view repmatch_gff3.xml @ 10:29082971b47c draft

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<?xml version="1.0"?>
<tool id="repmatch_gff3" name="RepMatch" version="@WRAPPER_VERSION@.0">
    <description>Match paired peaks from two or more replicates</description>
    <macros>
        <import>repmatch_gff3_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
        python $__tool_directory__/repmatch_gff3.py
        #for $i in $input:
             --input "${i}" "${i.hid}"
        #end for
        --method $method
        --distance $distance
        --step $step
        --replicates $replicates
        --low_limit $low_limit
        --up_limit $up_limit
        --output_files $output_files_cond.output_files
        --output_matched_peaks "$output_matched_peaks"
        #if str($output_files_cond.output_files) in ["all", "matched_peaks_unmatched_peaks"]:
            --output_unmatched_peaks "$output_unmatched_peaks"
        #end if
        #if str($output_files_cond.output_files) =="all":
            --output_detail "$output_detail"
            --output_statistics_table "$output_statistics_table"
            --output_statistics_histogram "$output_statistics_histogram"
        #end if
    </command>
    <inputs>
        <param  name="input" type="data" format="gff" multiple="True" min="2" label="Match paired peaks on" />
        <param name="distance" type="integer" value="50" min="0" label="Maximum distance between peaks in different replicates to allow merging" />
        <param name="method" type="select" label="Method of finding match">
            <option value="closest" selected="True">Closest</option>
            <option value="largest">Largest</option>
            <option value="all">All</option>
        </param>
        <param name="step" type="integer" value="0" min="0" label="Step size" help="Distance for each iteration" />
        <param name="replicates" type="integer" value="2" min="2" label="Minimum number of replicates that must be matched for merging to occur" />
        <param name="low_limit" type="integer" value="-1000" label="Lower limit for Crick-Watson distance filter" />
        <param name="up_limit" type="integer" value="1000" label="Upper limit for Crick-Watson distance filter" />
        <conditional name="output_files_cond">
            <param name="output_files" type="select" label="Restrict output to" help="Statistics will always be generated." >
                <option value="all" selected="True">no restrictions (output everything)</option>
                <option value="matched_peaks">matched paired peaks only</option>
                <option value="matched_peaks_unmatched_peaks">matched paired peaks and unmatched paired peaks only</option>
            </param>
            <when value="matched_peaks" />
            <when value="matched_peaks_unmatched_peaks" />
            <when value="all" />
        </conditional>
    </inputs>
    <outputs>
        <data name="output_statistics_table" format="tabular" label="Statistics Table: ${tool.name} on ${on_string}">
            <filter>output_files_cond["output_files"] == "all"</filter>
       </data>
        <data name="output_statistics_histogram" format="pdf" label="Statistics Histogram: ${tool.name} on ${on_string}">
            <filter>output_files_cond["output_files"] == "all"</filter>
       </data>
        <data name="output_detail" format="tabular" label="Data D: ${tool.name} on ${on_string}">
            <filter>output_files_cond["output_files"] == "all"</filter>
       </data>
        <data name="output_unmatched_peaks" format="tabular" label="Data UP: ${tool.name} on ${on_string}">
            <filter>output_files_cond["output_files"] in ["all", "matched_peaks_unmatched_peaks"]</filter>
        </data>
        <data name="output_matched_peaks" format="gff" label="Data MP: ${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <param name="input" value="closest_matched_pairs_input1.gff" ftype="gff" />
        <param name="input" value="largest_matched_pairs_input1.gff" ftype="gff" />
        <param name="distance" value="50" />
        <param name="method" value="closest" />
        <param name="step" value="0" />
        <param name="replicates" value="2" />
        <param name="low_limit" value="-1000" />
        <param name="up_limit" value="1000" />
        <param name="output_files" value="all" />
        <output name="output_statistics_table" file="statistics_table_out1.tabular" ftype="tabular" />
        <output name="output_statistics_histogram" file="statistics_histogram_out1.pdf" ftype="pdf" compare="sim_size" />
        <output name="output_detail" file="detail_out1.tabular" ftype="tabular" />
        <output name="output_unmatched_peaks" file="unmatched_peaks_out1.tabular" ftype="tabular" />
        <output name="output_matched_peaks" file="matched_peaks_out1.gff" ftype="gff" />
    </tests>
    <help>
**What it does**

Replicate matching - inspects paired peaks from two or more replicates and produces a list of matched
paired peaks and optionally a list of unmatched paired peaks.  Additional optional outputs include the
median read count for each input, details and a histogram.

-----

**Options**

* **Distance** - Maximum distance between peaks in different replicates to allow merging.
* **Method** - Method to use when calling replicates.
* **Step Size** - Distance for each iteration.
* **Replicates** - Minimum number of replicates to call a peak.  Number of replicates required must be at least 2.
* **Lower Limit** - Lower limit for the Crick-Watson distance filter.
* **Upper Limit** - Upper limit for the Crick-Watson distance filter.

    </help>
    <expand macro="citations" />
</tool>