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comparison edger.xml @ 5:fb9b9f0f2f06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 91bdcc6a5a46173be6546d590cdf3f311c2b1476
author iuc
date Tue, 05 Feb 2019 20:57:30 -0500
parents 4730985c816f
children 555659de7321
comparison
equal deleted inserted replaced
4:4730985c816f 5:fb9b9f0f2f06
1 <tool id="edger" name="edgeR" version="3.22.5"> 1 <tool id="edger" name="edgeR" version="3.24.1">
2 <description> 2 <description>
3 Perform differential expression of count data 3 Perform differential expression of count data
4 </description> 4 </description>
5 5
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3.22.5">bioconductor-edger</requirement> 7 <requirement type="package" version="3.24.1">bioconductor-edger</requirement>
8 <requirement type="package" version="3.36.5">bioconductor-limma</requirement> 8 <requirement type="package" version="3.38.3">bioconductor-limma</requirement>
9 <requirement type="package" version="0.2.20">r-rjson</requirement> 9 <requirement type="package" version="0.2.20">r-rjson</requirement>
10 <requirement type="package" version="1.20.2">r-getopt</requirement> 10 <requirement type="package" version="1.20.2">r-getopt</requirement>
11 <requirement type="package" version="1.4.30">r-statmod</requirement> 11 <requirement type="package" version="1.4.30">r-statmod</requirement>
12 <!-- required for alpha function used with plotMD --> 12 <!-- required for alpha function used with plotMD -->
13 <requirement type="package" version="1.0.0">r-scales</requirement> 13 <requirement type="package" version="1.0.0">r-scales</requirement>
422 </assert_contents> 422 </assert_contents>
423 </element> 423 </element>
424 <element name="edgeR_normcounts" ftype="tabular" > 424 <element name="edgeR_normcounts" ftype="tabular" >
425 <assert_contents> 425 <assert_contents>
426 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" /> 426 <has_text_matching expression="GeneID.*Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
427 <has_text_matching expression="11304.*15.7535" /> 427 <has_text_matching expression="11304.*15.75" />
428 </assert_contents> 428 </assert_contents>
429 </element> 429 </element>
430 </output_collection> 430 </output_collection>
431 </test> 431 </test>
432 <!-- Ensure likelihood ratio option works --> 432 <!-- Ensure likelihood ratio option works -->
501 </assert_contents> 501 </assert_contents>
502 </element> 502 </element>
503 <element name="edgeR_normcounts" ftype="tabular" > 503 <element name="edgeR_normcounts" ftype="tabular" >
504 <assert_contents> 504 <assert_contents>
505 <has_text_matching expression="Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" /> 505 <has_text_matching expression="Mut1.*Mut2.*Mut3.*WT1.*WT2.*WT3" />
506 <has_text_matching expression="11304.*Abca4.*15.7535" /> 506 <has_text_matching expression="11304.*Abca4.*15.75" />
507 </assert_contents> 507 </assert_contents>
508 </element> 508 </element>
509 </output_collection> 509 </output_collection>
510 </test> 510 </test>
511 <!-- Ensure filtering on CPM in Mnimum Samples works --> 511 <!-- Ensure filtering on CPM in Mnimum Samples works -->