comparison Get_ms-ms_observations.xml @ 5:034cfb96a482 draft

planemo upload commit b052261cf5cd6c2413e301a19d5c95d9794f1e81-dirty

4:299eb4a62e0c

<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.01.1">
    <description>[Peptide Atlas]</description>
    <requirements>
        <requirement type="package" version="3.4.1">R</requirement>
    </requirements>
    <stdio>

        #else
            --input="$input.file"
            --column_number="$input.ncol"
            --header="$input.header"
        #end if
        --atlas=${",".join([$__tool_directory__+"/"+str(ref) for ref in str($atlas).split(",")])}
        --output="$output"
    </command>

    <inputs>
        <conditional name="input" >

                </param>
            </when>
            <when value="file" >
                <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
                <param name="ncol" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
            </when>
        </conditional>
        <!-- Peptide Atlas options -->
        <param name="atlas" type="select" display="checkboxes" multiple="true" label="Proteomics dataset (biological sample)" optional="false" >
            <options from_data_table="proteore_peptide_atlas">

5:034cfb96a482

<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.26">
    <description>[Peptide Atlas]</description>
    <requirements>
        <requirement type="package" version="3.4.1">R</requirement>
    </requirements>
    <stdio>

        #else
            --input="$input.file"
            --column_number="$input.ncol"
            --header="$input.header"
        #end if
        --atlas=${",".join([str(ref) if "peptide_atlas" in str(ref).split("/") else $__tool_directory__+"/"+str(ref) for ref in str($atlas).split(",")])}
        --output="$output"
    </command>

    <inputs>
        <conditional name="input" >

                </param>
            </when>
            <when value="file" >
                <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
                <param name="ncol" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
                    <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
                </param>
            </when>
        </conditional>
        <!-- Peptide Atlas options -->
        <param name="atlas" type="select" display="checkboxes" multiple="true" label="Proteomics dataset (biological sample)" optional="false" >
            <options from_data_table="proteore_peptide_atlas">