<commit_before><tool id="macs2_predictd" name="MACS2 predictd" version="2.0.10.0">
    <description>Predict 'd' or fragment size from alignment results</description>
    <expand macro="requirements">
        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
    </expand>
    <expand macro="version_command" />
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <command>
        macs2 predictd
            -i 
            #for $infile in $infiles:
                "$infile"
            #end for
            @tag_size@
            @effective_genome_size@
            --bw $band_width
            --mfold $mfoldlo $mfoldhi
            &gt; $outfile;

        Rscript predicted_model.R &gt; $outfile_image
    </command>
    <expand macro="stdio" />
    <inputs>
        <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
        <expand macro="conditional_effective_genome_size" />
        <expand macro="tag_size" />

        <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
            help="This value is only used while building the shifting model. (--bw)" />

        <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
        <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>

    </inputs>

    <outputs>
        <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
        <data name="outfile_image" format="png" label="${tool.name} on ${on_string} - X-correlation image" />
    </outputs>
    <tests>
        <!--none yet for macs2-->
    </tests>
    <help>
**What it does**

bdgdiff from macs2


Note that pair-end data is not supposed to work with this command.


@citation@
    </help>
</tool><commit_msg>redirect stdout to the output file, fix generation of the R plot<commit_after><tool id="macs2_predictd" name="MACS2 predictd" version="2.0.10.0">
    <description>Predict 'd' or fragment size from alignment results</description>
    <expand macro="requirements">
        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
    </expand>
    <expand macro="version_command" />
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <command>
        macs2 predictd
            -i #echo ' '.join( map( str, $infiles) )#
            @tag_size@
            @effective_genome_size@
            --bw $band_width
            --mfold $mfoldlo $mfoldhi
            2&gt; $outfile;

        Rscript predictd;
    </command>
    <expand macro="stdio" />
    <inputs>
        <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
        <expand macro="conditional_effective_genome_size" />
        <expand macro="tag_size" />

        <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
            help="This value is only used while building the shifting model. (--bw)" />

        <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
        <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>

    </inputs>

    <outputs>
        <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
        <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" />
    </outputs>
    <tests>
        <!--none yet for macs2-->
    </tests>
    <help>
**What it does**

predictd from macs2


Note that pair-end data is not supposed to work with this command.


@citation@
    </help>
</tool>
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