view muse_sump.xml @ 5:723755ec06be draft

Uploaded

<tool id="muse" name="muse_sump" version="1.0.rc">
  <description>Second 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="0.2.5" >tabix</requirement>
  </requirements>
  <command> <![CDATA[bgzip -c $input2 > dbsnp.vcf.gz && tabix -p vcf -f dbsnp.vcf.gz && MuSE sump -O prova $selection -I $input1 -D dbsnp.vcf.gz]]></command>
  <inputs>
    <param format="txt" name="input1" type="data" label="MuSE call output" help="txt file from MuSE call"/>
    <param format="vcf" name="input2" type="data" label="dbSNP vcf file" help="dbSNP vcf file"/>
    <param name="selection" type="select" label="List Selection">
        <option value="-E" selected="true">input generated from whole exome sequencing</option>
        <option value="-G"                >input generated from whole genome sequencing</option>
    </param>
  </inputs>
  <outputs>
    <data format="vcf" name="output" from_work_dir="prova" label="${tool.name} on ${on_string}"/>
  </outputs>
  <tests>
      <test>
	<param name="input1" value="results.txt"/>
        <param name="input2" value="dbsnp.vcf"/>
        <output name="output" file="sump_results.vcf" lines_diff="10"/>
      </test>
  </tests>
  <help>
    **MuSE sump**, takes as input the output file from ‘MuSE call’ and the dbSNP file.
    More information at MuSE: http://bioinformatics.mdanderson.org/main/MuSE

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

                 Usage:   MuSE sump [options]
                          Options:
                                -I FILE    single input file generated by 'MuSE call'
                                -G         input generated from whole genome sequencing data
                                -E         input generated from whole exome sequencing data
                                -O STR     output file name (VCF format)
                                -D FILE    dbSNP vcf file that should be bgzip compressed,
                                           tabix indexed and based on the same reference
                                           genome used in 'MuSE call'.
	**IMPORTANT** the wrapper will automatically compress the vcf and create the tabix index

					   
    </help>
    <citations>
      <citation type="doi">10.1186/s13059-016-1029-6</citation>
    </citations>
</tool>