comparison spectra_plots.xml @ 9:0b7e00e5b9d2 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"

8:ebb7de263d49

    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.2.1">r-ggplot2</requirement>
        <requirement type="package" version="2.3">r-gridextra</requirement>
        <requirement type="package" version="1.0.0">r-scales</requirement>
    </expand>
    <command detect_errors="exit_code">
    <![CDATA[
        @INPUT_LINKING@
        cat '${MSI_mzplots}' &&

    </configfiles>
    <inputs>
        <expand macro="reading_msidata"/>
        <expand macro="pdf_filename"/>
        <conditional name="pixel_conditional">
            <param name="pixel_type" type="select" label="Choose spectra (pixel)">
                <option value="all_pixel" selected="True" >All spectra</option>
                <option value="tabular_pixel">Single spectra</option>
            </param>
            <when value="tabular_pixel">
                <param name="pixel_file" type="data" format="tabular" label="Load tabular file with pixel coordinates"

        </test>
        <test>
            <expand macro="processed_infile_imzml"/>
            <conditional name="processed_cond">
                <param name="processed_file" value="processed"/>
                <param name="accuracy" value="50"/>
                <param name="units" value="ppm"/>
            </conditional>
            <conditional name="pixel_conditional">
                <param name="pixel_type" value="all_pixel"/>
            </conditional>

9:0b7e00e5b9d2

    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="3.3.2">r-ggplot2</requirement>
        <requirement type="package" version="2.3">r-gridextra</requirement>
        <requirement type="package" version="1.1.1">r-scales</requirement>
    </expand>
    <command detect_errors="exit_code">
    <![CDATA[
        @INPUT_LINKING@
        cat '${MSI_mzplots}' &&

    </configfiles>
    <inputs>
        <expand macro="reading_msidata"/>
        <expand macro="pdf_filename"/>
        <conditional name="pixel_conditional">
            <param name="pixel_type" type="select" label="Choose spectra (pixel) and/or add spectra annotations">
                <option value="all_pixel" selected="True" >All spectra</option>
                <option value="tabular_pixel">Single spectra</option>
            </param>
            <when value="tabular_pixel">
                <param name="pixel_file" type="data" format="tabular" label="Load tabular file with pixel coordinates"

        </test>
        <test>
            <expand macro="processed_infile_imzml"/>
            <conditional name="processed_cond">
                <param name="processed_file" value="processed"/>
                <param name="accuracy" value="100"/>
                <param name="units" value="ppm"/>
            </conditional>
            <conditional name="pixel_conditional">
                <param name="pixel_type" value="all_pixel"/>
            </conditional>