Mercurial > repos > iuc > tximport
comparison tximport.xml @ 1:2c338211927c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
author | iuc |
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date | Thu, 23 Sep 2021 00:18:22 +0000 |
parents | 206a71a69161 |
children | 1906cb429215 |
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0:206a71a69161 | 1:2c338211927c |
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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> |