comparison mothur/tools/mothur/trim.seqs.xml @ 7:7bfe1f843858

Support Mothur v1.20 trim.seqs - added name parameter and optional trim.names output phylo.diversity - group optional, put group and groups in conditional - breaks get.lineage remove.lineage - allow multiple taxons dist.shared - added processors consensus.seqs - add cutoff parameter trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs new tools - chimera.uchime deunique.tree count.seqs shared/relabund files - Column headings refactor lib/galaxy/datatypes/metagenomics.py add filters to label and group selects in tool configs mothur_wrapper.py updated with new tools params

6:ce6e81622c6a

<tool id="mothur_trim_seqs" name="Trim.seqs" version="1.19.0" force_history_refresh="True">
 <description>Trim sequences - primers, barcodes, quality</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='trim.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.trim\.fasta$:'$trim_fasta,'^\S+\.trim\.qual$:'$trim_qual,'^\S+\.scrap\.fasta$:'$scrap_fasta,'^\S+\.scrap\.qual$:'$scrap_qual,'^\S+\.groups$:'$groups_file

   #end if
   $qual.qtrim
  #end if
  $flip 
  --fasta=$fasta
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/>
  <param name="minlength" type="integer" value="0" label="minlength - Minimum Sequence Length (default 0, ignored if &#060; 1 )"/>
  <param name="maxlength" type="integer" value="0" label="maxlength - Maximum Sequence Length (default 0, ignored if &#060; 1)"/>
  <param name="maxambig" type="integer" value="-1" label="maxambig - Maximum ambiguous bases (default -1, ignored if &#060; 0)"/>
  <param name="maxhomop" type="integer" value="0" label="maxhomop - Maximum homopolymers (default 0, ignored if &#060; 1)"/>
  <param name="keepfirst" type="integer" value="0" label="keepfirst - ignored if &#060; 0)" 

  <param name="flip" type="boolean" truevalue="--flip=true" falsevalue="" checked="false" label="flip - reverse complement the trimmed sequences"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="fasta" name="trim_fasta" label="${tool.name} on ${on_string}: trim.fasta"/>
  <data format_source="qfile" name="trim_qual" label="${tool.name} on ${on_string}: trim.qual">
   <filter>(qual['add'] == 'yes'  and len(qual['qfile'].__str__) > 0)</filter>
  </data>
  <data format_source="fasta" name="scrap_fasta" label="${tool.name} on ${on_string}: scrap.fasta"/>
  <data format_source="qfile" name="scrap_qual" label="${tool.name} on ${on_string}: scrap.qual">

7:7bfe1f843858

<tool id="mothur_trim_seqs" name="Trim.seqs" version="1.20.0" force_history_refresh="True">
 <description>Trim sequences - primers, barcodes, quality</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='trim.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.trim\.fasta$:'$trim_fasta,'^\S+\.trim\.qual$:'$trim_qual,'^\S+\.scrap\.fasta$:'$scrap_fasta,'^\S+\.scrap\.qual$:'$scrap_qual,'^\S+\.groups$:'$groups_file

   #end if
   $qual.qtrim
  #end if
  $flip 
  --fasta=$fasta
  #if $names.__str__ != "None" and len($names.__str__) > 0:
   --name=$names
  #end if

 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/>
  <param name="names" type="data" format="name" label="name - Sequence representative name list"/>
  <param name="minlength" type="integer" value="0" label="minlength - Minimum Sequence Length (default 0, ignored if &#060; 1 )"/>
  <param name="maxlength" type="integer" value="0" label="maxlength - Maximum Sequence Length (default 0, ignored if &#060; 1)"/>
  <param name="maxambig" type="integer" value="-1" label="maxambig - Maximum ambiguous bases (default -1, ignored if &#060; 0)"/>
  <param name="maxhomop" type="integer" value="0" label="maxhomop - Maximum homopolymers (default 0, ignored if &#060; 1)"/>
  <param name="keepfirst" type="integer" value="0" label="keepfirst - ignored if &#060; 0)" 

  <param name="flip" type="boolean" truevalue="--flip=true" falsevalue="" checked="false" label="flip - reverse complement the trimmed sequences"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="fasta" name="trim_fasta" label="${tool.name} on ${on_string}: trim.fasta"/>
  <data format_source="names" name="trim_names" label="${tool.name} on ${on_string}: trim.names">
   <filter>names != None</filter>
  </data>
  <data format_source="qfile" name="trim_qual" label="${tool.name} on ${on_string}: trim.qual">
   <filter>(qual['add'] == 'yes'  and len(qual['qfile'].__str__) > 0)</filter>
  </data>
  <data format_source="fasta" name="scrap_fasta" label="${tool.name} on ${on_string}: scrap.fasta"/>
  <data format_source="qfile" name="scrap_qual" label="${tool.name} on ${on_string}: scrap.qual">