comparison mothur/tools/mothur/get.seqs.xml @ 35:95d75b35e4d2

Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)

34:1be61ceb20d7

  #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="accnos" type="data" format="accnos" label="accnos - Accession Names"/>
  <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
  <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>

  <param name="group_in" type="data" format="groups" optional="true" label="group - Sequences Groups"/>
  <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/>
  <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"/>
  <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <!-- format should be set to match input -->
  <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">

  <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy">
   <filter>taxonomy_in != None</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

.. _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
.. _get.seqs: http://www.mothur.org/wiki/Get.seqs

 </help>
</tool>

35:95d75b35e4d2

  #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)
	#if $count.__str__ != "None" and len($count.__str__) > 0:
		--count=$count
	#end if
	#if $fastq.__str__ != "None" and len($fastq.__str__) > 0:
		--fastq=$fastq
	#end if
 </command>
 <inputs>
  <param name="accnos" type="data" format="accnos" label="accnos - Accession Names"/>
  <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
  <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>

  <param name="group_in" type="data" format="groups" optional="true" label="group - Sequences Groups"/>
  <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/>
  <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"/>
  <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/>
	<param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
	<param name="fastq" type="data" format="fastq" optional="true" label="count - a count_table" help="fastq - allows you to select sequences from your fastq file"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <!-- format should be set to match input -->
  <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">

  <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy">
   <filter>taxonomy_in != None</filter>
  </data>
 </outputs>
 <requirements>
<requirement type = "package" version ="1.33">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

.. _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
.. _get.seqs: http://www.mothur.org/wiki/Get.seqs

v.1.27.0 : Updated to Mothur 1.33, added count and fastq params

 </help>
</tool>