# HG changeset patch
# User greg
# Date 1448114506 18000
# Node ID 9ed566138ecb24660d45b3b4057c762122815133
# Parent  430a5bdc55a30cbcfa73bc9e1b4c78ae6baf745c
Uploaded

diff -r 430a5bdc55a3 -r 9ed566138ecb cwpair2.xml
--- a/cwpair2.xml	Sat Nov 21 09:01:35 2015 -0500
+++ b/cwpair2.xml	Sat Nov 21 09:01:46 2015 -0500
@@ -21,10 +21,7 @@
             #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
+            --output_files $output_files
             --sort_chromosome $sort_chromosome
             --sort_score $sort_score
             --statistics_output "$statistics_output"
@@ -53,24 +50,12 @@
                 <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="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>
@@ -83,137 +68,65 @@
     </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>
+            <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="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>
+            <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="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>
+            <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="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>
+            <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_cond["output_files"] in ["all", "simple_orphan_detail"] and method in ["all", "largest"]</filter>
+            <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_cond["output_files"] in ["all", "simple_orphan_detail"] and method in ["all", "mode"]</filter>
+            <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_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter>
+            <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="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>
+            <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="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>
+            <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="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>
+            <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_cond["output_files"] in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "largest"]</filter>
+            <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_cond["output_files"] in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "mode"]</filter>
+            <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_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter>
+            <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="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>
+            <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="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>
+            <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="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" />
@@ -260,7 +173,6 @@
             <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">
@@ -316,13 +228,14 @@
 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 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 a specified format: pdf, png or svg
+* **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 a specified format: pdf, png or svg
+* **closest/largest/mode P** - the preview plots graph in pdf format
 * **closest/largest/mode S** - the matched pairs in gff format
 
+-----
 
 **Options**
 
@@ -332,7 +245,6 @@
 * **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.