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comparison snpEff.xml @ 4:698ef30638a8 draft

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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
comparison
equal deleted inserted replaced
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 -->