comparison peakachu.xml @ 3:600360da3986 draft default tip

"planemo upload for repository https://github.com/tbischler/PEAKachu commit 23fac1009bde8648151e533ce12c9f3d2f787a65-dirty"

2:26304ccaca57

<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
    ]]>

            --het_p_val_threshold $mode.het_p_val_threshold
            --rep_pair_p_val_threshold $mode.rep_pair_p_val_threshold
        #end if
       --norm_method $mode.norm_method.norm_method_selector
        #if str($mode.norm_method.norm_method_selector) == 'manual':
            --size_factors $size_factors
        #end if
        --mad_multiplier $mad_multiplier
        --fc_cutoff $fc_cutoff
        --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';
        else 
            echo "No Peaks Found" >&2;
        fi 

            <when value="adaptive">
                <param argument="--min_cluster_expr_frac" label="Minimum cluster Expression Fraction" help="Minimum fraction of a block in a cluster for further consideration." type="float" value="0.01"/>
                <param argument="--min_block_overlap" label="Minimum Block Overlap" help="Minimum fraction of the width of blocks for merging." type="float" value="0.5"/>
                <param argument="--min_max_block_expr" label="Minimum Block Expression" help="Minimum fraction of expression of blocks for merging." type="float" value="0.1"/>
                <conditional name="norm_method">
                    <param name="norm_method_selector" type="select" label="Normalisation Method.">
                        <option value="deseq" selected="True">DESeq2</option>
                        <option value="manual">Manual</option>
                        <option value="none">None</option>
                    </param>
                    <when value="deseq"/>

                <param name="stat_test" type="select" label="Statistical Test">
                    <option value="gtest" selected="True">gtest</option>
                    <option value="deseq">DESeq2</option>
                </param>
                <conditional name="norm_method">
                    <param name="norm_method_selector" type="select" label="Normalisation Method.">
                        <option value="tmm" selected="True">TMM</option>
                        <option value="deseq">DESeq2</option>
                        <option value="count">Count</option>
                        <option value="manual">Manual</option>
                        <option value="none">None</option>

                    <when value="deseq"/>
                    <when value="tmm"/>
                    <when value="count"/>
                    <when value="none"/>
                    <when value="manual">
                        <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be seperated by SPACE">
                            <sanitizer>
                                <valid initial="default"/>
                            </sanitizer>
                        </param>
                    </when>

3:600360da3986

<tool id="peakachu" name="PEAKachu" version="0.2.0+galaxy0" profile="20.01">
    <description>Calls Peaks in CLIP data</description>
    <requirements>
        <requirement type="package" version="3.6">python</requirement>
        <requirement type="package" version="4.1.0">r-base</requirement>
        <requirement type="package" version="0.2.0">peakachu</requirement>
    </requirements>
    <version_command>
    <![CDATA[
        peakachu --version
    ]]>

            --het_p_val_threshold $mode.het_p_val_threshold
            --rep_pair_p_val_threshold $mode.rep_pair_p_val_threshold
        #end if
       --norm_method $mode.norm_method.norm_method_selector
        #if str($mode.norm_method.norm_method_selector) == 'manual':
            --size_factors '${mode.norm_method.size_factors}'
        #end if
        --mad_multiplier $mad_multiplier
        --fc_cutoff $fc_cutoff
        --padj_threshold $padj_threshold

        &&
        if ls ./tmp_output/peak_tables/*.csv > /dev/null;
        then 
            sed -n 1p ./tmp_output/peak_tables/*.csv > peaks.tsv &&
            tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
            mv peaks.tsv '$peak_tables' &&
            awk '/peak/ {print $0}' ./tmp_output/peak_annotations/*.gff > peak_annotations.gff &&
            mv peak_annotations.gff '$peak_annotations' &&
            mv ./tmp_output/plots/Initial*.png '$MA_plot';
        else 
            echo "No Peaks Found" >&2;
        fi 

            <when value="adaptive">
                <param argument="--min_cluster_expr_frac" label="Minimum cluster Expression Fraction" help="Minimum fraction of a block in a cluster for further consideration." type="float" value="0.01"/>
                <param argument="--min_block_overlap" label="Minimum Block Overlap" help="Minimum fraction of the width of blocks for merging." type="float" value="0.5"/>
                <param argument="--min_max_block_expr" label="Minimum Block Expression" help="Minimum fraction of expression of blocks for merging." type="float" value="0.1"/>
                <conditional name="norm_method">
                    <param name="norm_method_selector" type="select" label="Normalisation Method">
                        <option value="deseq" selected="True">DESeq2</option>
                        <option value="manual">Manual</option>
                        <option value="none">None</option>
                    </param>
                    <when value="deseq"/>

                <param name="stat_test" type="select" label="Statistical Test">
                    <option value="gtest" selected="True">gtest</option>
                    <option value="deseq">DESeq2</option>
                </param>
                <conditional name="norm_method">
                    <param name="norm_method_selector" type="select" label="Normalisation Method">
                        <option value="tmm" selected="True">TMM</option>
                        <option value="deseq">DESeq2</option>
                        <option value="count">Count</option>
                        <option value="manual">Manual</option>
                        <option value="none">None</option>

                    <when value="deseq"/>
                    <when value="tmm"/>
                    <when value="count"/>
                    <when value="none"/>
                    <when value="manual">
                        <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be separated by SPACE">
                            <sanitizer>
                                <valid initial="default"/>
                            </sanitizer>
                        </param>
                    </when>