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comparison deseq2_macros.xml @ 31:9a882d108833 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
author iuc
date Tue, 18 Jul 2023 14:58:52 +0000
parents 8fe98f7094de
children
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30:8fe98f7094de 31:9a882d108833
1 <macros>
2 <xml name="factor_repeat">
3 <repeat name="rep_factorName" title="Factor" min="1">
4 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers"
5 help="Only letters, numbers and underscores will be retained in this field">
6 <sanitizer>
7 <valid initial="string.letters,string.digits"><add value="_" /></valid>
8 </sanitizer>
9 </param>
10 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
11 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
12 help="Only letters, numbers and underscores will be retained in this field">
13 <sanitizer>
14 <valid initial="string.letters,string.digits"><add value="_" /></valid>
15 </sanitizer>
16 </param>
17 <yield/>
18 </repeat>
19 </repeat>
20 </xml>
21 <xml name="requirements">
22 <requirements>
23 <requirement type="package" version="1.34.0">bioconductor-deseq2</requirement>
24 <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->
25 <requirement type="package" version="2.38.0">bioconductor-rhdf5</requirement>
26 <requirement type="package" version="1.22.0">bioconductor-tximport</requirement>
27 <requirement type="package" version="1.46.1">bioconductor-genomicfeatures</requirement>
28 <requirement type="package" version="1.20.3">r-getopt</requirement>
29 <requirement type="package" version="0.9.1">r-ggrepel</requirement>
30 <requirement type="package" version="3.1.1">r-gplots</requirement>
31 <requirement type="package" version="1.0.12">r-pheatmap</requirement>
32 <requirement type="package" version="0.2.20">r-rjson</requirement>
33 </requirements>
34 </xml>
35 <token name="@TOOL_VERSION@">2.11.40.7</token>
36 <token name="@SUFFIX_VERSION@">2</token>
37 <xml name="edam_ontology">
38 <edam_topics>
39 <edam_topic>topic_3308</edam_topic>
40 </edam_topics>
41 <edam_operations>
42 <edam_operation>operation_3800</edam_operation>
43 </edam_operations>
44 </xml>
45 <xml name="citations">
46 <citations>
47 <citation type="doi">10.1186/s13059-014-0550-8</citation>
48 </citations>
49 </xml>
50 <xml name="xrefs">
51 <xrefs>
52 <xref type='bio.tools'>DESeq2</xref>
53 </xrefs>
54 </xml>
55 </macros>