view cluster-picker.xml @ 0:2040cda75d1f draft

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<tool id="cluster-pick" name="Cluster Picker" version="1.2.3">
  <description>cluster picker</description>
<requirements>
    <requirement type="package" version="1.2.3">cluster-picker</requirement>
</requirements>
<!-- <command> <![CDATA[cluster-picker sequence_file tree_file init_threshold main_threshold dis_threshold size genetic_distance]]> </command> -->
<command> <![CDATA[cluster-picker]]> </command>
<inputs>
  <param format="fasta" name="sequence_file" type="data" label="align"
    help="Please enter fasta format sequences file name to process"/>
  <param format="nwk" name="tree_file" type="data" label="tree"
    help="Please enter newick format tree, with branch lengths and node support"/>
  <param name="init_threshold" type="float" value="0.9" optional="true"
    help="Please enter initial support threshold for these initial subtrees" label="initial threshold">
  </param>
  <param name="main_threshold" type="float" value="0.9" optional="true"
    help="Please enter main support threshold for clusters" label="main threshold">
  </param>
  <param name="dis_threshold" type="float" value="0.045" optional="true"
    help="Please enter genetic distance threshold for clusters in %" label="distance threshold">
  </param>
  <param name="size" type="float" value="10" optional="true"
    help="To output all cluster names for clusters of size >= X enter X" label="size">
  </param>
  <param name="genetic_distance" type="select" label="genetic distance"
    help="Please enter scoring type for genetic distance\n
          abs      	= count absolute character differences\n
          gap      	= disregard sites with -, ~, or n\n
          valid    	= only count differences for sites with nucleotides: a, c, t, g in both sequences\n
          ambiguity	= disregard sites with -, ~, or n and do not count ambiguities as differences (e.g. a vs r is not a difference)">
      <option value="gap">gap</option>
      <option value="abs">abs</option>
      <option value="valid">valid</option>
      <option value="ambiguity">ambiguity</option>
  </param>
</inputs>
<outputs>
  <data format="figTree"/>
  <data format="nhx"/>
  <data format="txt"/>
  <data format="fasta"/>
</outputs>

<tests>
  <test>
    <param name="input" value="fa_gc_content_input.fa"/>
    <output name="out_file1" file="fa_gc_content_output.txt"/>
  </test>
</tests>

<help>
Cluster identification strategies differ between studies and as a consequence cluster definitions vary.
</help>
</tool>