comparison kegg_identification.xml @ 3:0308c2d81607 draft

planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty

2:60368fca9772

<tool id="kegg_identification" name="Pathways identification" version="2019.03.05">
    <description>and coverage [KEGG]</description>
    <requirements>
        <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        --species="$species"

    ]]></command>
    <inputs>
        <conditional name="input" >
            <param name="ids" type="select" label="Enter your IDs (Entrez gene IDs, KEGG gene IDs or UniProt Accession number)" help="Copy/paste or from a file (e.g. table)" >
                <option value="text">Copy/paste your IDs</option>
                <option value="file" selected="true">Input file containing your IDs</option>
            </param>
            <when value="text" >
                <param name="txt" type="text" label="Copy/paste your IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: hsa:3306 hsa:22948' >

Input can be either a list of IDs or a file containing multiple columns but with at least one column of IDs (e.g. hsa:04970). 
Input IDs type can be Entrez gene ID (e.g. 2243), KEGG gene ID (e.g. hsa:2243 in homo sapiens) or Uniprot accession number (e.g. P02671).

.. class:: warningmark  

If you use Uniprot accession number, it will be converted to KEGG gene ID; this step can be time consuming.

If your input file contains other type of ID, please use the ID_Converter tool.

-----

**Parameters**

.. class:: infomark

**Galaxy integration**

David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR

Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR

This work has been partially funded through the French National Agency for Research (ANR) IFB project.

Contact [e-mail] for any questions or concerns about the Galaxy implementation of this tool.

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubKEGGREST,

3:0308c2d81607

<tool id="kegg_identification" name="Pathways identification" version="2019.06.27">
    <description>and coverage [KEGG]</description>
    <requirements>
        <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        --species="$species"

    ]]></command>
    <inputs>
        <conditional name="input" >
            <param name="ids" type="select" label="Enter your IDs (Entrez gene IDs, KEGG IDs, UniProt Accession number)" help="Copy/paste or from a file (e.g. table)" >
                <option value="text">Copy/paste your IDs</option>
                <option value="file" selected="true">Input file containing your IDs</option>
            </param>
            <when value="text" >
                <param name="txt" type="text" label="Copy/paste your IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: hsa:3306 hsa:22948' >

Input can be either a list of IDs or a file containing multiple columns but with at least one column of IDs (e.g. hsa:04970). 
Input IDs type can be Entrez gene ID (e.g. 2243), KEGG gene ID (e.g. hsa:2243 in homo sapiens) or Uniprot accession number (e.g. P02671).

.. class:: warningmark  

If you use Uniprot accession number, it will be converted to KEGG gene ID; this step can be time consuming. KEGG database being "gene-centric" we recommend the use of Entrez gene IDs.

If your input file contains other type of ID (than those allowed), please use the ID_Converter tool.

In copy/paste mode, the number of IDs considered in input is limited to 5000.

-----

**Parameters**

.. class:: infomark

**Galaxy integration**

David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR

Sandra Dérozier, Olivier Rué, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR

This work has been partially funded through the French National Agency for Research (ANR) IFB project.

Help: [e-mail] for any questions or concerns about this tool.

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubKEGGREST,