| Previous changeset 1:13191d4914f7 (2016-06-07) Next changeset 3:563d1bdb7b80 (2016-12-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f |
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modified:
snpSift_dbnsfp.xml snpSift_macros.xml |
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removed:
tool_dependencies.xml |
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| diff -r 13191d4914f7 -r c838e7136a40 snpSift_dbnsfp.xml --- a/snpSift_dbnsfp.xml Tue Jun 07 10:04:48 2016 -0400 +++ b/snpSift_dbnsfp.xml Mon Dec 05 12:06:13 2016 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.0"> +<tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.1"> <description>Add Annotations from dbNSFP or similar annotation DBs</description> <macros> <import>snpSift_macros.xml</import> @@ -7,7 +7,8 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ - java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" dbnsfp -v + @CONDA_SNPSIFT_JAR_PATH@ && + java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp -v #if $db.dbsrc == 'cached': -db "$db.dbnsfp" #if $db.annotations and str($db.annotations) != '': @@ -60,17 +61,21 @@ <data format="vcf" name="output" /> </outputs> <tests> + <!-- This cannot be tested at the moment because test_dbnsfpdb.tabular + is converted from dbnsfp.tabular to snpsiftdbnsfp format on-the-fly + when this tool is run and annotation metadata is not available + until after the conversion is completed. <test> - <param name="input" ftype="vcf" value="test_annotate_in.vcf.vcf"/> + <param name="input" ftype="vcf" value="test_annotate_in.vcf"/> <param name="dbsrc" value="history"/> <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" /> - <annotations value="aaref,aaalt,genename,aapos,SIFT_score"/> + <param name="annotations" value="aaref,aaalt,genename,aapos,SIFT_score"/> <output name="output"> <assert_contents> <has_text text="dbNSFP_SIFT_score=0.15" /> </assert_contents> </output> - </test> + </test> --> </tests> <help><![CDATA[ @@ -279,9 +284,6 @@ @EXTERNAL_DOCUMENTATION@ http://snpeff.sourceforge.net/SnpSift.html#dbNSFP - -@CITATION_SECTION@ - ]]> </help> <expand macro="citations"> |
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| diff -r 13191d4914f7 -r c838e7136a40 snpSift_macros.xml --- a/snpSift_macros.xml Tue Jun 07 10:04:48 2016 -0400 +++ b/snpSift_macros.xml Mon Dec 05 12:06:13 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> |
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| diff -r 13191d4914f7 -r c838e7136a40 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jun 07 10:04:48 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="snpEff" version="4.1"> - <repository changeset_revision="374c7f8421fb" name="package_snpeff_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |