comparison mothur/tools/mothur/pre.cluster.xml @ 2:e990ac8a0f58

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

1:fcc0778f6987

<tool id="mothur_pre_cluster" name="Pre.cluster" version="1.16.0">
 <description>Remove sequences due to pyrosequencing errors</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='pre.cluster'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.precluster\.fasta$:'$fasta_out,'^\S+\.precluster\.names$:'$names_out
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  #if $matrix.name.__str__ != "None" and len($matrix.name.__str__) > 0:
   --name=$name
  #if 20 >= int($diffs.__str__) >= 0:
   --diffs=$diffs
  #end if
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequence Fasta"/>
  <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <param name="diffs" type="integer" value="1" label="diffs - Number of mismatched bases to allow between sequences in a group (default 1)"/>

2:e990ac8a0f58

<tool id="mothur_pre_cluster" name="Pre.cluster" version="1.19.0">
 <description>Remove sequences due to pyrosequencing errors</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  ## adds .precluster before the last extension to the input file
  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.precluster.\2',$os.path.basename($fasta.__str__)) + ":'" + $fasta_out.__str__]
  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.precluster.names',$os.path.basename($fasta.__str__)) + ":'" + $names_out.__str__]
  --cmd='pre.cluster'
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  #if $name.__str__ != "None" and len($name.__str__) > 0:
   --name=$name
  #end if
  #if 20 >= int($diffs.__str__) >= 0:
   --diffs=$diffs
  #end if
  --result=#echo ','.join($results)
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Sequence Fasta"/>
  <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <param name="diffs" type="integer" value="1" label="diffs - Number of mismatched bases to allow between sequences in a group (default 1)"/>