Mercurial > repos > jjohnson > snpeff
annotate snpSift_int.xml @ 9:937367efb1da default tip
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 18 Sep 2013 10:49:56 -0500 |
| parents | 13b6ad2ddace |
| children |
| rev | line source |
|---|---|
| 8 | 1 <tool id="snpSift_int" name="SnpSift Intervals" version="3.2"> |
| 0 | 2 <description>Filter variants using intervals </description> |
| 3 <!-- | |
| 4 You will need to change the path to wherever your installation is. | |
| 5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
| 6 --> | |
| 7 <requirements> | |
| 8 | 8 <requirement type="package" version="3.2">snpEff</requirement> |
| 0 | 9 </requirements> |
| 10 <command> | |
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9
937367efb1da
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
Jim Johnson <jj@umn.edu>
parents:
8
diff
changeset
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11 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output |
| 0 | 12 </command> |
| 13 <inputs> | |
| 14 <param format="vcf" name="input" type="data" label="VCF input"/> | |
| 15 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/> | |
| 8 | 16 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" |
| 17 help="Filter out (exclude) VCF entries that match any interval in the BED files"/> | |
| 0 | 18 </inputs> |
| 19 <outputs> | |
| 20 <data format="vcf" name="output" /> | |
| 21 </outputs> | |
| 22 <stdio> | |
| 23 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 24 <exit_code range="1:" level="fatal" description="Error" /> | |
| 25 </stdio> | |
| 5 | 26 <tests> |
| 8 | 27 |
| 5 | 28 <test> |
| 29 <param name="input" ftype="vcf" value="annotate_5.vcf"/> | |
|
6
ec16dae84230
Fix tests for SnpSift caseControl and intervals
Jim Johnson <jj@umn.edu>
parents:
5
diff
changeset
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30 <param name="bedFile" ftype="bed" value="interval.bed"/> |
| 8 | 31 <param name="exclude" value="False"/> |
| 5 | 32 <output name="output"> |
| 33 <assert_contents> | |
| 34 <has_text text="872687" /> | |
| 35 <not_has_text text="1195966" /> | |
| 36 </assert_contents> | |
| 37 </output> | |
| 38 </test> | |
| 39 | |
| 8 | 40 <test> |
| 41 <param name="input" ftype="vcf" value="annotate_5.vcf"/> | |
| 42 <param name="bedFile" ftype="bed" value="interval.bed"/> | |
| 43 <param name="exclude" value="True"/> | |
| 44 <output name="output"> | |
| 45 <assert_contents> | |
| 46 <has_text text="1195966" /> | |
| 47 <not_has_text text="872687" /> | |
| 48 </assert_contents> | |
| 49 </output> | |
| 50 </test> | |
| 51 | |
| 5 | 52 </tests> |
| 53 | |
| 0 | 54 <help> |
| 55 | |
| 56 You can filter using intervals (BED file) | |
| 57 | |
| 58 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals | |
| 59 | |
| 60 </help> | |
| 61 </tool> |