comparison mothur/tools/mothur/remove.groups.xml @ 12:370b3fc4e7d3

Mothur galaxy tool updates for Mothur version 1.21.0, fix help section warnings

11:11867a45a43d

<tool id="mothur_remove_groups" name="Remove.groups" version="1.19.0">
 <description>Remove groups from groups,fasta,names,list,taxonomy</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]

    --accnos=$groupnames.accnos
   #end if
  #end if
  #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0:
   --fasta=$fasta_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__]
  #end if
  #if $name_in.__str__ != "None" and len($name_in.__str__) > 0:
   --name=$name_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__]
  #end if
  #if $list_in.__str__ != "None" and len($list_in.__str__) > 0:
   --list=$list_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__]
  #end if
  #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0:
   --taxonomy=$taxonomy_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__]
  #end if
  --result=#echo ','.join($results)

 </command>
 <inputs>
  <param name="group_in" type="data" format="groups" label="group - Groups"/>
  <conditional name="groupnames">
   <param name="source" type="select" label="Select Group Names from">

   </when>
  </conditional>
  <param name="fasta_in" type="data" format="fasta,align" optional="true" label="fasta - Fasta Sequences"/>
  <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/>
  <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/>

  <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name">
   <filter>name_in != None</filter>
  </data>
  <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list">
   <filter>list_in != None</filter>
  </data>
  <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy">
   <filter>taxonomy_in != None</filter>
  </data>
 </outputs>

12:370b3fc4e7d3

<tool id="mothur_remove_groups" name="Remove.groups" version="1.21.0">
 <description>Remove groups from groups,fasta,names,list,taxonomy</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]

    --accnos=$groupnames.accnos
   #end if
  #end if
  #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0:
   --fasta=$fasta_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__]
  #end if
  #if $name_in.__str__ != "None" and len($name_in.__str__) > 0:
   --name=$name_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__]
  #end if
  #if $list_in.__str__ != "None" and len($list_in.__str__) > 0:
   --list=$list_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__]
  #end if
  #if $shared_in.__str__ != "None" and len($shared_in.__str__) > 0:
   --shared=$shared_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.*\\.pick\\.\2',$os.path.basename($shared_in.__str__)) + ":'" + $shared_out.__str__]
  #end if
  #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0:
   --taxonomy=$taxonomy_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__]
  #end if
  --result=#echo ','.join($results)
 </command>
 <inputs>
  <param name="group_in" type="data" format="groups" label="group - Groups"/>
  <conditional name="groupnames">
   <param name="source" type="select" label="Select Group Names from">

   </when>
  </conditional>
  <param name="fasta_in" type="data" format="fasta,align" optional="true" label="fasta - Fasta Sequences"/>
  <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/>
  <param name="shared_in" type="data" format="shared" optional="true" label="shared - OTU Shared"/>
  <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/>

  <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name">
   <filter>name_in != None</filter>
  </data>
  <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list">
   <filter>list_in != None</filter>
  </data>
  <data format="shared" name="shared_out" label="${tool.name} on ${on_string}: pick.shared">
   <filter>shared_in != None</filter>
  </data>
  <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy">
   <filter>taxonomy_in != None</filter>
  </data>
 </outputs>