Mercurial > repos > jjohnson > snpsift
annotate snpSift_int.xml @ 9:88f4997ccb02 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
| author | jjohnson |
|---|---|
| date | Mon, 11 Apr 2016 09:31:49 -0400 |
| parents | 2f40467536cf |
| children |
| rev | line source |
|---|---|
| 4 | 1 <tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.0"> |
| 0 | 2 <description>Filter variants using intervals</description> |
| 3 <!-- | |
| 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
| 5 --> | |
| 4 | 6 <macros> |
| 7 <import>snpSift_macros.xml</import> | |
| 8 </macros> | |
| 0 | 9 <expand macro="requirements" /> |
| 4 | 10 <expand macro="stdio" /> |
| 11 <expand macro="version_command" /> | |
| 12 <command><![CDATA[ | |
|
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2f40467536cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
jjohnson
parents:
4
diff
changeset
|
13 java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output" |
| 4 | 14 ]]> |
| 0 | 15 </command> |
| 16 <inputs> | |
| 17 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> | |
| 18 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/> | |
| 19 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" | |
| 20 help="Filter out (exclude) VCF entries that match any interval in the BED files"/> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data format="vcf" name="output" /> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 <test> | |
| 27 <param name="input" ftype="vcf" value="annotate_5.vcf"/> | |
| 28 <param name="bedFile" ftype="bed" value="interval.bed"/> | |
| 29 <param name="exclude" value="False"/> | |
| 30 <output name="output"> | |
| 31 <assert_contents> | |
| 32 <has_text text="872687" /> | |
| 33 <not_has_text text="1195966" /> | |
| 34 </assert_contents> | |
| 35 </output> | |
| 36 </test> | |
| 37 <test> | |
| 38 <param name="input" ftype="vcf" value="annotate_5.vcf"/> | |
| 39 <param name="bedFile" ftype="bed" value="interval.bed"/> | |
| 40 <param name="exclude" value="True"/> | |
| 41 <output name="output"> | |
| 42 <assert_contents> | |
| 43 <has_text text="1195966" /> | |
| 44 <not_has_text text="872687" /> | |
| 45 </assert_contents> | |
| 46 </output> | |
| 47 </test> | |
| 48 </tests> | |
| 4 | 49 <help><![CDATA[ |
| 0 | 50 |
| 51 You can filter using intervals (BED file). | |
| 52 | |
| 53 @EXTERNAL_DOCUMENTATION@ | |
| 4 | 54 http://snpeff.sourceforge.net/SnpSift.html#intervals |
| 0 | 55 |
| 4 | 56 ]]> |
| 0 | 57 </help> |
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2f40467536cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
jjohnson
parents:
4
diff
changeset
|
58 <expand macro="citations" /> |
| 0 | 59 </tool> |