comparison phylorelatives.xml @ 41:9453ba52f46b draft

tool now uses multiple selection for input fasta files

40:dd39849c2ff1

    <requirement type="package" version="2.2.6">rpy2</requirement>
    <requirement type="package" version="3.12.0">dendropy</requirement>
    <requirement type="package" version="3.0-8">ape</requirement>
  </requirements>
  <command interpreter="python">phylorelatives.py
     #for $sequence in $sequences:
         -i "${sequence.sequence}"
     #end for
     -m "${multifasta}"
     -b "$iterations"
     $pairwise
     $major_only
     #if str($root.root_selector)=="upload_root":
      -r "${root.root_fa}"
     #end if
     --relatives-out "$siblings"
     --newick-out "$newick"
     --trees-out "$plot"

  </command>
  <inputs>
    <repeat name="sequences" title="Input FASTA file" min="1" help="Files will be concatenated into a single FASTA multiple alignment file, thus equal length homologous sequences are required">
      <param format="fasta" name="sequence" type="data" label="FASTA file" help="Minor allele sequences must be labeled &quot;_minor&quot; or &quot;_test&quot; e.g. &quot;>sample1_minor&quot;">
      </param>
    </repeat>
    <conditional name="root">
      <param name="root_selector" type="select" label=" Root sequence">
        <option value="unrooted" selected="True"></option>
        <option value="upload_root"></option>
      </param>
      <when value="unrooted">
      </when>           
      <when value="upload_root">
        <param name="root_fa" format="fasta" type="data"  label="Root tree using" help="Must have the same length as input sequences"/>
      </when>
    </conditional>
    <param name="pairwise" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Use pairwise deletion of gaps/missing data" help="Defaults to &quot;Complete deletion&quot;"/>
    <param name="iterations" type="integer" value="1000" label="Change number of bootstrap replicas" help="0 to deactivate"/>

    <data format="png" name="plot"  label="${tool.name} on ${on_string}: tree plot"/>
  </outputs>
  <tests>
    <test>
      <param name="iterations" value="0"/>
      <param name="sequence" value="test.fa"/>
      <output name="siblings" file="test.fa-siblings.tab"/>
    </test>
  </tests>

  <help>

41:9453ba52f46b

    <requirement type="package" version="2.2.6">rpy2</requirement>
    <requirement type="package" version="3.12.0">dendropy</requirement>
    <requirement type="package" version="3.0-8">ape</requirement>
  </requirements>
  <command interpreter="python">phylorelatives.py
     #for $sequence in ( $sequences ):
         -i "${sequence}"
     #end for
     -m "${multifasta}"
     -b "$iterations"
     $pairwise
     $major_only
     #if str($root.root_selector)=="add_root":
      -r "${root.root_fa}"
     #end if
     --relatives-out "$siblings"
     --newick-out "$newick"
     --trees-out "$plot"
  </command>
  <inputs>
      <param format="fasta" name="sequences" type="data" label="FASTA file" multiple="TRUE" help="Minor allele sequences must be labeled &quot;_minor&quot; or &quot;_test&quot; e.g. &quot;>sample1_minor&quot;">
      </param>
    <conditional name="root">
      <param name="root_selector" type="select" label=" Root sequence">
        <option value="unrooted" selected="True"></option>
        <option value="add_root"></option>
      </param>
      <when value="unrooted">
      </when>           
      <when value="add_root">
        <param name="root_fa" format="fasta" type="data"  label="Root tree using" help="Must have the same length as input sequences"/>
      </when>
    </conditional>
    <param name="pairwise" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Use pairwise deletion of gaps/missing data" help="Defaults to &quot;Complete deletion&quot;"/>
    <param name="iterations" type="integer" value="1000" label="Change number of bootstrap replicas" help="0 to deactivate"/>

    <data format="png" name="plot"  label="${tool.name} on ${on_string}: tree plot"/>
  </outputs>
  <tests>
    <test>
      <param name="iterations" value="0"/>
      <param name="sequences" value="test.fa"/>
      <output name="siblings" file="test.fa-siblings.tab"/>
    </test>
  </tests>

  <help>