Lint warnings

bgruening · Oct 17, 2024 · fb0edfb · fb0edfb
1 parent 0130d8f
commit fb0edfb
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Showing 6 changed files with 31 additions and 22 deletions.
diff --git a/tools/rna_tools/infernal/cmalign.xml b/tools/rna_tools/infernal/cmalign.xml
@@ -3,9 +3,9 @@
  <macros>
  <import>macros.xml</import>
  </macros>
+ <expand macro="xrefs"/>
  <expand macro="requirements" />
  <expand macro="stdio" />
- <expand macro="xrefs"/>
  <command>
 <![CDATA[
 
@@ -76,7 +76,7 @@
  </param>
  <when value="db">
  <param name="database" type="select" label="Covariance models">
- <options from_file="infernal.loc">
+ <options from_data_table="infernal.loc">
  <column name="value" index="0"/>
  <column name="name" index="1"/>
  <column name="path" index="2"/>
@@ -105,8 +105,11 @@
  </when>
  </conditional>
  <conditional name="notrunc_opt">
- <param argument="--notrunc" truevalue="" falsevalue="--notrunc" checked="true" type="boolean"
- label="Use truncated alignment algorithm" help=""/>
+ <param argument="--notrunc" truevalue="" falsevalue="--notrunc" type="select"
+ label="Use truncated alignment algorithm">
+ <option value="">Yes</option>
+ <option value="--notrunc">No</option>
+ </param>
  <when value=""></when>
  <when value="--notrunc">
  <param argument="--sub" type="boolean" truevalue="--sub" falsevalue="" checked="false"
@@ -143,8 +146,11 @@
 
  <section name="other_opts" title="Other options">
  <conditional name="mapali_opt">
- <param name="mapali_cond" type="boolean" checked="false"
- label="Read the aligment file that used to build the CM" help="The alignment from the file is held fixed. This allows you to align sequences to a model with cmalign and view them in the context of an existing trusted multiple alignment."/>
+ <param name="mapali_cond" type="select"
+ label="Read the aligment file that used to build the CM" help="The alignment from the file is held fixed. This allows you to align sequences to a model with cmalign and view them in the context of an existing trusted multiple alignment.">
+ <option value="true">Yes</option>
+ <option value="false">No</option>
+ </param>
  <when value="true">
  <param argument="--mapali" type="data" format="fasta"
  label="The aligment file that used to build the CM" help=""/>

diff --git a/tools/rna_tools/infernal/cmbuild.xml b/tools/rna_tools/infernal/cmbuild.xml
@@ -4,9 +4,9 @@
  <import>macros.xml</import>
  </macros>
  <!--parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" merge_outputs="cmfile_outfile"></parallelism-->
+ <expand macro="xrefs"/>
  <expand macro="requirements" />
  <expand macro="stdio" />
- <expand macro="xrefs"/>
  <command>
 <![CDATA[
  cmbuild
@@ -196,19 +196,22 @@
  <option value="--cyk">align with the CYK algorithm</option>
  </param>
 
- <param name="refine_output" truevalue="" falsevalue="" checked="False" type="boolean"
+ <param name="refine_output" truevalue="--refine" falsevalue="" checked="False" type="boolean"
  label="Output the refined alignment file as it is used to build the covariance model" help=""/>
 
  </when>
  </conditional>
 
- <param name="is_summery_output" truevalue="" falsevalue="" checked="False" type="boolean"
+ <param name="is_summery_output" truevalue="-o" falsevalue="" checked="False" type="boolean"
  label="Output a summery file?" help=""/>
 
  <!-- calibrate options -->
  <conditional name="Calibrate">
- <param name="selector" type="boolean" checked="true" label="Calibrate the covariance model"
- help="A CM file must be calibrated with cmcalibrate before it can be used in cmsearch or cmscan. cmcalibrate is very slow. It takes a couple of hours to calibrate a single average sized CM on a single CPU"/>
+ <param name="selector" type="select" label="Calibrate the covariance model"
+ help="A CM file must be calibrated with cmcalibrate before it can be used in cmsearch or cmscan. cmcalibrate is very slow. It takes a couple of hours to calibrate a single average sized CM on a single CPU">
+ <option value="true">Yes</option>
+ <option value="false">No</option>
+ </param>
  <when value="false"/>
  <when value="true">
  <param argument="-L" type="float" value="1.6" min="0.01" max="160" label="Total length of random sequences to search" help="Set random seq length to search in Mb (megabases)"/>
@@ -325,7 +328,7 @@
  </outputs>
 
  <tests>
- <test>
+ <test expect_num_outputs="1">
  <param name="alignment_infile" value="cmbuild_input_tRNA5.sto"/>
  <conditional name="Calibrate">
  <param name="selector" value="true"/>
@@ -338,7 +341,7 @@
  </output>
  </test>
  <!-- Test emax seq parameter -->
- <test>
+ <test expect_num_outputs="1">
  <param name="alignment_infile" value="cmbuild_input_tRNA5.sto"/>
  <conditional name="Calibrate">
  <param name="selector" value="true"/>

diff --git a/tools/rna_tools/infernal/cmpress.xml b/tools/rna_tools/infernal/cmpress.xml
@@ -3,9 +3,9 @@
  <macros>
  <import>macros.xml</import>
  </macros>
+ <expand macro="xrefs"/>
  <expand macro="requirements" />
  <expand macro="stdio" />
- <expand macro="xrefs"/>
  <command detect_errors="aggressive">
 <![CDATA[
  mkdir -p ./cm_model &&
@@ -28,7 +28,7 @@
  </param>
  <when value="db">
  <param name="database" type="select" label="Covariance models">
- <options from_file="infernal.loc">
+ <options from_data_table="infernal.loc">
  <column name="value" index="0"/>
  <column name="name" index="1"/>
  <column name="path" index="2"/>

diff --git a/tools/rna_tools/infernal/cmscan.xml b/tools/rna_tools/infernal/cmscan.xml
@@ -3,9 +3,9 @@
  <macros>
  <import>macros.xml</import>
  </macros>
+ <expand macro="xrefs"/>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
- <expand macro="xrefs"/>
  <command>
 <![CDATA[
  ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
@@ -100,7 +100,7 @@
  </param>
  <when value="db">
  <param name="database" type="select" label="Covariance models">
- <options from_file="infernal.loc">
+ <options from_data_table="infernal.loc">
  <column name="value" index="0"/>
  <column name="name" index="1"/>
  <column name="path" index="2"/>

diff --git a/tools/rna_tools/infernal/cmsearch.xml b/tools/rna_tools/infernal/cmsearch.xml
@@ -4,9 +4,9 @@
  <import>macros.xml</import>
  </macros>
  <!--parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="500" merge_outputs="outfile,multiple_alignment_output"></parallelism-->
+ <expand macro="xrefs"/>
  <expand macro="requirements"/>
  <expand macro="stdio" />
- <expand macro="xrefs"/>
  <command>
 <![CDATA[
  ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
@@ -89,7 +89,7 @@
  </param>
  <when value="db">
  <param name="database" type="select" label="Covariance models">
- <options from_file="infernal.loc">
+ <options from_data_table="infernal.loc">
  <column name="value" index="0"/>
  <column name="name" index="1"/>
  <column name="path" index="2"/>
@@ -243,7 +243,7 @@
 
  </outputs>
  <tests>
- <test>
+ <test expect_num_outputs="1">
  <conditional name="cm_opts">
  <param name="cm_opts_selector" value="histdb"/>
  <param name="cmfile" value="cmsearch_input1.cm"/>

diff --git a/tools/rna_tools/infernal/cmstat.xml b/tools/rna_tools/infernal/cmstat.xml
@@ -3,9 +3,9 @@
  <macros>
  <import>macros.xml</import>
  </macros>
+ <expand macro="xrefs"/>
  <expand macro="requirements"/>
  <expand macro="stdio" />
- <expand macro="xrefs"/>
  <command>
 <![CDATA[
  ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
@@ -32,7 +32,7 @@
  </param>
  <when value="db">
  <param name="database" type="select" label="Covariance models">
- <options from_file="infernal.loc">
+ <options from_data_table="infernal.loc">
  <column name="value" index="0"/>
  <column name="name" index="1"/>
  <column name="path" index="2"/>