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comparison goseq.xml @ 10:43798b4caee0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 21f3eae641dd20a0f8724e0a05910396df8d028f
author iuc
date Thu, 09 Jun 2022 13:01:48 +0000
parents ef2ad746b589
children 602de62d995b
comparison
equal deleted inserted replaced
9:ef2ad746b589 10:43798b4caee0
1 <tool id="goseq" name="goseq" version="@VERSION@+@GALAXY_VERSION@"> 1 <tool id="goseq" name="goseq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>tests for overrepresented gene categories</description> 2 <description>tests for overrepresented gene categories</description>
3 <xrefs> 3 <xrefs>
4 <xref type="bio.tools">goseq</xref> 4 <xref type="bio.tools">goseq</xref>
5 </xrefs> 5 </xrefs>
6 <edam_topics> 6 <edam_topics>
8 </edam_topics> 8 </edam_topics>
9 <edam_operations> 9 <edam_operations>
10 <edam_operation>operation_2436</edam_operation> 10 <edam_operation>operation_2436</edam_operation>
11 </edam_operations> 11 </edam_operations>
12 <macros> 12 <macros>
13 <token name="@VERSION@">1.44.0</token> 13 <token name="@TOOL_VERSION@">1.44.0</token>
14 <token name="@GALAXY_VERSION@">galaxy0</token> 14 <token name="@VERSION_SUFFIX@">2</token>
15 </macros> 15 </macros>
16 <requirements> 16 <requirements>
17 <requirement type="package" version="@VERSION@">bioconductor-goseq</requirement> 17 <requirement type="package" version="@TOOL_VERSION@">bioconductor-goseq</requirement>
18 <requirement type="package" version="3.13.0">bioconductor-org.hs.eg.db</requirement> 18 <requirement type="package" version="3.13.0">bioconductor-org.hs.eg.db</requirement>
19 <requirement type="package" version="3.13.0">bioconductor-org.dm.eg.db</requirement> 19 <requirement type="package" version="3.13.0">bioconductor-org.dm.eg.db</requirement>
20 <requirement type="package" version="3.13.0">bioconductor-org.dr.eg.db</requirement> 20 <requirement type="package" version="3.13.0">bioconductor-org.dr.eg.db</requirement>
21 <requirement type="package" version="3.13.0">bioconductor-org.mm.eg.db</requirement> 21 <requirement type="package" version="3.13.0">bioconductor-org.mm.eg.db</requirement>
22 <requirement type="package" version="1.0.6">r-dplyr</requirement> 22 <requirement type="package" version="3.13.0">bioconductor-org.rn.eg.db</requirement>
23 <requirement type="package" version="3.3.3">r-ggplot2</requirement> 23 <requirement type="package" version="1.0.9">r-dplyr</requirement>
24 <requirement type="package" version="1.6.6">r-optparse</requirement> 24 <requirement type="package" version="3.3.6">r-ggplot2</requirement>
25 <requirement type="package" version="1.7.1">r-optparse</requirement>
26 <requirement type="package" version="1.1.1o">openssl</requirement>
25 </requirements> 27 </requirements>
26 <stdio> 28 <stdio>
27 <regex match="Execution halted" 29 <regex match="Execution halted"
28 source="both" 30 source="both"
29 level="fatal" 31 level="fatal"
102 <param name="genome" type="select" label="Select a genome to use"> 104 <param name="genome" type="select" label="Select a genome to use">
103 <option value="hg38">Human (hg38)</option> 105 <option value="hg38">Human (hg38)</option>
104 <option value="mm10">Mouse (mm10)</option> 106 <option value="mm10">Mouse (mm10)</option>
105 <option value="dm6">Fruit fly (dm6)</option> 107 <option value="dm6">Fruit fly (dm6)</option>
106 <option value="danRer10">Zebrafish (danRer10)</option> 108 <option value="danRer10">Zebrafish (danRer10)</option>
109 <option value="rn6">Rat (rn6)</option>
107 </param> 110 </param>
108 <param name="gene_id" type="select" label="Select Gene ID format" help="Supported Gene IDs to automatically fetch categories should either be Entrez, Ensembl, or gene symbols."> 111 <param name="gene_id" type="select" label="Select Gene ID format" help="Supported Gene IDs to automatically fetch categories should either be Entrez, Ensembl, or gene symbols.">
109 <option value="ensGene">Ensembl Gene ID</option> 112 <option value="ensGene">Ensembl Gene ID</option>
110 <option value="knownGene">Entrez Gene ID</option> 113 <option value="knownGene">Entrez Gene ID</option>
111 <option value="geneSymbol">Gene Symbol</option> 114 <option value="geneSymbol">Gene Symbol</option>