Mercurial > repos > jjohnson > snpeff
annotate snpSift_int.xml @ 7:b26a1aff7f81
Fix issues with snpEff commandline template and add test cases
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 28 Mar 2013 12:29:45 -0500 |
| parents | ec16dae84230 |
| children | 13b6ad2ddace |
| rev | line source |
|---|---|
| 0 | 1 <tool id="snpSift_int" name="SnpSift Intervals" version="3.1"> |
| 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 <requirement type="package" version="3.1">snpEff</requirement> | |
| 9 </requirements> | |
| 10 <command> | |
| 11 cat $input | java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output | |
| 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)"/> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format="vcf" name="output" /> | |
| 19 </outputs> | |
| 20 <stdio> | |
| 21 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 22 <exit_code range="1:" level="fatal" description="Error" /> | |
| 23 </stdio> | |
| 5 | 24 <tests> |
| 25 <test> | |
| 26 <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
|
27 <param name="bedFile" ftype="bed" value="interval.bed"/> |
| 5 | 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 | |
| 36 </tests> | |
| 37 | |
| 0 | 38 <help> |
| 39 | |
| 40 You can filter using intervals (BED file) | |
| 41 | |
| 42 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals | |
| 43 | |
| 44 </help> | |
| 45 </tool> |