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comparison deseq2.xml @ 20:89d26b11d452 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
author iuc
date Thu, 06 Dec 2018 15:49:22 -0500
parents c56e0689e46e
children a6fc9228e1a0
comparison
equal deleted inserted replaced
19:c56e0689e46e 20:89d26b11d452
346 <assert_contents> 346 <assert_contents>
347 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" /> 347 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
348 </assert_contents> 348 </assert_contents>
349 </output> 349 </output>
350 </test> 350 </test>
351 <!--Ensure Sailfish/Salmon input with GFF3 annotation works--> 351 <!--Ensure Sailfish/Salmon input with GFF3 annotation from NCBI works-->
352 <test expect_num_outputs="1"> 352 <test expect_num_outputs="1">
353 <repeat name="rep_factorName"> 353 <repeat name="rep_factorName">
354 <param name="factorName" value="Treatment"/> 354 <param name="factorName" value="Treatment"/>
355 <repeat name="rep_factorLevel"> 355 <repeat name="rep_factorLevel">
356 <param name="factorLevel" value="Treated"/> 356 <param name="factorLevel" value="Treated"/>
367 <param name="mapping_format_selector" value="gtf"/> 367 <param name="mapping_format_selector" value="gtf"/>
368 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/> 368 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/>
369 <output name="deseq_out" > 369 <output name="deseq_out" >
370 <assert_contents> 370 <assert_contents>
371 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" /> 371 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
372 </assert_contents>
373 </output>
374 </test>
375 <!--Ensure Sailfish/Salmon input with GTF annotation from Ensembl works-->
376 <test expect_num_outputs="1">
377 <repeat name="rep_factorName">
378 <param name="factorName" value="Treatment"/>
379 <repeat name="rep_factorLevel">
380 <param name="factorLevel" value="Treated"/>
381 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
382 </repeat>
383 <repeat name="rep_factorLevel">
384 <param name="factorLevel" value="Untreated"/>
385 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
386 </repeat>
387 </repeat>
388 <param name="pdf" value="False"/>
389 <param name="tximport_selector" value="tximport"/>
390 <param name="txtype" value="sailfish"/>
391 <param name="mapping_format_selector" value="gtf"/>
392 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
393 <output name="deseq_out" >
394 <assert_contents>
395 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" />
372 </assert_contents> 396 </assert_contents>
373 </output> 397 </output>
374 </test> 398 </test>
375 </tests> 399 </tests>
376 <help><![CDATA[ 400 <help><![CDATA[