Mercurial > repos > devteam > varscan_version_2
changeset 1:44d514f3df8f draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:30:51 -0500 |
| parents | 6f8cead3dc93 |
| children | bc1e0cd41241 |
| files | varscan_mpileup.xml |
| diffstat | 1 files changed, 13 insertions(+), 15 deletions(-) [+] |
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--- a/varscan_mpileup.xml Sun Nov 17 11:08:56 2013 -0500 +++ b/varscan_mpileup.xml Wed Nov 11 12:30:51 2015 -0500 @@ -5,15 +5,17 @@ <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>&1 | head -n 1</version_command> - --> + <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>&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 <= NF; i++) { print \$i; } }' > samples_list.txt; + echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt; #end if ## Set up command + input. @@ -63,11 +65,6 @@ <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> @@ -96,10 +93,8 @@ 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 +.. _VarScan: http://dkoboldt.github.io/varscan/ +.. _online: http://dkoboldt.github.io/varscan/using-varscan.html **Input** @@ -150,6 +145,9 @@ variants Report only variant (SNP/indel) positions [0] + </help> - </help> + <citations> + <citation type="doi">10.1101/gr.129684.111</citation> + </citations> </tool>