comparison varscan_mpileup.xml @ 1:44d514f3df8f draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7

0:6f8cead3dc93

    <requirements>
        <requirement type="package" version="2.3.6">varscan</requirement>
    </requirements>

    <!-- 
    The version command string is not yet a template that can be filled in, so version command is not yet possible.
    <version_command>java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/varscan/VarScan.jar 2>&amp;1 | head -n 1</version_command>
    -->

    <command>
        ## Set up samples list file.
        #if $sample_names.strip() != '':
	       echo $sample_names | awk -F ',' '{ for (i = 1; i &lt;= NF; i++) { print \$i; } }' > samples_list.txt;
        #end if

        ## Set up command + input.
        java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar ${cmd} ${input}
        --min-coverage ${min_coverage} 

            <option value="yes">yes</option>
        </param>
        <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
    </inputs>

    <stdio>
        <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

    <outputs>
        <data name="output" format="vcf"/>
    </outputs>

    <trackster_conf>

    <help>
**VarScan Overview**

VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. It calls variants from a mpileup dataset and produces a VCF 4.1 Full documentation is available online_.

Please cite: Koboldt, D., Zhang, Q., Larson, D., Shen, D., McLellan, M., Lin, L., Miller, C., Mardis, E., Ding, L., and Wilson, R. (2012). VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing Genome Research DOI: 10.1101/gr.129684.111 

.. _VarScan: http://varscan.sourceforge.net/
.. _online: http://varscan.sourceforge.net/using-varscan.html

**Input**

::

  vcf-sample-list
    For VCF output, a list of sample names in order, one per line
  
  variants
    Report only variant (SNP/indel) positions [0]

    </help>
</tool>

1:44d514f3df8f

    <requirements>
        <requirement type="package" version="2.3.6">varscan</requirement>
    </requirements>

    <stdio>
        <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

    <version_command>java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&amp;1 | head -n 1</version_command>

    <command>
        ## Set up samples list file.
        #if $sample_names.strip() != '':
           echo $sample_names | awk -F ',' '{ for (i = 1; i &lt;= NF; i++) { print \$i; } }' > samples_list.txt;
        #end if

        ## Set up command + input.
        java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar ${cmd} ${input}
        --min-coverage ${min_coverage} 

            <option value="yes">yes</option>
        </param>
        <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
    </inputs>

    <outputs>
        <data name="output" format="vcf"/>
    </outputs>

    <trackster_conf>

    <help>
**VarScan Overview**

VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. It calls variants from a mpileup dataset and produces a VCF 4.1 Full documentation is available online_.

.. _VarScan: http://dkoboldt.github.io/varscan/
.. _online: http://dkoboldt.github.io/varscan/using-varscan.html

**Input**

::

  vcf-sample-list
    For VCF output, a list of sample names in order, one per line
  
  variants
    Report only variant (SNP/indel) positions [0]
    </help>

    <citations>
        <citation type="doi">10.1101/gr.129684.111</citation>
    </citations>
</tool>