comparison peakachu.xml @ 2:49a5a2e86c84 draft

planemo upload for repository https://github.com/tbischler/PEAKachu commit c5d9e7d26c36c03b485d1a29154018bc9b0fa069

1:68656d100a7f

<tool id="peakachu" name="PEAKachu" version="0.1.0.1">
    <description>Calls Peaks in CLIP data</description>
    <requirements>
        <requirement type="package" version="3.6">python</requirement>
        <requirement type="package" version="0.1.0">peakachu</requirement>
    </requirements>
    <version_command>
    <![CDATA[
        peakachu --version

        --padj_threshold $padj_threshold

        &&
        if ls ./tmp_output/peak_tables/*.csv > /dev/null;
        then 
            head -n 1 -q ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv &&
            tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
            mv peaks.tsv '$peak_tables' &&
            cat ./tmp_output/peak_annotations/*.gff | awk '/peak/ {print $0}' > peak_annotations.gff &&
            mv peak_annotations.gff '$peak_annotations' &&
            mv ./tmp_output/plots/Initial*.png '$MA_plot';

        <data format="gff" name="peak_annotations" label="${tool.name} ${mode.mode_selector} on ${on_string}: peak_annotations"/>
        <data format="png" name="MA_plot" label="${tool.name} ${mode.mode_selector} on ${on_string}: MA plot"/>
    </outputs>
    <tests>
        <test>
            <param name="experimentLibs" value="test1_+xl.bam"/>
            <param name="controlLibs" value="test1_-xl.bam"/>
            <output name="peak_tables" ftype="tabular" file="test1_peaks.tsv"/>
            <output name="peak_annotations" ftype="gff" file="test1_peak_annotations.gff"/>
        </test>
    </tests>
    <help>

2:49a5a2e86c84

<tool id="peakachu" name="PEAKachu" version="0.1.0.2">
    <description>Calls Peaks in CLIP data</description>
    <requirements>
        <requirement type="package" version="3.6">python</requirement>
        <requirement type="package" version="3.4.1">r-base</requirement>
        <requirement type="package" version="0.1.0">peakachu</requirement>
    </requirements>
    <version_command>
    <![CDATA[
        peakachu --version

        --padj_threshold $padj_threshold

        &&
        if ls ./tmp_output/peak_tables/*.csv > /dev/null;
        then 
            cat ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv &&
            tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
            mv peaks.tsv '$peak_tables' &&
            cat ./tmp_output/peak_annotations/*.gff | awk '/peak/ {print $0}' > peak_annotations.gff &&
            mv peak_annotations.gff '$peak_annotations' &&
            mv ./tmp_output/plots/Initial*.png '$MA_plot';

        <data format="gff" name="peak_annotations" label="${tool.name} ${mode.mode_selector} on ${on_string}: peak_annotations"/>
        <data format="png" name="MA_plot" label="${tool.name} ${mode.mode_selector} on ${on_string}: MA plot"/>
    </outputs>
    <tests>
        <test>
            <param name="experimentLibs" value="test1_plus-xl.bam"/>
            <param name="controlLibs" value="test1_minus-xl.bam"/>
            <output name="peak_tables" ftype="tabular" file="test1_peaks.tsv"/>
            <output name="peak_annotations" ftype="gff" file="test1_peak_annotations.gff"/>
        </test>
    </tests>
    <help>