Mercurial > repos > iuc > snpsift
diff snpSift_macros.xml @ 2:bf8c1526871b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
| author | iuc |
|---|---|
| date | Mon, 05 Dec 2016 12:11:18 -0500 |
| parents | 98708b88af9f |
| children | 20c7d583fec1 |
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--- a/snpSift_macros.xml Tue Jun 07 10:04:09 2016 -0400 +++ b/snpSift_macros.xml Mon Dec 05 12:11:18 2016 -0500 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="4.1">snpEff</requirement> + <requirement type="package" version="4.1">snpsift</requirement> </requirements> </xml> <xml name="stdio"> @@ -10,8 +10,12 @@ <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> + <token name="@CONDA_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi</token> <xml name="version_command"> - <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command> + <version_command><![CDATA[ + if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi && + java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1 + ]]></version_command> </xml> <token name="@WRAPPER_VERSION@">4.1</token> <token name="@EXTERNAL_DOCUMENTATION@"> @@ -20,16 +24,6 @@ http://snpeff.sourceforge.net/SnpEff_manual.html </token> - <token name="@CITATION_SECTION@">------ - -**Citation** - -For the underlying tool, please cite the following two publications: - -SnpSift citation: -"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3:35, 2012. - - </token> <xml name="citations"> <citations> <citation type="doi">10.3389/fgene.2012.00035</citation>