Mercurial > repos > proteore > proteore_kegg_pathways_coverage
comparison kegg_identification.xml @ 2:60368fca9772 draft
planemo upload commit 89cd1b5f2ca7b135abfe2d9ed18bf2478a59e099-dirty
| author | proteore |
|---|---|
| date | Tue, 05 Mar 2019 09:37:56 -0500 |
| parents | d600ce7f2484 |
| children | 0308c2d81607 |
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| 1:d600ce7f2484 | 2:60368fca9772 |
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| 1 <tool id="kegg_identification" name="KEGG pathways identification" version="2018.12.12"> | 1 <tool id="kegg_identification" name="Pathways identification" version="2019.03.05"> |
| 2 <description>and coverage</description> | 2 <description>and coverage [KEGG]</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement> | 4 <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
| 7 Rscript $__tool_directory__/kegg_identification.R | 7 Rscript $__tool_directory__/kegg_identification.R |
| 39 </param> | 39 </param> |
| 40 </when> | 40 </when> |
| 41 <when value="file" > | 41 <when value="file" > |
| 42 <param name="file" type="data" format="txt,tabular,tsv" label="Select your file" help="" /> | 42 <param name="file" type="data" format="txt,tabular,tsv" label="Select your file" help="" /> |
| 43 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> | 43 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> |
| 44 <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> | 44 <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> |
| 45 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> | |
| 46 </param> | |
| 45 </when> | 47 </when> |
| 46 </conditional> | 48 </conditional> |
| 47 <param name="id_type" type="select" label="Select IDs" > | 49 <param name="id_type" type="select" label="Select IDs" > |
| 48 <option value="ncbi-geneid" selected="true">Entrez Gene ID</option> | 50 <option value="ncbi-geneid" selected="true">Entrez Gene ID</option> |
| 49 <option value="kegg-id">KEGG gene ID</option> | 51 <option value="kegg-id">KEGG gene ID</option> |