comparison weeder2_wrapper.xml @ 2:3c5f10f7dd40 draft

Updated to tool version 2.0.1 (use data table to locate freqfiles).

1:571cb77ab9e7

<tool id="motiffinding_weeder2" name="Weeder2" version="2.0.0">
  <description>Motif discovery in sequences from coregulated genes of a single species</description>
  <command interpreter="bash">weeder2_wrapper.sh
  $sequence_file $species_code
  $output_motifs_file $output_matrix_file
  $strands
  #if $chipseq.use_chipseq
     -chipseq -top $chipseq.top
  #end if

     -maxm $advanced_options.n_motifs_report
     -b $advanced_options.n_motifs_build
     -sim $advanced_options.sim_threshold
     -em $advanced_options.em_cycles
  #end if
</command>
  <requirements>
    <requirement type="package" version="2.0">weeder</requirement>
  </requirements>
  <inputs>
    <param name="sequence_file" type="data" format="fasta" label="Input sequence" />
    <param name="species_code" type="select" label="Species to use for background comparison">
      <!-- Hard code options for now
	   See weeder's "organisms.txt" for full list
      -->
      <option value="HS">Homo sapiens (HS)</option>
      <option value="MM">Mus musculus (MM)</option>
      <option value="DM">Drosophila melanogaster (DM)</option>
      <option value="SC">Saccharomyces cerevisiae (SC)</option>
      <option value="AT">Arabidopsis thaliana (AT)</option>
    </param>
    <param name="strands" label="Use both strands of sequence" type="boolean"
	   truevalue="" falsevalue="-ss" checked="True"
	   help="If not checked then use -ss option" />
    <conditional name="chipseq">

2:3c5f10f7dd40

<tool id="motiffinding_weeder2" name="Weeder2" version="2.0.1">
  <description>Motif discovery in sequences from coregulated genes of a single species</description>
  <requirements>
    <requirement type="package" version="2.0">weeder</requirement>
  </requirements>
  <command interpreter="bash">weeder2_wrapper.sh
  $sequence_file $species_code ${species_code.fields.path}
  $output_motifs_file $output_matrix_file
  $strands
  #if $chipseq.use_chipseq
     -chipseq -top $chipseq.top
  #end if

     -maxm $advanced_options.n_motifs_report
     -b $advanced_options.n_motifs_build
     -sim $advanced_options.sim_threshold
     -em $advanced_options.em_cycles
  #end if
  </command>
  <inputs>
    <param name="sequence_file" type="data" format="fasta" label="Input sequence" />
    <param name="species_code" type="select" label="Species to use for background comparison">
      <options from_data_table="weeder2">
      </options>
    </param>
    <param name="strands" label="Use both strands of sequence" type="boolean"
	   truevalue="" falsevalue="-ss" checked="True"
	   help="If not checked then use -ss option" />
    <conditional name="chipseq">