Mercurial > repos > iuc > snpeff
comparison snpEff.xml @ 4:698ef30638a8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
| author | iuc |
|---|---|
| date | Fri, 16 Sep 2016 13:06:42 -0400 |
| parents | b24873564cf6 |
| children | 2950d5afa3fe |
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| 3:b24873564cf6 | 4:698ef30638a8 |
|---|---|
| 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> | 9 <command> |
| 10 <![CDATA[ | 10 <![CDATA[ |
| 11 @CONDA_SNPEFF_JAR_PATH@ && | |
| 11 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff | 12 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff |
| 12 -c "\$SNPEFF_JAR_PATH/snpEff.config" | 13 -c "\$SNPEFF_JAR_PATH/snpEff.config" |
| 13 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength | 14 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength |
| 14 #if $spliceSiteSize and str($spliceSiteSize) != '': | 15 #if $spliceSiteSize and str($spliceSiteSize) != '': |
| 15 -spliceSiteSize "$spliceSiteSize" | 16 -spliceSiteSize "$spliceSiteSize" |
| 357 --> | 358 --> |
| 358 <param name="generate_stats" value="False"/> | 359 <param name="generate_stats" value="False"/> |
| 359 <output name="snpeff_output"> | 360 <output name="snpeff_output"> |
| 360 <assert_contents> | 361 <assert_contents> |
| 361 <!-- Check that deleletions were evaluated --> | 362 <!-- Check that deleletions were evaluated --> |
| 362 <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" /> | 363 <has_text_matching expression="Y\t59030478\t.*intergenic_region" /> |
| 363 <!-- Check that insertion on last line was NOT evaluated --> | 364 <!-- Check that insertion on last line was NOT evaluated --> |
| 364 <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" /> | 365 <has_text_matching expression="Y\t59032947\t.*\tGT" /> |
| 365 </assert_contents> | 366 </assert_contents> |
| 366 </output> | 367 </output> |
| 367 </test> | 368 </test> |
| 368 | 369 |
| 369 <!-- Check that NO UPSTREAM effect was added --> | 370 <!-- Check that NO UPSTREAM effect was added --> |