comparison mothur/tools/mothur/screen.seqs.xml @ 3:b849cd7e132a

workflow cleanup_param_values recurses through paramnames whenever they start with a paramname_, so change input to input_fasta

2:e990ac8a0f58

 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='screen.seqs'
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input.__str__)) + ":'" + $out_file.__str__]
  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.bad.accnos',$os.path.basename($input.__str__)) + ":'" + $bad_accnos.__str__]
  --outputdir='$logfile.extra_files_path'
  --tmpdir='${logfile.extra_files_path}/input'
  --fasta=$input
  #if int($start) >= 0:
   --start=$start
  #end if
  #if int($end) >= 0:
   --end=$end

  #end if
  --result=#echo ','.join($results)
  --processors=2
 </command>
 <inputs>
  <param name="input" type="data" format="fasta,align" label="fasta - Fasta to screen"/>
  <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/>
  <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/>
  <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/>
  <param name="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/>
  <param name="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/>

  <param name="input_groups" type="data" format="groups" optional="true" label="group - Groups to screen"/>
  <param name="input_alignreport" type="data" format="align.report" optional="true" label="alignreport - Align Report to screen"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="input" name="out_file" label="${tool.name} on ${on_string}: good.${input.datatype.file_ext}" />
  <data format="accnos" name="bad_accnos" label="${tool.name} on ${on_string}: bad.accnos" />
  <data format_source="input_qfile" name="output_qfile" label="${tool.name} on ${on_string}: qfile" >
   <filter>input_qfile != None</filter>
  </data>
  <data format="names" name="output_names" label="${tool.name} on ${on_string}: names" >

3:b849cd7e132a

 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='screen.seqs'
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_fasta.__str__)) + ":'" + $out_file.__str__]
  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.bad.accnos',$os.path.basename($input_fasta.__str__)) + ":'" + $bad_accnos.__str__]
  --outputdir='$logfile.extra_files_path'
  --tmpdir='${logfile.extra_files_path}/input'
  --fasta=$input_fasta
  #if int($start) >= 0:
   --start=$start
  #end if
  #if int($end) >= 0:
   --end=$end

  #end if
  --result=#echo ','.join($results)
  --processors=2
 </command>
 <inputs>
  <param name="input_fasta" type="data" format="fasta,align" label="fasta - Fasta to screen"/>
  <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/>
  <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/>
  <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/>
  <param name="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/>
  <param name="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/>

  <param name="input_groups" type="data" format="groups" optional="true" label="group - Groups to screen"/>
  <param name="input_alignreport" type="data" format="align.report" optional="true" label="alignreport - Align Report to screen"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="input_fasta" name="out_file" label="${tool.name} on ${on_string}: good.${input_fasta.datatype.file_ext}" />
  <data format="accnos" name="bad_accnos" label="${tool.name} on ${on_string}: bad.accnos" />
  <data format_source="input_qfile" name="output_qfile" label="${tool.name} on ${on_string}: qfile" >
   <filter>input_qfile != None</filter>
  </data>
  <data format="names" name="output_names" label="${tool.name} on ${on_string}: names" >