Mercurial > repos > iuc > snpsift
annotate snpSift_int.xml @ 11:b884686a80dc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
| author | iuc |
|---|---|
| date | Mon, 04 May 2015 22:37:06 -0400 |
| parents | f0faaa4d6ee5 |
| children | ed810da439cc |
| rev | line source |
|---|---|
| 0 | 1 <tool id="snpSift_int" name="SnpSift Intervals" version="4.0.0"> |
| 2 <description>Filter variants using intervals</description> | |
|
11
b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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0
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|
3 <!-- |
| 0 | 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) |
| 5 --> | |
| 6 <macros> | |
| 7 <import>snpSift_macros.xml</import> | |
| 8 </macros> | |
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11
b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
0
diff
changeset
|
9 <expand macro="requirements" /> |
|
b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
0
diff
changeset
|
10 <expand macro="stdio" /> |
| 0 | 11 <command> |
| 12 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> | |
| 16 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/> | |
|
11
b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
0
diff
changeset
|
17 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" |
| 0 | 18 help="Filter out (exclude) VCF entries that match any interval in the BED files"/> |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data format="vcf" name="output" /> | |
| 22 </outputs> | |
| 23 <tests> | |
| 24 <test> | |
| 25 <param name="input" ftype="vcf" value="annotate_5.vcf"/> | |
| 26 <param name="bedFile" ftype="bed" value="interval.bed"/> | |
| 27 <param name="exclude" value="False"/> | |
| 28 <output name="output"> | |
| 29 <assert_contents> | |
| 30 <has_text text="872687" /> | |
| 31 <not_has_text text="1195966" /> | |
| 32 </assert_contents> | |
| 33 </output> | |
| 34 </test> | |
| 35 <test> | |
| 36 <param name="input" ftype="vcf" value="annotate_5.vcf"/> | |
| 37 <param name="bedFile" ftype="bed" value="interval.bed"/> | |
| 38 <param name="exclude" value="True"/> | |
| 39 <output name="output"> | |
| 40 <assert_contents> | |
| 41 <has_text text="1195966" /> | |
| 42 <not_has_text text="872687" /> | |
| 43 </assert_contents> | |
| 44 </output> | |
| 45 </test> | |
| 46 </tests> | |
| 47 <help> | |
| 48 | |
| 49 You can filter using intervals (BED file). | |
| 50 | |
| 51 @EXTERNAL_DOCUMENTATION@ | |
| 52 http://snpeff.sourceforge.net/SnpSift.html#intervals | |
| 53 | |
| 54 @CITATION_SECTION@ | |
| 55 | |
| 56 </help> | |
| 57 </tool> |