view mutationseq.xml @ 0:3f5545f5f0c8 draft

planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty

<tool id="mutationseq" name="MutationSeq" version="4.3.6">
  <description>
    a feature based classifier for somatic mutation detection
  </description>
  <requirements>
    <requirement type="package" version="4.3.6">mutationseq</requirement>
    <requirement type="package" version="4.3.6">mutationseq_python_environment</requirement>
  </requirements>
  <macros>
    <import>citations.xml</import>
  </macros>  
  <command>

  <!-- Linking BAM Indexs to current working directory -->
  #if $model_source.model_source_selector == "standard" or $model_source.model_source_selector == "solid" or $model_source.model_source_selector == "deepseq" or $model_source.model_source_selector == "titan_mode"
    ln -s $model_source.normal normal.bam;
    ln -s $model_source.normal.metadata.bam_index normal.bam.bai;
    ln -s $model_source.tumour tumour.bam;
    ln -s $model_source.tumour.metadata.bam_index tumour.bam.bai;

  #else
    ln -s $model_source.input input.bam;
    ln -s $model_source.input.metadata.bam_index input.bam.bai;

  #end if

  <!-- Index Reference if from History -->
  #if $reference_source.reference_source_selector == "history":
    ln -s $reference_source.ref_file ref.fa;
    samtools faidx ref.fa;
  #end if

  <!-- Run Mutation Seq -->
  #if $interval:
    for i in \$(cat $interval); do
  #end if

  #if $model_source.model_source_selector == "titan_mode":
    \$MUTATIONSEQ_PYTHON_ENVIRONMENT_ROOT_DIR/bin/python2.7 \$MUTATIONSEQ_ROOT_DIR/preprocess.py
  #else:
    \$MUTATIONSEQ_PYTHON_ENVIRONMENT_ROOT_DIR/bin/python2.7 \$MUTATIONSEQ_ROOT_DIR/classify.py
  #end if

  #if $reference_source.reference_source_selector == "history":
    reference:ref.fa
  #else:
    reference:${reference_source.ref_file.fields.path}
  #end if

  #if $model_source.model_source_selector == "titan_mode":
    normal:normal.bam
    tumour:tumour.bam
    model:\$MUTATIONSEQ_ROOT_DIR/model_single_v4.0.2.npz
    --single

  #elif $model_source.model_source_selector == "standard"
    normal:normal.bam
    tumour:tumour.bam
    model:\$MUTATIONSEQ_ROOT_DIR/model_v4.1.2.npz

  #elif $model_source.model_source_selector == "standard_single"
    normal:input.bam
    model:\$MUTATIONSEQ_ROOT_DIR/model_single_v4.0.2.npz
    --single

  #elif $model_source.model_source_selector == "solid"
    normal:normal.bam
    tumour:tumour.bam
    model:\$MUTATIONSEQ_ROOT_DIR/model_solid_v4.1.2.npz

  #elif $model_source.model_source_selector == "deepseq"
    normal:normal.bam
    tumour:tumour.bam
    model:\$MUTATIONSEQ_ROOT_DIR/model_deep_v0.2.npz
    --deep

  #elif $model_source.model_source_selector == "deepseq_single"
    normal:input.bam
    model:\$MUTATIONSEQ_ROOT_DIR/model_deep_single_v0.2.npz
    --single
    --deep

  #end if

  #if $advancedsettings.filter.value == "all"
    --all
  #elif $advancedsettings.filter.value == "no_filter"
    --no_filter
  #end if

  #if $interval
    -i \$i 
  #end if

  #if $advancedsettings.positions:
    -f $advancedsettings.positions
  #end if
    
  --threshold $advancedsettings.filter_prob

  | grep -v ".*no somatic mutation calls.*" >> $output

  #if $interval
    ; done
  #end if
  ;
  </command>
  <inputs>
    <conditional name="reference_source">
      <param label="Choose the source for the reference genome" name="reference_source_selector" type="select">
        <option value="cached">Use a built-in genome</option>
        <option value="history">Use a genome from the history</option>
      </param>
      <when value="cached">
        <param label="Reference Genome File" name="ref_file" type="select">
          <options from_data_table="fasta_indexes"/>
        </param>
      </when>
      <when value="history">
        <param label="Reference Genome File" name="ref_file" type="data" format="fasta"/>
      </when>
    </conditional>
    <conditional name="model_source">
      <param type="select" name="model_source_selector" label="Choose the model for MutationSeq">
        <option value="standard" selected="true">Matched Sample Illumina Model</option>
        <option value="solid">Matched Sample Solid Model</option>
        <option value="deepseq">Matched Sample Deepseq Model</option>
        <option value="standard_single">Single Sample Illumina Model</option>
        <option value="deepseq_single">Single Sample Deepseq Model</option>
        <option value="titan_mode">TITAN Mode</option>
      </param>
      <when value="standard">
        <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
        <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/>
      </when>
      <when value="solid">
        <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
        <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/>
      </when>
      <when value="deepseq">
        <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
        <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/>
      </when>
      <when value="standard_single">
        <param type="data" format="bam" name="input" label="Sequence Alignment File"/>
      </when>
      <when value="deepseq_single">
        <param type="data" format="bam" name="input" label="Sequence Alignment File"/>
      </when>
      <when value="titan_mode">
        <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
        <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/> 
      </when>
    </conditional>
    <param type="data" format="txt" optional="true" name="interval" label="Specify Interval"/>    
    <section name="advancedsettings" title="Advanced Settings" expanded="false">
      <param type="select" name="filter" label="Filter Method">
        <option value="standard" selected="true">Print Probablistic Positions</option>
        <option value="all">Print Positions Regardless of Classified Probabilitly</option>
        <option value="no_filter">Print Positions Regardless of Initial Criteira</option>
      </param>
      <param type="data" format="txt" optional="true" name="positions" label="Positions File"/>
      <param type="float" value="0.85" min="0" max="1" name="filter_prob" label="Probabililty Filter Threshold"/>
    </section>
  </inputs>
  <outputs>
    <data format="vcf" name="output"/>
  </outputs>
  <citations>
    <expand macro="morinlab_citation" />
    <expand macro="galaxy_citation" />
    <expand macro="mutationseq_citation" />
  </citations>
</tool>