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bgruening · Aug 31, 2023 · 2696517 · 2696517
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Showing 2 changed files with 9 additions and 5 deletions.
diff --git a/tools/rna_tools/sortmerna/macros.xml b/tools/rna_tools/sortmerna/macros.xml
@@ -8,8 +8,8 @@
  </requirements>
  </xml>
  <xml name="db_prep">
- <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
- <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored (--max_pos)"/>
+ <param name="seed_length" argument="-L" type="integer" min="0" max="100" value="18" label="Seed length" help="Seed length for database indexing"/>
+ <param argument="--max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored"/>
  </xml>
  <xml name="reads_macro">
  <param argument="--reads" type="data" format="fasta,fastq,fastq.gz" label="Querying sequences"/>

diff --git a/tools/rna_tools/sortmerna/sortmerna.xml b/tools/rna_tools/sortmerna/sortmerna.xml
@@ -30,6 +30,8 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
  
  mkdir -p './aligned' &&
  mkdir -p './kvdb_folder' &&
+ mkdir -p './idx_folder' &&
+ mkdir -p './readb_folder' &&
 
  sortmerna
  #for $i, $reference in enumerate($ref)
@@ -80,6 +82,8 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
  --threads \${GALAXY_SLOTS:-1}
  -m \${GALAXY_MEMORY_MB:-8192}
  --kvdb 'kvdb_folder'
+ --idx-dir 'idx_folder'
+ --readb 'readb_folder'
  #if $aligned_fastx.aligned_fastx_selector == '--fastx' and str($sequencing_type.sequencing_type_selector) == 'paired'
  --out2
  #end if
@@ -100,8 +104,8 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
  <expand macro="reads_macro"/>
  </when>
  <when value="paired">
- <param name="forward_reads" type="data" format="fasta,fastq,fastq.gz" label="Forward reads"/>
- <param name="reverse_reads" type="data" format="fasta,fastq,fastq.gz" label="Reverse reads"/>
+ <param name="forward_reads" type="data" format="fasta,fastq,fastq.gz,fasta.gz" label="Forward reads"/>
+ <param name="reverse_reads" type="data" format="fasta,fastq,fastq.gz,fasta.gz" label="Reverse reads"/>
  <expand macro="paired_type_macro"/>
  </when>
  <when value="interleaved">
@@ -136,7 +140,7 @@ sortmerna --version 2>&1|grep 'SortMeRNA version'
  <expand macro="db_prep"/>
  </when>
  <when value="history">
- <param name="database_name" type="data" format="fasta" multiple="true" label="rRNA databases" help="Your databases will be indexed first, which may take up to several minutes."/>
+ <param name="database_name" type="data" format="fasta,fasta.gz" multiple="true" label="rRNA databases" help="Your databases will be indexed first, which may take up to several minutes."/>
  <expand macro="db_prep"/>
  </when>
  </conditional>