diff repmatch_gff3.xml @ 0:d33030c8e2cc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repmatch_gff3.xml	Tue Nov 17 14:26:08 2015 -0500
@@ -0,0 +1,118 @@
+<?xml version="1.0"?>
+<tool id="repmatch_gff3" name="RepMatch" version="@WRAPPER_VERSION@.0">
+    <description>Match paired peaks from two or more replicates</description>
+    <macros>
+        <import>repmatch_gff3_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+        python $__tool_directory__/repmatch_gff3.py
+        #for $i in $input:
+             --input "${i}" "${i.hid}"
+        #end for
+        --method $method
+        --distance $distance
+        --step $step
+        --replicates $replicates
+        --low_limit $low_limit
+        --up_limit $up_limit
+        --output_files $output_files_cond.output_files
+        --output_summary "$output_summary"
+        #if str($output_files_cond.output_files) in ["all", "simple_orphan"]:
+            --output_orphan "$output_orphan"
+        #end if
+        #if str($output_files_cond.output_files) =="all":
+            --plot_format $output_files_cond.plot_format
+            --output_detail "$output_detail"
+            --output_key "$output_key"
+            --output_histogram "$output_histogram"
+        #end if
+    </command>
+    <inputs>
+        <param  name="input" type="data" format="gff" multiple="True" min="2" label="Match paired peaks on" />
+        <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" />
+        <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>
+                <option value="simple">matched pairs only</option>
+                <option value="simple_orphan">matched pairs and orphans only</option>
+            </param>
+            <when value="simple" />
+            <when value="simple_orphan" />
+            <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>
+    </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}">
+            <filter>output_files_cond["output_files"] == "all"</filter>
+       </data>
+        <data name="output_key" format="tabular" label="Key: ${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>
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="output_files_cond.plot_format" />
+                 </action>
+           </actions>
+       </data>
+    </outputs>
+    <tests>
+        <param name="input" value="closest_s_input1.gff" ftype="gff" />
+        <param name="input" value="largest_s_input1.gff" ftype="gff" />
+        <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" />
+        <param name="plot_format" value="png" />
+        <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" />
+    </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.
+
+]]>
+
+**Options**
+
+* **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>