# HG changeset patch
# User greg
# Date 1449090950 18000
# Node ID 29082971b47ca5456914472813382a399ae8d173
# Parent  39cb3eeacdbddd04db654afc1a6c6da886acfd96
Uploaded

diff -r 39cb3eeacdbd -r 29082971b47c repmatch_gff3.xml
--- a/repmatch_gff3.xml	Wed Dec 02 16:15:42 2015 -0500
+++ b/repmatch_gff3.xml	Wed Dec 02 16:15:50 2015 -0500
@@ -17,24 +17,24 @@
         --low_limit $low_limit
         --up_limit $up_limit
         --output_files $output_files_cond.output_files
-        --output_summary "$output_summary"
-        #if str($output_files_cond.output_files) in ["all", "simple_orphan"]:
-            --output_orphan "$output_orphan"
+        --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 "$output_detail"
-            --output_key "$output_key"
-            --output_histogram "$output_histogram"
+            --output_statistics_table "$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="distance" type="integer" value="50" min="0" label="Maximum distance between peaks in different replicates to allow merging" />
         <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" />
@@ -42,64 +42,63 @@
         <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="simple">matched pairs only</option>
-                <option value="simple_orphan">matched pairs and orphans only</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="simple" />
-            <when value="simple_orphan" />
+            <when value="matched_peaks" />
+            <when value="matched_peaks_unmatched_peaks" />
             <when value="all" />
         </conditional>
     </inputs>
     <outputs>
-        <data name="output_summary" format="gff" label="Matched pairs: ${tool.name} on ${on_string}" />
-        <data name="output_orphan" format="tabular" label="Orphans: ${tool.name} on ${on_string}">
-            <filter>output_files_cond["output_files"] in ["all", "simple_orphan"]</filter>
-       </data>
-        <data name="output_detail" format="tabular" label="Details: ${tool.name} on ${on_string}">
+        <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_key" format="tabular" label="Key: ${tool.name} on ${on_string}">
+        <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_histogram" format="pdf" label="Histogram: ${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_s_input1.gff" ftype="gff" />
-        <param name="input" value="largest_s_input1.gff" ftype="gff" />
+        <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="distance" value="50" />
         <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_summary" file="summary_out1.gff" ftype="gff" />
-        <output name="output_orphan" file="orphan_out1.tabular" ftype="tabular" />
-        <output name="output_detail" file="orphan_detail1.tabular" ftype="tabular" />
-        <output name="output_key" file="key_out1.tabular" ftype="tabular" />
-        <output name="output_histogram" file="histogram_out1.pdf" ftype="pdf" compare="sim_size" />
+        <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**
-<![CDATA[
 
-Replicate matching - matches paired peaks from two or more replicates and produces a list of matched
-groups and optionally a list of matched orphans.  Additional optional outputs include the median read
-count for each input, details and a histogram.
+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.
-* **Distance** - Maximum distance between peaks in different replicates to allow merging.
 * **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.
-* **Plot Format** - Output format for graph.  The options are PNG or SVG.
+
     </help>
     <expand macro="citations" />
 </tool>