view falco-call.xml @ 38:f1b32c09deaf draft

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<tool id="falco-call" name="falco-call" version="0.0.1">
  
  <requirements>
    
    <requirement type="package" version="0.1.19">samtools</requirement>
    <requirement type="package" version="3.1.0">R</requirement>
    <requirement type="package" version="2">bcftools</requirement> 
    <!--
    <requirement type="package" version="3.4">snpeff</requirement>
    <requirement type="package" version="2">varscan</requirement> 
    
    -->
    <!--
    
    <requirement type="set_environment">JAVA_JAR_PATH</requirement>
    <requirement type="set_environment">SNPEFF_JAR_PATH</requirement>
    
    <requirement type="set_environment">JAR_PATH1</requirement>
    <requirement type="set_environment">JAR_PATH2</requirement>
    -->
    <requirement type="set_environment">TOOL_DIR</requirement>
    
  </requirements>

  <description>FALCO: Amplicon Analysis Pipeline</description>
  
  <!-- command block to call script with specific R installation (set full paths) -->
  <!--
  <command>
    /full/path/to/Rscript 
    /full/path/to/QDNAseq.R 
    $qdnaseq_cfg
  </command>
  -->

  <!-- command block to call script with default R environment -->
  <command interpreter="bash">
    <!--falco.sh $bam $bam.name $html_output $vcf_output ${html_output.files_path} &amp;&amp;; echo "ECHO PRINT"; -->
    <!-- falco.sh $falco_cfg \$JAVA_JAR_PATH \$SNPEFF_JAR_PATH; -->
    falco-call.sh $falco_cfg;
  </command>
  <!--
  <command interpreter="bash">
    falco/amplicon-VcAn-TSACP.sh $bam $bam.name;
    echo "DONE"
  </command>
  <command interpreter="perl">
    falco.pl $htmlFile ${htmlFile.files_path} $bam $bam.name;
  </command>
  -->

  <stdio>
    <!-- Anything higher than 0 means the bash script didnt finish -->
    <exit_code range="1:" level="fatal" description="Bash script didnt finish correctly, check log" />
  </stdio>
  
  <inputs>
    <!-- ==================== -->
    <!-- General inputs -->
    <!-- ==================== -->
    <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST">
      <validator type="empty_field" />
      <validator type="regex" message="This field may contain only non-whitespace characters">\S+</validator>
    </param>
    <param name="bam" type="data" multiple="false" optional="false" format="bam" label="Input BAM" help="Select BAM file" />

    <param format="fasta" name="reference" type="data" metadata_name="dbkey" label="Reference File"/>
    <param format="bed" name="design_file" optional="True" type="data" label="BED File" help="When left empty, default Cancer Panel is used"/>
    <param format="txt" name="manifest_file" optional="True" type="data" label="MANIFEST File" help="When left empty, default Cancer Panel is used"/>

    <!-- ==================== -->
    <!-- Option to use your own bin annotations -->
    <!-- ==================== -->
  
  </inputs>
  
  <!-- ==================== -->
  <!-- This config is sourced by tool -->
  <!-- ==================== -->
  <configfiles>
    <configfile name="falco_cfg">
      design_file=$design_file
      manifest_file=$manifest_file
      bam_file=$bam
      bam_name=$bam.name
      html_out=$html_output
      vcf_out=$vcf_output
      out_path=${vcf_output.files_path}
    </configfile>
  </configfiles>
      <!--
      jar_path1=$JAR_PATH1
      jar_path2=$JAR_PATH2
      jar_path3=$JAVA_JAR_PATH
      jar_path4=$SNPEFF_JAR_PATH
    -->
  <!-- ==================== -->
  <!-- Main output is an html based report, additional on request -->
  <!-- ==================== -->
  <outputs>
    <data format="html" name="html_output" label="FALCO AAP (${jobName})" />
    <data format="vcf" name="vcf_output" label="FALCO AAP (${jobName}): VCF" />
  </outputs>

  <!-- ==================== -->
  <!-- Tests still to be done -->
  <!-- ==================== -->

  <!-- 
  <tests>
    <test>
      <param name="input1" value="input1" />   
      <param name="input2" value="input2" />   
    </test>
  </tests>
  -->

  <help>
.. class:: infomark

**Introduction**

This tool is a wrapper for the Amplicon Analysis Pipeline (AAP) FALCO_

.. _FALCO: https://bitbucket.org/daoud/falco

Calls and annotates genomic variants for each amplicon in a design.

-----

**Citation**

For the underlying tool please cite: Daoud Sie et al. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology (Cell Oncol 2014 Oct;37(5):353-61).

  </help>

</tool>