Mercurial > repos > jjohnson > snpsift_dbnsfp

comparison snpSift_dbnsfp.xml @ 4:772825adad2f draft default tip

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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
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3:b5e03b2cb813 4:772825adad2f
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command><![CDATA[ 9 <command><![CDATA[
10 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar dbnsfp -v 10 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" dbnsfp -v
11 #if $db.dbsrc == 'cached' : 11 #if $db.dbsrc == 'cached':
12 -db $db.dbnsfp 12 -db "$db.dbnsfp"
13 #if $db.annotations and $db.annotations.__str__ != '': 13 #if $db.annotations and str($db.annotations) != '':
14 -f "$db.annotations" 14 -f "$db.annotations"
15 #end if 15 #end if
16 #else : 16 #else:
17 -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}" 17 -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}"
18 #if $db.annotations and $db.annotations.__str__ != '': 18 #if $db.annotations and str($db.annotations) != '':
19 -f "$db.annotations" 19 -f "$db.annotations"
20 #end if 20 #end if
21 #end if 21 #end if
22 $input > $output 22 "$input" > "$output"
23 2> tmp.err && grep -v file tmp.err 23 2> tmp.err && grep -v file tmp.err
24 ]]> 24 ]]>
25 </command> 25 </command>
26 <inputs> 26 <inputs>
27 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/> 27 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
282 282
283 @CITATION_SECTION@ 283 @CITATION_SECTION@
284 284
285 ]]> 285 ]]>
286 </help> 286 </help>
287 <expand macro="citations">
288 <citation type="doi">DOI: 10.1002/humu.21517</citation>
289 <citation type="doi">DOI: 10.1002/humu.22376</citation>
290 <citation type="doi">DOI: 10.1002/humu.22932</citation>
291 <citation type="doi">doi: 10.1093/hmg/ddu733</citation>
292 <citation type="doi">doi: 10.1093/nar/gku1206</citation>
293 <citation type="doi">doi: 10.3389/fgene.2012.00035</citation>
294 </expand>
287 </tool> 295 </tool>