comparison mothur/tools/mothur/list.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_list_seqs" name="List.seqs" version="1.16.0">
 <description>Lists the names of the sequences</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='list.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.accnos$:'$out_file
  --outputdir='$logfile.extra_files_path'
  #if $search.type == "fasta":
   --fasta=$search.input
  #elif $search.type == "name":
   --name=$search.input
  #else if search.type == "group":
   --group=$search.input
  #elif $search.type == "alignreport":
   --alignreport=$search.input
  #elif $search.type == "list":
   --list=$search.input

   </when>
   <when value="list">
    <param name="input" type="data" format="list" label="list - OTU List"/>
   </when>
   <when value="taxonomy">
    <param name="input" type="data" format="taxonomy" label="taxonomy - Sequence Taxonomy"/>
   </when>
  </conditional>
 </inputs>
 <outputs>
  <!-- fix format -->

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

**Command Documenation**

The list.seqs_ command writes out the names of the sequences found within a fasta, name, group, list, or align.report file.

.. _list.seqs: http://www.mothur.org/wiki/list.seqs


 </help>
</tool>

2:e990ac8a0f58

<tool id="mothur_list_seqs" name="List.seqs" version="1.19.0">
 <description>Lists the names (accnos) of the sequences</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='list.seqs'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.accnos$:'$out_file
  --outputdir='$logfile.extra_files_path'
  #if $search.type == "fasta":
   --fasta=$search.input
  #elif $search.type == "name":
   --name=$search.input
  #else if $search.type == "group":
   --group=$search.input
  #elif $search.type == "alignreport":
   --alignreport=$search.input
  #elif $search.type == "list":
   --list=$search.input

   </when>
   <when value="list">
    <param name="input" type="data" format="list" label="list - OTU List"/>
   </when>
   <when value="taxonomy">
    <param name="input" type="data" format="seq.taxonomy" label="taxonomy - Sequence Taxonomy"/>
   </when>
  </conditional>
 </inputs>
 <outputs>
  <!-- fix format -->

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

**Command Documenation**

The list.seqs_ command writes out the names of the sequences found within a fasta, name_, group_, list_, align.report_ or taxonomy_ file.

.. _name: http://www.mothur.org/wiki/Name_file
.. _group: http://www.mothur.org/wiki/Group_file
.. _list: http://www.mothur.org/wiki/List_file
.. _align.report: http://www.mothur.org/wiki/Align.seqs
.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
.. _list.seqs: http://www.mothur.org/wiki/list.seqs


 </help>
</tool>