comparison mothur/tools/mothur/screen.seqs.xml @ 2:e990ac8a0f58

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

1:fcc0778f6987

<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.16.0">
 <description>Screen sequences</description>
 <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

   --criteria=$criteria
  #end if
  #if $optimize != None and $optimize.__str__ != "None":
   --optimize=$optimize
  #end if
  #if $input_names != None and $input_names.__str__ != "None":
   --name=$input_names
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.good.\2',$os.path.basename($input_names.__str__)) + ":'" + $output_names.__str__]
  #end if
  #if $input_groups != None and $input_groups.__str__ != "None":
   --group=$input_groups
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.good.\2',$os.path.basename($input_groups.__str__)) + ":'" + $output_groups.__str__]
  #end if
  #if $input_alignreport != None and $input_alignreport.__str__ != "None":
   --alignreport=$input_alignreport
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.good.\2',$os.path.basename($input_alignreport.__str__)) + ":'" + $output_alignreport.__str__]
  #end if
  --result=#echo ','.join($results)
  --processors=2
 </command>
 <inputs>

   <option value="minlength">minlength</option>
   <option value="maxlength">maxlength</option>
   <option value="maxambig">maxambig</option>
   <option value="maxhomop">maxhomop</option>
  </param>
  <param name="input_names" type="data" format="names" optional="true" label="name - Sequece Names to screen"/>
  <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 ${on_string}: logfile" />
  <data format="fasta" name="out_file" label="${tool.name} on ${on_string}: good.${input.datatype.file_ext}" >
   <change_format>
    <when input_dataset="input" attribute="ext" value="align" format="align"/>
   </change_format>
  </data>
  <data format="accnos" name="bad_accnos" label="${tool.name} on ${on_string}: bad.accnos" />
  <data format="names" name="output_names" label="${tool.name} on ${on_string}: names" >
   <filter>input_names != None</filter>
  </data>
  <data format="groups" name="output_groups" label="${tool.name} on ${on_string}: groups" >
   <filter>input_groups != None</filter>

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a names, group, or align.report file. 

.. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs


 </help>
</tool>

2:e990ac8a0f58

<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.19.0">
 <description>Screen sequences</description>
 <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

   --criteria=$criteria
  #end if
  #if $optimize != None and $optimize.__str__ != "None":
   --optimize=$optimize
  #end if
  #if $input_qfile != None and $input_qfile.__str__ != "None":
   --qfile=$input_qfile
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_qfile.__str__)) + ":'" + $output_qfile.__str__]
  #end if
  #if $input_names != None and $input_names.__str__ != "None":
   --name=$input_names
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_names.__str__)) + ":'" + $output_names.__str__]
  #end if
  #if $input_groups != None and $input_groups.__str__ != "None":
   --group=$input_groups
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_groups.__str__)) + ":'" + $output_groups.__str__]
  #end if
  #if $input_alignreport != None and $input_alignreport.__str__ != "None":
   --alignreport=$input_alignreport
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_alignreport.__str__)) + ":'" + $output_alignreport.__str__]
  #end if
  --result=#echo ','.join($results)
  --processors=2
 </command>
 <inputs>

   <option value="minlength">minlength</option>
   <option value="maxlength">maxlength</option>
   <option value="maxambig">maxambig</option>
   <option value="maxhomop">maxhomop</option>
  </param>
  <param name="input_qfile" type="data" format="qual" optional="true" label="qfile - Sequence Quality file  to screen"/>
  <param name="input_names" type="data" format="names" optional="true" label="name - Sequence Names to screen"/>
  <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 ${on_string}: names" >
   <filter>input_names != None</filter>
  </data>
  <data format="groups" name="output_groups" label="${tool.name} on ${on_string}: groups" >
   <filter>input_groups != None</filter>

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a name_, group_, or align.report_ file. 

.. _name: http://www.mothur.org/wiki/Name_file
.. _group: http://www.mothur.org/wiki/Group_file
.. _align.report: http://www.mothur.org/wiki/Align.seqs
.. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs


 </help>
</tool>