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comparison tximport.xml @ 1:3e2f1aef1aac draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
author iuc
date Thu, 23 Sep 2021 00:17:50 +0000
parents d53de4a14836
children 865d5bc8f531
comparison
equal deleted inserted replaced
0:d53de4a14836 1:3e2f1aef1aac
1 <tool id="tximport" name="tximport" version="0.1"> 1 <tool id="tximport" name="tximport" version="@TOOL_VERSION@" profile="20.09">
2 <macros>
3 <token name="@TOOL_VERSION@">1.20.0</token>
4 </macros>
2 <description>Summarize transcript-level estimates for gene-level analysis</description> 5 <description>Summarize transcript-level estimates for gene-level analysis</description>
6 <xrefs>
7 <xref type="bio.tools">tximport</xref>
8 </xrefs>
3 <requirements> 9 <requirements>
4 <requirement type="package">bioconductor-tximport</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">bioconductor-tximport</requirement>
5 <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement> 11 <requirement type="package" version="1.44.0">bioconductor-genomicfeatures</requirement>
6 <requirement type="package" version="1.20.2">r-getopt</requirement> 12 <requirement type="package" version="1.20.3">r-getopt</requirement>
7 </requirements> 13 </requirements>
8 14
9 <stdio> 15 <stdio>
10 <exit_code range="1:" level="fatal" description="Error code returned" /> 16 <exit_code range="1:" level="fatal" description="Error code returned" />
11 <regex match="is not TRUE" 17 <regex match="is not TRUE"
121 </conditional> 127 </conditional>
122 </when> 128 </when>
123 </conditional> 129 </conditional>
124 <param name="counts_from_abundance" type="select" label="Summarization using the abundance (TPM) values?"> 130 <param name="counts_from_abundance" type="select" label="Summarization using the abundance (TPM) values?">
125 <option value="no">No</option> 131 <option value="no">No</option>
126 <option value="scaled_TPM">Scaled up to library size</option> 132 <option value="scaledTPM">Scaled up to library size</option>
127 <option value="length_scaled_TPM">Scaled using the avg. transcript legth over samples and then the library size</option> 133 <option value="lengthScaledTPM">Scaled using the avg. transcript legth over samples and then the library size</option>
128 <option value="dtu_scaled_TPM">Scaled using the median transcript length among isoforms of a gene, and then the library size</option> 134 <option value="dtuScaledTPM">Scaled using the median transcript length among isoforms of a gene, and then the library size</option>
129 </param> 135 </param>
130 </inputs> 136 </inputs>
131 <outputs> 137 <outputs>
132 <data name="gene_level_values" format="tabular" label="Gene level summarization on ${on_string}"/> 138 <data name="gene_level_values" format="tabular" label="Gene level summarization on ${on_string}"/>
133 </outputs> 139 </outputs>