Mercurial > repos > jjohnson > snpsift_dbnsfp
changeset 4:772825adad2f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
| author | jjohnson |
|---|---|
| date | Sat, 09 Apr 2016 11:54:31 -0400 |
| parents | b5e03b2cb813 |
| children | |
| files | snpSift_dbnsfp.xml snpSift_macros.xml tool-data/snpsift_dbnsfp.loc.sample tool_dependencies.xml |
| diffstat | 4 files changed, 20 insertions(+), 10 deletions(-) [+] |
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--- a/snpSift_dbnsfp.xml Wed Dec 09 14:07:32 2015 -0500 +++ b/snpSift_dbnsfp.xml Sat Apr 09 11:54:31 2016 -0400 @@ -7,19 +7,19 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ - java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar dbnsfp -v - #if $db.dbsrc == 'cached' : - -db $db.dbnsfp - #if $db.annotations and $db.annotations.__str__ != '': + java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" dbnsfp -v + #if $db.dbsrc == 'cached': + -db "$db.dbnsfp" + #if $db.annotations and str($db.annotations) != '': -f "$db.annotations" #end if - #else : + #else: -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}" - #if $db.annotations and $db.annotations.__str__ != '': + #if $db.annotations and str($db.annotations) != '': -f "$db.annotations" #end if - #end if - $input > $output + #end if + "$input" > "$output" 2> tmp.err && grep -v file tmp.err ]]> </command> @@ -284,4 +284,12 @@ ]]> </help> + <expand macro="citations"> + <citation type="doi">DOI: 10.1002/humu.21517</citation> + <citation type="doi">DOI: 10.1002/humu.22376</citation> + <citation type="doi">DOI: 10.1002/humu.22932</citation> + <citation type="doi">doi: 10.1093/hmg/ddu733</citation> + <citation type="doi">doi: 10.1093/nar/gku1206</citation> + <citation type="doi">doi: 10.3389/fgene.2012.00035</citation> + </expand> </tool>
--- a/snpSift_macros.xml Wed Dec 09 14:07:32 2015 -0500 +++ b/snpSift_macros.xml Sat Apr 09 11:54:31 2016 -0400 @@ -11,7 +11,7 @@ </stdio> </xml> <xml name="version_command"> - <version_command>java -jar $SNPEFF_JAR_PATH/SnpEff.jar -version</version_command> + <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command> </xml> <token name="@WRAPPER_VERSION@">4.1</token> <token name="@EXTERNAL_DOCUMENTATION@">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpsift_dbnsfp.loc.sample Sat Apr 09 11:54:31 2016 -0400 @@ -0,0 +1,2 @@ +#id desc path annotations +#GRCh37_dbNSFP2.1 GRCh37 dbNSFP2.1 /depot/snpeff/ SIFT_pred,Uniprot_acc
--- a/tool_dependencies.xml Wed Dec 09 14:07:32 2015 -0500 +++ b/tool_dependencies.xml Sat Apr 09 11:54:31 2016 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="snpEff" version="4.1"> - <repository changeset_revision="02a5e07a4121" name="package_snpeff_4_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="625bc8f7929d" name="package_snpeff_4_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>