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<?xml version="1.0"?>
<tool id="cwpair2" name="CWPair2" version="@WRAPPER_VERSION@.0">
    <description>find matched pairs and unmatched orphans</description>
    <macros>
        <import>cwpair2_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
        <![CDATA[
            python $__tool_directory__/cwpair2.py
            #for $i in $input:
                 --input "${i}" "${i.hid}"
            #end for
            --method $method
            --up_distance $up_distance
            --down_distance $down_distance
            --binsize $binsize
            --threshold_format $threshold_format_cond.threshold_format
            #if str($threshold_format_cond.threshold_format) == "absolute_threshold":
                --absolute_threshold $threshold_format_cond.absolute_threshold
            #elif str($threshold_format_cond.threshold_format) == "relative_threshold":
                --relative_threshold $threshold_format_cond.relative_threshold
            #end if
            --output_files $output_files
            --sort_chromosome $sort_chromosome
            --sort_score $sort_score
            --statistics_output "$statistics_output"
        ]]>
    </command>
    <inputs>
        <param  name="input" type="data" format="gff" multiple="True" label="Find matched pairs on" />
        <param name="method" type="select" label="Method of finding a match">
            <option value="mode" selected="True">Mode</option>
            <option value="closest">Closest</option>
            <option value="largest">Largest</option>
            <option value="all">All</option>
        </param>
        <param name="up_distance" type="integer" value="50" min="0" label="Distance upstream from a peak to allow a pair" />
        <param name="down_distance" type="integer" value="100" min="0" label="Distance downstream from a peak to allow a pair" />
        <param name="binsize" type="integer" value="1" min="0" label="Width of bins for frequency plots and mode calculation" help="Value 1 implies no bins" />
        <conditional name="threshold_format_cond">
            <param name="threshold_format" type="select" label="Filter using">
                <option value="relative_threshold" selected="True">Relative threshold</option>
                <option value="absolute_threshold">Absolute threshold</option>
            </param>
            <when value="relative_threshold">
                <param  name="relative_threshold" type="float" value="0.0" min="0.0" label="Percentage of the 95 percentile value to filter below" help="Value 0 results in no filtering" />
            </when>
            <when value="absolute_threshold">
                <param name="absolute_threshold" type="float" value="0.0" min="0.0" label="Absolute value to filter below" />
            </when>
        </conditional>
        <param name="output_files" type="select" label="Restrict output to" help="Statistics will always be generated." >
            <option value="simple" selected="True">matched pairs only (S)</option>
            <option value="simple_orphan">matched pairs and orphans only (O,S)</option>
            <option value="simple_orphan_detail">matched pairs, orphans and details only (D,O,S)</option>
            <option value="all">no restrictions (output everything: C,D,F,O,P,S)</option>
        </param>
        <param name="sort_chromosome" type="select" label="Sort output by chromosomes in" help="Chromosome strings that are not numeric will not be sorted" >
            <option value="asc" selected="True">ascending order</option>
            <option value="desc">descending order</option>
        </param>
        <param name="sort_score" type="select" label="Sort output by score?">
            <option value="no" selected="True">No</option>
            <option value="asc">Yes, in ascending order</option>
            <option value="desc">Yes, in descending order</option>
        </param>
    </inputs>
    <outputs>
        <collection name="closest_C_pdf" type="list" label="closest C: ${tool.name} on ${on_string}">
            <filter>output_files == "all" and method in ["all", "closest"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_C" ext="pdf" visible="false" />
        </collection>
        <collection name="largest_C_pdf" type="list" label="largest C: ${tool.name} on ${on_string}">
            <filter>output_files == "all" and method in ["all", "largest"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_C" ext="pdf" visible="false" />
        </collection>
        <collection name="mode_C_pdf" type="list" label="mode C: ${tool.name} on ${on_string}">
            <filter>output_files == "all" and method in ["all", "mode"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_C" ext="pdf" visible="false" />
        </collection>
        <collection name="closest_D" type="list" label="closest D: ${tool.name} on ${on_string}">
            <filter>output_files in ["all", "simple_orphan_detail"] and method in ["all", "closest"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_D" ext="tabular" visible="false" />
        </collection>
        <collection name="largest_D" type="list" label="largest D: ${tool.name} on ${on_string}">
            <filter>output_files in ["all", "simple_orphan_detail"] and method in ["all", "largest"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_D" ext="tabular" visible="false" />
        </collection>
        <collection name="mode_D" type="list" label="mode D: ${tool.name} on ${on_string}">
            <filter>output_files in ["all", "simple_orphan_detail"] and method in ["all", "mode"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_D" ext="tabular" visible="false" />
        </collection>
        <collection name="closest_F_pdf" type="list" label="closest F: ${tool.name} on ${on_string}">
            <filter>output_files == "all" and method in ["all", "closest"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_F" ext="pdf" visible="false" />
        </collection>
        <collection name="largest_F_pdf" type="list" label="largest F: ${tool.name} on ${on_string}">
            <filter>output_files == "all" and method in ["all", "largest"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_F" ext="pdf" visible="false" />
        </collection>
        <collection name="mode_F_pdf" type="list" label="mode F: ${tool.name} on ${on_string}">
            <filter>output_files == "all" and method in ["all", "mode"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_F" ext="pdf" visible="false" />
        </collection>
        <collection name="closest_O" type="list" label="closest O: ${tool.name} on ${on_string}">
            <filter>output_files in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "closest"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_O" ext="tabular" visible="false" />
        </collection>
        <collection name="largest_O" type="list" label="largest O: ${tool.name} on ${on_string}">
            <filter>output_files in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "largest"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_O" ext="tabular" visible="false" />
        </collection>
        <collection name="mode_O" type="list" label="mode O: ${tool.name} on ${on_string}">
            <filter>output_files in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "mode"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_O" ext="tabular" visible="false" />
        </collection>
        <collection name="closest_P_pdf" type="list" label="closest P: ${tool.name} on ${on_string}">
            <filter>output_files == "all" and method in ["all", "closest"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_P" ext="pdf" visible="false" />
        </collection>
        <collection name="largest_P_pdf" type="list" label="largest P: ${tool.name} on ${on_string}">
            <filter>output_files == "all" and method in ["all", "largest"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_P" ext="pdf" visible="false" />
        </collection>
        <collection name="mode_P_pdf" type="list" label="mode P: ${tool.name} on ${on_string}">
            <filter>output_files == "all" and method in ["all", "mode"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_P" ext="pdf" visible="false" />
        </collection>
        <collection name="closest_S" type="list" label="closest S: ${tool.name} on ${on_string}">
            <filter>method in ["all", "closest"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_S" ext="gff" visible="false" />
        </collection>
        <collection name="largest_S" type="list" label="largest S: ${tool.name} on ${on_string}">
            <filter>method in ["all", "largest"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_S" ext="gff" visible="false" />
        </collection>
        <collection name="mode_S" type="list" label="mode S: ${tool.name} on ${on_string}">
            <filter>method in ["all", "mode"]</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_S" ext="gff" visible="false" />
        </collection>
        <data name="statistics_output" format="tabular" label="Statistics: ${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="cwpair2_input1.gff" />
            <param name="method" value="all" />
            <param name="up_distance" value="25" />
            <param name="down_distance" value="100" />
            <param name="binsize" value="1" />
            <param name="threshold_format" value="relative_threshold" />
            <param name="relative_threshold" value="0.0" />
            <param name="output_files" value="simple" />
            <param name="sort_chromosome" value="asc" />
            <param name="sort_score" value="asc" />
            <output_collection name="closest_S" type="list">
                <element name="closest_S_data_1_f0u25d100b1" file="closest_s_output1.gff" ftype="gff" />
            </output_collection>
            <output_collection name="largest_S" type="list">
                <element name="largest_S_data_1_f0u25d100b1" file="largest_s_output1.gff" ftype="gff" />
            </output_collection>
            <output_collection name="mode_S" type="list">
                <element name="mode_S_data_1_f0u25d100b1" file="mode_s_output1.gff" ftype="gff" />
            </output_collection>
            <output name="statistics_output" file="statistics1.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="input" value="cwpair2_input1.gff" />
            <param name="method" value="all" />
            <param name="up_distance" value="50" />
            <param name="down_distance" value="100" />
            <param name="binsize" value="1" />
            <param name="threshold_format" value="relative_threshold" />
            <param name="relative_threshold" value="0.0" />
            <param name="output_files" value="all" />
            <param name="sort_chromosome" value="asc" />
            <param name="sort_score" value="no" />
            <output_collection name="closest_D" type="list">
                <element name="closest_D_data_1_f0u50d100b1" file="closest_d_output2.tabular" ftype="tabular" />
            </output_collection>
            <output_collection name="closest_F" type="list">
                <element name="closest_F_data_1_f0u50d100b1" file="closest_f_output2.pdf" ftype="pdf" compare="sim_size" />
            </output_collection>
            <output_collection name="closest_O" type="list">
                <element name="closest_O_data_1_f0u50d100b1" file="closest_o_output2.tabular" ftype="tabular" />
            </output_collection>
            <output_collection name="closest_S" type="list">
                <element name="closest_S_data_1_f0u50d100b1" file="closest_s_output2.gff" ftype="gff" />
            </output_collection>
            <output_collection name="largest_D" type="list">
                <element name="largest_D_data_1_f0u50d100b1" file="largest_d_output2.tabular" ftype="tabular" />
            </output_collection>
            <output_collection name="largest_F" type="list">
                <element name="largest_F_data_1_f0u50d100b1" file="largest_f_output2.pdf" ftype="pdf" compare="sim_size" />
            </output_collection>
            <output_collection name="largest_O" type="list">
                <element name="largest_O_data_1_f0u50d100b1" file="largest_o_output2.tabular" ftype="tabular" />
            </output_collection>
            <output_collection name="largest_S" type="list">
                <element name="largest_S_data_1_f0u50d100b1" file="largest_s_output2.gff" ftype="gff" />
            </output_collection>
            <output_collection name="mode_C" type="list">
                <element name="mode_C_data_1_f0u50d100b1" file="mode_c_output2.pdf" ftype="pdf" compare="sim_size" />
            </output_collection>
            <output_collection name="mode_D" type="list">
                <element name="mode_D_data_1_f0u50d100b1" file="mode_d_output2.tabular" ftype="tabular" />
            </output_collection>
            <output_collection name="mode_F" type="list">
                <element name="mode_F_data_1_f0u50d100b1" file="mode_f_output2.pdf" ftype="pdf" compare="sim_size" />
            </output_collection>
            <output_collection name="mode_O" type="list">
                <element name="mode_O_data_1_f0u50d100b1" file="mode_o_output2.tabular" ftype="tabular" />
            </output_collection>
            <output_collection name="mode_P" type="list">
                <element name="mode_P_data_1_f0u50d100b1" file="mode_p_output2.pdf" ftype="pdf" compare="sim_size" />
            </output_collection>
            <output_collection name="mode_S" type="list">
                <element name="mode_S_data_1_f0u50d100b1" file="mode_s_output2.gff" ftype="gff" />
            </output_collection>
            <output name="statistics_output" file="statistics2.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>
**What it does**

Takes a list of called peaks on both strands and produces a list of matched pairs and a list of unmatched orphans
using a specified method for finding matched pairs.  Methods for finding matched pairs are mode, closest, largest
or all (where the analysis is run for each method).  A statistics dataset is generated and a collection of datasets
is produced for each method as follows.

* **closest/largest/mode C** - the stastics graph in pdf format
* **closest/largest/mode D** - the details in tabular format
* **closest/largest/mode F** - the final plots graph in pdf format
* **closest/largest/mode O** - the orphans in tabular format
* **closest/largest/mode P** - the preview plots graph in pdf format
* **closest/largest/mode S** - the matched pairs in gff format

-----

**Options**

* **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types.
* **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method).
* **Distance upstream from a peak to allow a pair** - Distance upstream from a Watson peak to allow a Crick pair.
* **Distance downstream from a peak to allow a pair** - Distance downstream from a Watson peak to allow a Crick pair.
* **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold.
* **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold.
* **Sort output by chromosomes in** - Output will be sorted by chromsome in the specified order.
* **Sort output by score?** - If yes, output will be sorted by score in the specified order.
* **Summary output format** - Format for summary output.

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