| Previous changeset 3:b24873564cf6 (2016-06-07) Next changeset 5:2950d5afa3fe (2016-12-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d |
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modified:
snpEff.xml snpEff_databases.xml snpEff_download.xml snpEff_macros.xml |
| b |
| diff -r b24873564cf6 -r 698ef30638a8 snpEff.xml --- a/snpEff.xml Tue Jun 07 10:03:17 2016 -0400 +++ b/snpEff.xml Fri Sep 16 13:06:42 2016 -0400 |
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| @@ -8,6 +8,7 @@ <expand macro="version_command" /> <command> <![CDATA[ + @CONDA_SNPEFF_JAR_PATH@ && java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff -c "\$SNPEFF_JAR_PATH/snpEff.config" -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength @@ -359,9 +360,9 @@ <output name="snpeff_output"> <assert_contents> <!-- Check that deleletions were evaluated --> - <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" /> + <has_text_matching expression="Y\t59030478\t.*intergenic_region" /> <!-- Check that insertion on last line was NOT evaluated --> - <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" /> + <has_text_matching expression="Y\t59032947\t.*\tGT" /> </assert_contents> </output> </test> |
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| diff -r b24873564cf6 -r 698ef30638a8 snpEff_databases.xml --- a/snpEff_databases.xml Tue Jun 07 10:03:17 2016 -0400 +++ b/snpEff_databases.xml Fri Sep 16 13:06:42 2016 -0400 |
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| @@ -8,6 +8,7 @@ <expand macro="version_command" /> <command> <![CDATA[ + @CONDA_SNPEFF_JAR_PATH@ && java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > "$snpeff_dbs" ]]> </command> |
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| diff -r b24873564cf6 -r 698ef30638a8 snpEff_download.xml --- a/snpEff_download.xml Tue Jun 07 10:03:17 2016 -0400 +++ b/snpEff_download.xml Fri Sep 16 13:06:42 2016 -0400 |
| [ |
| @@ -8,6 +8,7 @@ <expand macro="version_command" /> <command> <![CDATA[ + @CONDA_SNPEFF_JAR_PATH@ && java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" download -c "\$SNPEFF_JAR_PATH/snpEff.config" -dataDir "$snpeff_db.files_path" -v "$genome_version" ]]> </command> |
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| diff -r b24873564cf6 -r 698ef30638a8 snpEff_macros.xml --- a/snpEff_macros.xml Tue Jun 07 10:03:17 2016 -0400 +++ b/snpEff_macros.xml Fri Sep 16 13:06:42 2016 -0400 |
| [ |
| @@ -10,8 +10,13 @@ <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> + <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token> <xml name="version_command"> - <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command> + <version_command><![CDATA[ + if [ -z "$SNPEFF_JAR_PATH" ]; then + export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff))); + fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version + ]]></version_command> </xml> <token name="@WRAPPER_VERSION@">4.1</token> <token name="@SNPEFF_VERSION@">SnpEff4.1</token> @@ -22,16 +27,6 @@ http://snpeff.sourceforge.net/SnpEff_manual.html </token> - <token name="@CITATION_SECTION@">------ - -**Citation** - -For the underlying tool, please cite the following two publications: - -SnpEff citation: -"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly 6(2):80-92, 2012 - - </token> <xml name="citations"> <citations> <citation type="doi">10.4161/fly.19695</citation> |