# HG changeset patch
# User greg
# Date 1449106341 18000
# Node ID 91e663440ca48584c73349b3fa15e5dfb1b7a3a0
# Parent  29082971b47ca5456914472813382a399ae8d173
Uploaded

diff -r 29082971b47c -r 91e663440ca4 repmatch_gff3.xml
--- a/repmatch_gff3.xml	Wed Dec 02 16:15:50 2015 -0500
+++ b/repmatch_gff3.xml	Wed Dec 02 20:32:21 2015 -0500
@@ -12,10 +12,7 @@
         #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($output_files_cond.output_files) in ["all", "matched_peaks_unmatched_peaks"]:
@@ -26,19 +23,21 @@
             --output_statistics_table "$output_statistics_table"
             --output_statistics_histogram "$output_statistics_histogram"
         #end if
+        #if str($advanced_options_cond.advanced_options) == "on":
+            --step $advanced_options_cond.step
+            --low_limit $advanced_options_cond.low_limit
+            --up_limit $advanced_options_cond.up_limit
+        #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="distance" type="integer" value="50" min="0" label="Maximum distance between peaks in different replicates to allow merging" />
         <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>
@@ -49,6 +48,18 @@
             <when value="matched_peaks_unmatched_peaks" />
             <when value="all" />
         </conditional>
+        <conditional name="advanced_options_cond">
+            <param name="advanced_options" type="select" label="Advanced options">
+                <option value="off" selected="true">Hide advanced options</option>
+                <option value="on">Display advanced options</option>
+            </param>
+            <when value="on">
+                <param name="step" type="integer" value="0" min="0" label="Step size" help="Distance for each iteration" />
+                <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" />
+            </when>
+            <when value="off" />
+        </conditional>
     </inputs>
     <outputs>
         <data name="output_statistics_table" format="tabular" label="Statistics Table: ${tool.name} on ${on_string}">
@@ -68,13 +79,13 @@
     <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="method" value="closest" />
         <param name="distance" value="50" />
-        <param name="method" value="closest" />
+        <param name="replicates" value="2" />
+        <param name="output_files" value="all" />
         <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" />