comparison mothur/tools/mothur/trim.flows.xml @ 35:95d75b35e4d2

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

34:1be61ceb20d7

<tool id="mothur_trim_flows" name="Trim.flows" version="1.22.0" force_history_refresh="True">
 <description>partition by barcode, trim to length, cull by lenght and mismatches</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='trim.flows'

  </param>
  <param name="noise" type="float" value="" optional="true" label="noise - treat any intensity signal less than this threshold as noise" 
         help="default .7">
   <validator type="in_range" message="signal between 0. and 1." min="0.0" max="1.0"/>
  </param>
  <param name="order" type="text" value="" label="order - flow order for nucleotides in the sequencer" 
         help="default is TACG"/>

  <param name="fasta" type="boolean" truevalue="--fasta=true" falsevalue="" checked="false" label="fasta - translate the flowgram data to fasta sequence format"/>

 </inputs>
 <outputs>

  <data format_source="fasta" name="flow_fasta" label="${tool.name} on ${on_string}: flow.fasta">
   <filter>fasta == True</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**mothur overview**

35:95d75b35e4d2

<tool id="mothur_trim_flows" name="Trim.flows" version="1.23.0" force_history_refresh="True">
 <description>partition by barcode, trim to length, cull by lenght and mismatches</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='trim.flows'

  </param>
  <param name="noise" type="float" value="" optional="true" label="noise - treat any intensity signal less than this threshold as noise" 
         help="default .7">
   <validator type="in_range" message="signal between 0. and 1." min="0.0" max="1.0"/>
  </param>
  <param name="order" type="text" value="A" label="order - flow order for nucleotides in the sequencer"
         help="default is A, was TACG. Also accepts B or I"/>

  <param name="fasta" type="boolean" truevalue="--fasta=true" falsevalue="" checked="false" label="fasta - translate the flowgram data to fasta sequence format"/>

 </inputs>
 <outputs>

  <data format_source="fasta" name="flow_fasta" label="${tool.name} on ${on_string}: flow.fasta">
   <filter>fasta == True</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="package" version="1.33">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**mothur overview**