Mercurial > repos > proteore > proteore_maps_visualization

comparison kegg_maps_visualization.xml @ 10:a4db9efe1e43 draft

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"planemo upload commit 78a50fa16dcea6afd93a2f4de17ed193a2aa7dd3-dirty"
author proteore
date Mon, 02 Mar 2020 09:23:05 +0000
parents 9ac0ade20b3f
children 7d04efde2526
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9:9ac0ade20b3f 10:a4db9efe1e43
1 <tool id="kegg_maps_visualization" name="Pathways visualization" version="2020.01.08"> 1 <tool id="kegg_maps_visualization" name="KEGG pathways mapping and visualization" version="2020.03.02">
2 <description>of (differentially expressed) genes/proteins [KEGG]</description> 2 <description>[PathView]</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.6.2" >R</requirement> 4 <requirement type="package" version="3.6.2" >R</requirement>
5 <requirement type="package" version="1.26.0">bioconductor-pathview</requirement> 5 <requirement type="package" version="1.26.0">bioconductor-pathview</requirement>
6 <requirement type="package" version="1.26.0">bioconductor-keggrest</requirement> 6 <requirement type="package" version="1.26.0">bioconductor-keggrest</requirement>
7 <requirement type="package" version="1.30.10">r-biocmanager</requirement>
7 </requirements> 8 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 Rscript $__tool_directory__/kegg_maps_visualization.R 10 Rscript $__tool_directory__/kegg_maps_visualization.R
10 #if $input.ids == "text" 11 #if $input.ids == "text"
11 --id_list="$input.txt" 12 --id_list="$input.txt"
259 - giving a list of KEGG pathway IDs (e.g.hsa00010) (copy/paste mode) 260 - giving a list of KEGG pathway IDs (e.g.hsa00010) (copy/paste mode)
260 - selecting a list from a dataset (column) - for instance, output from the "KEGG pathways identification and coverage" tool can be used (1st column, c1) 261 - selecting a list from a dataset (column) - for instance, output from the "KEGG pathways identification and coverage" tool can be used (1st column, c1)
261 2. "Select ID type for genes to map on the pathway(s)": Identifiers to map can be either a list of Entrez genes IDs, KEGG genes ID or Uniprot accession number. IDs to be mapped can be either provided by copy/paste or a file (tabular, tsv, txt) with a column containing the IDs. 262 2. "Select ID type for genes to map on the pathway(s)": Identifiers to map can be either a list of Entrez genes IDs, KEGG genes ID or Uniprot accession number. IDs to be mapped can be either provided by copy/paste or a file (tabular, tsv, txt) with a column containing the IDs.
262 3. "Map quantitative data on the pathway ?": Yes/No (default is No). Fold change values (up to three columns) from a dataset (same file as identifiers to map) can be graphically represented on the final figure (using a range of color representing the fold-change values). 263 3. "Map quantitative data on the pathway ?": Yes/No (default is No). Fold change values (up to three columns) from a dataset (same file as identifiers to map) can be graphically represented on the final figure (using a range of color representing the fold-change values).
263 264
265 .. class:: warningmark
266
267 Some pathway ids causes error with the KEGG API: **hsa04215**, **mmu04723**. These ids will not be used if present in input.
268
269
264 Below is an example of an input file with identifiers (uniprot_AC) and fold_change values. 270 Below is an example of an input file with identifiers (uniprot_AC) and fold_change values.
265 271
266 .. csv-table:: Simulated data 272 .. csv-table:: Simulated data
267 :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3" 273 :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3"
268 274