comparison kegg_maps_visualization.xml @ 6:eb140217a9f1 draft default tip

"planemo upload commit 1f9a98db2496834cc38a281cbe3d4b11de2bc3d2-dirty"

5:4a3056be0774

<tool id="kegg_maps_visualization" name="KEGG pathways mapping and visualization" version="2020.01.23">
    <description>[PathView]</description>
    <requirements>
        <requirement type="package" version="3.6.2" >R</requirement>
        <requirement type="package" version="1.26.0">bioconductor-pathview</requirement>
        <requirement type="package" version="1.26.0">bioconductor-keggrest</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript $__tool_directory__/kegg_maps_visualization.R 
        #if $input.ids == "text"
            --id_list="$input.txt"

    - giving a list of KEGG pathway IDs (e.g.hsa00010) (copy/paste mode)
    - selecting a list from a dataset (column) - for instance, output from the "KEGG pathways identification and coverage" tool can be used (1st column, c1)
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. 
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).

Below is an example of an input file with identifiers (uniprot_AC) and fold_change values.

.. csv-table:: Simulated data
   :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3"

6:eb140217a9f1

<tool id="kegg_maps_visualization" name="KEGG pathways mapping and visualization" version="2020.03.05">
    <description>[PathView]</description>
    <requirements>
        <requirement type="package" version="3.6.2" >R</requirement>
        <requirement type="package" version="1.26.0">bioconductor-pathview</requirement>
        <requirement type="package" version="1.26.0">bioconductor-keggrest</requirement>
        <requirement type="package" version="1.30.10">r-biocmanager</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript $__tool_directory__/kegg_maps_visualization.R 
        #if $input.ids == "text"
            --id_list="$input.txt"

    - giving a list of KEGG pathway IDs (e.g.hsa00010) (copy/paste mode)
    - selecting a list from a dataset (column) - for instance, output from the "KEGG pathways identification and coverage" tool can be used (1st column, c1)
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. 
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).

.. class:: warningmark 

Some pathway ids causes error with the KEGG API: **hsa04215**, **mmu04723**. These ids will not be used if present in input.


Below is an example of an input file with identifiers (uniprot_AC) and fold_change values.

.. csv-table:: Simulated data
   :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3"