\\\", \\\"minfrac\\\": \\\"0.9\\\", \\\"minqual\\\": \\\"100.0\\\", \\\"rename_cons\\\": \\\"false\\\", \\\"rgid\\\": \\\"\\\"}\", \"__page__\": null, \"outputs\": \"[\\\"outvcf\\\", \\\"outtab\\\", \\\"outzip\\\"]\", \"__rerun_remap_job_id__\": null, \"fastq_input\": \"{\\\"__current_case__\\\": 2, \\\"fastq_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired_collection\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 1, \\\"ref_file\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\"}\"}",
+ "id": 2,
+ "tool_shed_repository": {
+ "owner": "iuc",
+ "changeset_revision": "3fe8ef358d66",
+ "name": "snippy",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "uuid": "06a306e1-aea1-4139-8f87-30fc25662625",
+ "errors": null,
+ "name": "snippy",
+ "post_job_actions": {
+ "HideDatasetActionoutdir": {
+ "output_name": "outdir",
+ "action_type": "HideDatasetAction",
+ "action_arguments": {}
+ },
+ "DeleteIntermediatesActionsnpvcf": {
+ "output_name": "snpvcf",
+ "action_type": "DeleteIntermediatesAction",
+ "action_arguments": {}
+ },
+ "HideDatasetActionsnptab": {
+ "output_name": "snptab",
+ "action_type": "HideDatasetAction",
+ "action_arguments": {}
+ },
+ "HideDatasetActionsnpvcf": {
+ "output_name": "snpvcf",
+ "action_type": "HideDatasetAction",
+ "action_arguments": {}
+ }
+ },
+ "label": null,
+ "inputs": [],
+ "position": {
+ "top": 371.5,
+ "left": 457.5
+ },
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.4.5+galaxy2",
+ "type": "tool"
+ },
+ "3": {
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/4.4.5+galaxy2",
+ "tool_version": "4.4.5+galaxy2",
+ "outputs": [
+ {
+ "type": "fasta",
+ "name": "alignment_fasta"
+ }
+ ],
+ "workflow_outputs": [],
+ "input_connections": {
+ "reference_source|ref_file": {
+ "output_name": "output",
+ "id": 1
+ },
+ "indirs": {
+ "output_name": "outdir",
+ "id": 2
+ }
+ },
+ "tool_state": "{\"__page__\": null, \"outputs\": \"[\\\"outaln\\\"]\", \"__rerun_remap_job_id__\": null, \"indirs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 1, \\\"ref_file\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\"}\"}",
+ "id": 3,
+ "tool_shed_repository": {
+ "owner": "iuc",
+ "changeset_revision": "3fe8ef358d66",
+ "name": "snippy",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "uuid": "a9cea341-b168-4470-872b-994a6137dcb2",
+ "errors": null,
+ "name": "snippy-core",
+ "post_job_actions": {
+ "HideDatasetActionalignment_fasta": {
+ "output_name": "alignment_fasta",
+ "action_type": "HideDatasetAction",
+ "action_arguments": {}
+ },
+ "RenameDatasetActionalignment_fasta": {
+ "output_name": "alignment_fasta",
+ "action_type": "RenameDatasetAction",
+ "action_arguments": {
+ "newname": "core_snps_pre_filter.fasta"
+ }
+ }
+ },
+ "label": null,
+ "inputs": [],
+ "position": {
+ "top": 192.5,
+ "left": 795.5
+ },
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/4.4.5+galaxy2",
+ "type": "tool"
+ },
+ "4": {
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_clean_full_aln/4.4.5+galaxy0",
+ "tool_version": "4.4.5+galaxy0",
+ "outputs": [
+ {
+ "type": "fasta",
+ "name": "clean_full_aln"
+ }
+ ],
+ "workflow_outputs": [
+ {
+ "output_name": "clean_full_aln",
+ "uuid": "85f2141d-bf40-4f92-bb71-30fa55502bdf",
+ "label": null
+ }
+ ],
+ "input_connections": {
+ "full_aln": {
+ "output_name": "alignment_fasta",
+ "id": 3
+ }
+ },
+ "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"custom_char\": \"{\\\"__current_case__\\\": 0, \\\"custom_char_selector\\\": \\\"false\\\"}\", \"full_aln\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}",
+ "id": 4,
+ "tool_shed_repository": {
+ "owner": "iuc",
+ "changeset_revision": "3fe8ef358d66",
+ "name": "snippy",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "uuid": "3b5f8cca-ff1b-42da-85f5-b15d86a61c85",
+ "errors": null,
+ "name": "snippy-clean_full_aln",
+ "post_job_actions": {
+ "RenameDatasetActionclean_full_aln": {
+ "output_name": "clean_full_aln",
+ "action_type": "RenameDatasetAction",
+ "action_arguments": {
+ "newname": "core_snps_pre_recomb_filter.fasta"
+ }
+ }
+ },
+ "label": null,
+ "inputs": [],
+ "position": {
+ "top": 373.5,
+ "left": 797
+ },
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_clean_full_aln/4.4.5+galaxy0",
+ "type": "tool"
+ },
+ "5": {
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/0.1.0",
+ "tool_version": "0.1.0",
+ "outputs": [
+ {
+ "type": "gff3",
+ "name": "recomb_pred_gff"
+ },
+ {
+ "type": "fasta",
+ "name": "filt_polymorph_fna"
+ },
+ {
+ "type": "vcf",
+ "name": "sum_snp_vcf"
+ }
+ ],
+ "workflow_outputs": [
+ {
+ "output_name": "recomb_pred_gff",
+ "uuid": "3898caa7-a07f-4791-9d21-eddca257aafc",
+ "label": null
+ }
+ ],
+ "input_connections": {
+ "alignment_file": {
+ "output_name": "clean_full_aln",
+ "id": 4
+ }
+ },
+ "tool_state": "{\"adv\": \"{\\\"conv_meth\\\": \\\"weighted_robinson_foulds\\\", \\\"iters\\\": \\\"5\\\", \\\"outgroup\\\": \\\"\\\"}\", \"__page__\": null, \"really_adv\": \"{\\\"filter_percentage\\\": \\\"25\\\", \\\"max_window_size\\\": \\\"10000\\\", \\\"min_snps\\\": \\\"3\\\", \\\"min_window_size\\\": \\\"100\\\", \\\"remove_duplicates\\\": \\\"false\\\", \\\"tree_builder\\\": \\\"raxml\\\"}\", \"__rerun_remap_job_id__\": null, \"alignment_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"outfiles\": \"[\\\"gff\\\", \\\"vcf\\\", \\\"fpoly\\\"]\"}",
+ "id": 5,
+ "tool_shed_repository": {
+ "owner": "iuc",
+ "changeset_revision": "637ec5d5368c",
+ "name": "gubbins",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
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+ "post_job_actions": {
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+ "output_name": "recomb_pred_gff",
+ "action_type": "RenameDatasetAction",
+ "action_arguments": {
+ "newname": "predicted_recombinant_sites.gff"
+ }
+ },
+ "HideDatasetActionsum_snp_vcf": {
+ "output_name": "sum_snp_vcf",
+ "action_type": "HideDatasetAction",
+ "action_arguments": {}
+ },
+ "HideDatasetActionfilt_polymorph_fna": {
+ "output_name": "filt_polymorph_fna",
+ "action_type": "HideDatasetAction",
+ "action_arguments": {}
+ }
+ },
+ "label": null,
+ "inputs": [],
+ "position": {
+ "top": 536.5,
+ "left": 800.5
+ },
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/0.1.0",
+ "type": "tool"
+ },
+ "6": {
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0",
+ "tool_version": "2.5.1+galaxy0",
+ "outputs": [
+ {
+ "type": "fasta",
+ "name": "output_fasta"
+ }
+ ],
+ "workflow_outputs": [
+ {
+ "output_name": "output_fasta",
+ "uuid": "3e062429-6aa3-4259-8cd8-3dbdb7a38e43",
+ "label": null
+ }
+ ],
+ "input_connections": {
+ "input_fasta": {
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+ "id": 5
+ }
+ },
+ "tool_state": "{\"input_fasta\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"out_type\": \"{\\\"__current_case__\\\": 0, \\\"b\\\": \\\"false\\\", \\\"c\\\": \\\"false\\\", \\\"formats\\\": [\\\"-m\\\"], \\\"ot_select\\\": \\\"alignment\\\"}\", \"__page__\": null}",
+ "id": 6,
+ "tool_shed_repository": {
+ "owner": "iuc",
+ "changeset_revision": "5804f786060d",
+ "name": "snp_sites",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "uuid": "e5872aa0-4c49-4305-91ea-947351bd4375",
+ "errors": null,
+ "name": "Finds SNP sites",
+ "post_job_actions": {
+ "RenameDatasetActionoutput_fasta": {
+ "output_name": "output_fasta",
+ "action_type": "RenameDatasetAction",
+ "action_arguments": {
+ "newname": "core_snps_post_recomb_filter.fasta"
+ }
+ }
+ },
+ "label": null,
+ "inputs": [],
+ "position": {
+ "top": 772,
+ "left": 800.5
+ },
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snp_sites/snp_sites/2.5.1+galaxy0",
+ "type": "tool"
+ },
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+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.3",
+ "tool_version": "1.5.5.3",
+ "outputs": [
+ {
+ "type": "nhx",
+ "name": "bionj"
+ },
+ {
+ "type": "nhx",
+ "name": "treefile"
+ },
+ {
+ "type": "nhx",
+ "name": "contree"
+ },
+ {
+ "type": "mldist",
+ "name": "mldist"
+ },
+ {
+ "type": "nex",
+ "name": "splits.nex"
+ },
+ {
+ "type": "iqtree",
+ "name": "iqtree"
+ }
+ ],
+ "workflow_outputs": [
+ {
+ "output_name": "iqtree",
+ "uuid": "ee1b66aa-c4a8-4a14-a9cf-752fe5e8ad88",
+ "label": null
+ },
+ {
+ "output_name": "mldist",
+ "uuid": "9620a86f-e574-48ed-8ee8-14cd673d2f9a",
+ "label": null
+ },
+ {
+ "output_name": "treefile",
+ "uuid": "df766ed3-11a0-4e7f-826a-c00de7f6708c",
+ "label": null
+ }
+ ],
+ "input_connections": {
+ "general_options|s": {
+ "output_name": "output_fasta",
+ "id": 6
+ }
+ },
+ "tool_state": "{\"__page__\": null, \"general_options\": \"{\\\"keep_ident\\\": \\\"false\\\", \\\"s\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"safe\\\": \\\"false\\\", \\\"seed\\\": \\\"\\\", \\\"short_alignments\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"st\\\": \\\"DNA\\\", \\\"t\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"te\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"modelling_parameters\": \"{\\\"automatic_model\\\": {\\\"cmax\\\": \\\"10\\\", \\\"cmin\\\": \\\"2\\\", \\\"cond_model\\\": {\\\"__current_case__\\\": 0, \\\"m\\\": \\\"GTR+G+ASC\\\", \\\"opt_custommodel\\\": \\\"true\\\"}, \\\"madd\\\": \\\"\\\", \\\"mdef\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"merit\\\": \\\"AIC\\\", \\\"mfreq\\\": \\\"\\\", \\\"mrate\\\": \\\"\\\", \\\"mset\\\": \\\"\\\", \\\"msub\\\": \\\"nuclear\\\", \\\"mtree\\\": \\\"false\\\", \\\"rcluster\\\": \\\"\\\"}, \\\"partition_model\\\": {\\\"q\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"spp\\\": \\\"false\\\"}, \\\"rate_heterogeneity\\\": {\\\"a\\\": \\\"\\\", \\\"gmedian\\\": \\\"false\\\", \\\"i\\\": \\\"\\\", \\\"opt_gamma_inv\\\": \\\"false\\\", \\\"wsr\\\": \\\"false\\\"}, \\\"site_specific_frequency\\\": {\\\"fmax\\\": \\\"false\\\", \\\"fs\\\": \\\"\\\", \\\"ft\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"specifying_substitution\\\": {\\\"mwopt\\\": \\\"false\\\"}}\", \"bootstrap_parameters\": \"{\\\"nonparametric_bootstrap\\\": {\\\"b\\\": \\\"\\\", \\\"bc\\\": \\\"false\\\", \\\"bo\\\": \\\"false\\\"}, \\\"ultrafast_bootstrap\\\": {\\\"bb\\\": \\\"\\\", \\\"bcor\\\": \\\"0.99\\\", \\\"beps\\\": \\\"0.5\\\", \\\"bnni\\\": \\\"false\\\", \\\"bspec\\\": \\\"\\\", \\\"nm\\\": \\\"1000\\\", \\\"nstep\\\": \\\"100\\\", \\\"wbt\\\": \\\"false\\\", \\\"wbtl\\\": \\\"false\\\"}}\", \"miscellaneous_options\": \"{\\\"fconst\\\": \\\"\\\"}\", \"likelihood_mapping\": \"{\\\"lmap\\\": \\\"\\\", \\\"lmclust\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"wql\\\": \\\"false\\\"}\", \"tree_parameters\": \"{\\\"computing_robinson_foulds\\\": {\\\"rf\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"rf_adj\\\": \\\"false\\\", \\\"rf_all\\\": \\\"false\\\"}, \\\"constructing_consensus\\\": {\\\"bi\\\": \\\"\\\", \\\"con\\\": \\\"false\\\", \\\"minsup\\\": \\\"0.0\\\", \\\"net\\\": \\\"false\\\", \\\"sup\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"suptag\\\": \\\"\\\"}, \\\"generating_random\\\": {\\\"r\\\": \\\"\\\", \\\"rbal\\\": \\\"false\\\", \\\"rcat\\\": \\\"false\\\", \\\"rcsg\\\": \\\"false\\\", \\\"rlen\\\": \\\"\\\", \\\"ru\\\": \\\"false\\\"}, \\\"single_branch\\\": {\\\"abayes\\\": \\\"false\\\", \\\"alrt\\\": \\\"\\\", \\\"lbp\\\": \\\"\\\"}, \\\"tree_search\\\": {\\\"allnni\\\": \\\"false\\\", \\\"djc\\\": \\\"false\\\", \\\"g\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"n\\\": \\\"\\\", \\\"nbest\\\": \\\"5\\\", \\\"ninit\\\": \\\"100\\\", \\\"nstop\\\": \\\"100\\\", \\\"ntop\\\": \\\"20\\\", \\\"pers\\\": \\\"0.5\\\", \\\"sprrad\\\": \\\"6\\\"}, \\\"tree_topology\\\": {\\\"au\\\": \\\"false\\\", \\\"z\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"zb\\\": \\\"\\\", \\\"zw\\\": \\\"false\\\"}}\"}",
+ "id": 7,
+ "tool_shed_repository": {
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+ "name": "iqtree",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
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+ "errors": null,
+ "name": "IQ-TREE",
+ "post_job_actions": {
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+ "action_type": "HideDatasetAction",
+ "action_arguments": {}
+ },
+ "RenameDatasetActioniqtree": {
+ "output_name": "iqtree",
+ "action_type": "RenameDatasetAction",
+ "action_arguments": {
+ "newname": "tree_report.txt"
+ }
+ },
+ "RenameDatasetActiontreefile": {
+ "output_name": "treefile",
+ "action_type": "RenameDatasetAction",
+ "action_arguments": {
+ "newname": "max_likelihood_tree.newick"
+ }
+ },
+ "HideDatasetActioncontree": {
+ "output_name": "contree",
+ "action_type": "HideDatasetAction",
+ "action_arguments": {}
+ },
+ "HideDatasetActionsplits.nex": {
+ "output_name": "splits.nex",
+ "action_type": "HideDatasetAction",
+ "action_arguments": {}
+ },
+ "RenameDatasetActionmldist": {
+ "output_name": "mldist",
+ "action_type": "RenameDatasetAction",
+ "action_arguments": {
+ "newname": "distance_matrix.txt"
+ }
+ }
+ },
+ "label": null,
+ "inputs": [
+ {
+ "name": "general_options",
+ "description": "runtime parameter for tool IQ-TREE"
+ },
+ {
+ "name": "general_options",
+ "description": "runtime parameter for tool IQ-TREE"
+ },
+ {
+ "name": "general_options",
+ "description": "runtime parameter for tool IQ-TREE"
+ },
+ {
+ "name": "general_options",
+ "description": "runtime parameter for tool IQ-TREE"
+ },
+ {
+ "name": "likelihood_mapping",
+ "description": "runtime parameter for tool IQ-TREE"
+ }
+ ],
+ "position": {
+ "top": 196.5,
+ "left": 1184.5
+ },
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.3",
+ "type": "tool"
+ }
+ },
+ "annotation": "",
+ "a_galaxy_workflow": "true"
+}
diff --git a/src/main/resources/workflows/0.1.1/messages_en.properties b/src/main/resources/workflows/0.1.1/messages_en.properties
new file mode 100644
index 0000000..342590a
--- /dev/null
+++ b/src/main/resources/workflows/0.1.1/messages_en.properties
@@ -0,0 +1,27 @@
+#Pipeline Info Properties
+#Fri Jan 31 13:50:04 PST 2020
+workflow.label.share-analysis-samples.SNIPPY_PHYLOGENOMICS=Save Results to Project Line List Metadata
+workflow.SNIPPY_PHYLOGENOMICS.title=Snippy Phylogenomics Pipeline
+workflow.SNIPPY_PHYLOGENOMICS.description=Call core genome SNPs with Snippy, identify recombination with Gubbins and build a maximum likelihood tree with IQ-TREE
+pipeline.title.snippy-phylogenomics=Pipelines - Snippy Phylogenomics
+pipeline.parameters.modal-title.snippy-phylogenomics=Snippy Phylogenomics Pipeline Parameters
+pipeline.h1.snippy-phylogenomics=Snippy Phylogenomics Pipeline
+
+#Tool Parameters - Tool: snippy - Workflow Step #: 2
+#Fri Jan 31 13:50:04 PST 2020
+pipeline.parameters.snippy-phylogenomics.snippy-2-adv.mincov=Snippy: Minimum coverage of variant site
+pipeline.parameters.snippy-phylogenomics.snippy-2-adv.minfrac=Snippy: Minumum allele fraction for variant evidence
+pipeline.parameters.snippy-phylogenomics.snippy-2-adv.mapqual=Snippy: Minimum mapping quality to allow
+pipeline.parameters.snippy-phylogenomics.snippy-2-adv.minqual=Snippy: Minimum variant quality to allow
+
+#Tool Parameters - Tool: gubbins - Workflow Step #: 5
+#Fri Jan 31 13:50:04 PST 2020
+pipeline.parameters.snippy-phylogenomics.gubbins-5-really_adv.min_window_size=Gubbins: Minimum Window Size
+pipeline.parameters.snippy-phylogenomics.gubbins-5-really_adv.min_snps=Gubbins: Minimum SNPS
+pipeline.parameters.snippy-phylogenomics.gubbins-5-really_adv.max_window_size=Gubbins: Maximum Window Size
+pipeline.parameters.snippy-phylogenomics.gubbins-5-really_adv.filter_percentage=Gubbins: Filter Percentage
+
+#Tool Parameters - Tool: iqtree - Workflow Step #: 7
+#Fri Jan 31 13:50:04 PST 2020
+pipeline.parameters.snippy-phylogenomics.iqtree-7-modelling_parameters.automatic_model.cond_model.m=Tree Model
+pipeline.parameters.snippy-phylogenomics.iqtree-8-general_options.short_alignments=Short Alignments