--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cwpair2.xml	Tue Nov 17 14:06:28 2015 -0500
@@ -0,0 +1,342 @@
+<?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 $output_files_cond.output_files
+            #if str($output_files_cond.output_files) == "all"
+                --plot_format $output_files_cond.plot_format
+            #end if
+            --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>
+        <conditional name="output_files_cond">
+            <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>
+            <when value="simple" />
+            <when value="simple_orphan" />
+            <when value="simple_orphan_detail" />
+            <when value="all">
+                <param name="plot_format" type="select" label="Output format for graph">
+                    <option value="pdf" selected="True">Pdf</option>
+                    <option value="png">Png</option>
+                    <option value="svg">Svg</option>
+                </param>
+            </when>
+        </conditional>
+        <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_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_C" ext="pdf" visible="false" />
+        </collection>
+        <collection name="closest_C_png" type="list" label="closest C: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "closest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_C" ext="png" visible="false" />
+        </collection>
+        <collection name="closest_C_svg" type="list" label="closest C: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and  output_files_cond['plot_format'] == "svg" and method in ["all", "closest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_C" ext="svg" visible="false" />
+        </collection>
+        <collection name="largest_C_pdf" type="list" label="largest C: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "largest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_C" ext="pdf" visible="false" />
+        </collection>
+        <collection name="largest_C_png" type="list" label="largest C: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "largest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_C" ext="png" visible="false" />
+        </collection>
+        <collection name="largest_C_svg" type="list" label="largest C: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "largest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_C" ext="svg" visible="false" />
+        </collection>
+        <collection name="mode_C_pdf" type="list" label="mode C: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "mode"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_C" ext="pdf" visible="false" />
+        </collection>
+        <collection name="mode_C_png" type="list" label="mode C: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "mode"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_C" ext="png" visible="false" />
+        </collection>
+        <collection name="mode_C_svg" type="list" label="mode C: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "mode"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_C" ext="svg" visible="false" />
+        </collection>
+        <collection name="closest_D" type="list" label="closest D: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["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_cond["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_cond["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_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_F" ext="pdf" visible="false" />
+        </collection>
+        <collection name="closest_F_png" type="list" label="closest F: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "closest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_F" ext="png" visible="false" />
+        </collection>
+        <collection name="closest_F_svg" type="list" label="closest F: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "closest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_F" ext="svg" visible="false" />
+        </collection>
+        <collection name="largest_F_pdf" type="list" label="largest F: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "largest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_F" ext="pdf" visible="false" />
+        </collection>
+        <collection name="largest_F_png" type="list" label="largest F: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "largest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_F" ext="png" visible="false" />
+        </collection>
+        <collection name="largest_F_svg" type="list" label="largest F: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "largest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_F" ext="svg" visible="false" />
+        </collection>
+        <collection name="mode_F_pdf" type="list" label="mode F: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "mode"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_F" ext="pdf" visible="false" />
+        </collection>
+        <collection name="mode_F_png" type="list" label="mode F: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "mode"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_F" ext="png" visible="false" />
+        </collection>
+        <collection name="mode_F_svg" type="list" label="mode F: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "mode"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_F" ext="svg" visible="false" />
+        </collection>
+        <collection name="closest_O" type="list" label="closest O: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["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_cond["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_cond["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_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_P" ext="pdf" visible="false" />
+        </collection>
+        <collection name="closest_P_png" type="list" label="closest P: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "closest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_P" ext="png" visible="false" />
+        </collection>
+        <collection name="closest_P_svg" type="list" label="closest P: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "closest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_P" ext="svg" visible="false" />
+        </collection>
+        <collection name="largest_P_pdf" type="list" label="largest P: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "largest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_P" ext="pdf" visible="false" />
+        </collection>
+        <collection name="largest_P_png" type="list" label="largest P: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "largest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_P" ext="png" visible="false" />
+        </collection>
+        <collection name="largest_P_svg" type="list" label="largest P: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "largest"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_P" ext="svg" visible="false" />
+        </collection>
+        <collection name="mode_P_pdf" type="list" label="mode P: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "mode"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_P" ext="pdf" visible="false" />
+        </collection>
+        <collection name="mode_P_png" type="list" label="mode P: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "mode"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_P" ext="png" visible="false" />
+        </collection>
+        <collection name="mode_P_svg" type="list" label="mode P: ${tool.name} on ${on_string}">
+            <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "mode"]</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_P" ext="svg" 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="plot_format" value="pdf" />
+            <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 a specified format: pdf, png or svg
+* **closest/largest/mode D** - the details in tabular format
+* **closest/largest/mode F** - the final plots graph in a specified format: pdf, png or svg
+* **closest/largest/mode O** - the orphans in tabular format
+* **closest/largest/mode P** - the preview plots graph in a specified format: pdf, png or svg
+* **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.
+* **Output format for graph** - Output format for graph.
+* **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>