view muse_call.xml @ 1:fe9b86b5da79 draft

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<tool id="muse_call" name="muse call" version="1.0.rc">
  <description>First step of somatic point mutation caller for tumor-normal paired samples in next-generation sequencing data.</description>
  <requirements>
        <requirement type="package" version="1.0.rc" >muse</requirement>
        <requirement type="package" version="1.7">samtools</requirement>
  </requirements>
  <macros>
    <import>muse_macros.xml</import>
  </macros>
  <command> <![CDATA[
    ##creation of the bam indexes and execution of the MuSE call command with all the advanced options
  
   	samtools index $input2 && samtools index $input3 && 
        
        MuSE call -O variant_call
         #if $reference_source.reference_source_selector == "history"
         -f $reference_source.reference
        #end if
        #if $reference_source.reference_source_selector == "cached"
        -f $reference_source.ref_file.fields.path
        #end if
 
        $input2 $input3

    #if $region
      -r $region
    #end if
    #if $positions
      -l $positions
    #end if]]>
  </command>
  <inputs>
    <expand macro="reference_loc"/>
    <param format="bam" name="input2" type="data" label="tumor bam" help="tumor sample bamfile"/>
    <param format="bam" name="input3" type="data" label="normal bam" help="normal sample bamfile"/>
    <param name="region" type="text" optional="true" label="region" help="(chr:pos-pos)"/>
    <param format="txt,bed" name="positions" type="data" optional="true" label="list of regions" help="file txt or BED (chr:pos-pos or BED),with one region per line" />
  </inputs>
  <outputs>
    <data format="txt" name="output" from_work_dir="variant_call.MuSE.txt" label="${tool.name} on ${on_string}"/>
  </outputs>
  <tests>
      <test>
	<param name="input1" value="test_fasta.fa" ftype="fasta"/>
        <param name="input2" value="Muse_test_tumoral.bam"/>
        <param name="input3" value="Muse_test_normal.bam"/>
        <output name="output" file="results.txt" lines_diff="8"/>
      </test>
  </tests>
  <help>
     **MuSE call**, takes as input the indexed reference genome FASTA file  and the BAM file from normal and tumoral sample.
     The BAM files require aligning all the sequence reads against the reference genome using the Burrows-Wheeler alignment tool (BWA),
     with either the backtrack or the maximal exact matches (MEM) algorithm. In addition,
     the BAM files need to be processed by following the Genome Analysis Toolkit (GATK) Best Practices that include:
     Marking duplicates,realigning the paired tumor-normal BAMs jointly recalibrating base quality scores.
     More information at MuSE: http://bioinformatics.mdanderson.org/main/MuSE

         Galaxy wrapper for MuSE call implements all options available through the command line. Supported options are described below.

                Usage:   MuSE call [options] tumor.bam matched_normal.bam
                        Options:
                             -f FILE    faidx indexed reference sequence file
                             -r STR     single region (chr:pos-pos) where somatic
                                        mutations are called
                             -l FILE    list of regions (chr:pos-pos or BED), one
                                        region per line
                             -O STR     output file name (suffix '.MuSE.txt' is
                                        automatically added)
  </help>
  <citations>
    <citation type="doi">10.1186/s13059-016-1029-6</citation>
  </citations>
</tool>