# HG changeset patch
# User greg
# Date 1448114257 18000
# Node ID fa85ca6c9cf80f09ba8722a4a69f51fe22af988f
# Parent  551630d1fae3f27b82548b06e2c8a0ff01924a68
Uploaded

diff -r 551630d1fae3 -r fa85ca6c9cf8 genetrack.xml
--- a/genetrack.xml	Sat Nov 21 08:57:27 2015 -0500
+++ b/genetrack.xml	Sat Nov 21 08:57:37 2015 -0500
@@ -8,8 +8,8 @@
     <command>
         python $__tool_directory__/genetrack.py
         --input_format $input_format_cond.input_format
-        #if str($input_format_cond.input_format) == "ssccidx":
-            #for $i in $input_format_cond.input_ssccidx:
+        #if str($input_format_cond.input_format) == "scidx":
+            #for $i in $input_format_cond.input_scidx:
                  --input "${i}" "${i.hid}"
             #end for
         #elif str($input_format_cond.input_format) == "gff":
@@ -27,11 +27,11 @@
     <inputs>
         <conditional name="input_format_cond">
             <param name="input_format" type="select" label="Format of files for conversion">
-                <option value="ssccidx">SsccIdx</option>
-                <option value="gff" selected="True">Gff</option>
+                <option value="scidx" selected="True">ScIdx</option>
+                <option value="gff">Gff</option>
             </param>
-            <when value="ssccidx">
-                <param name="input_ssccidx" type="data" format="ssccidx" multiple="True" label="Predict peaks on" />
+            <when value="scidx">
+                <param name="input_scidx" type="data" format="scidx" multiple="True" label="Predict peaks on" />
             </when>
             <when value="gff">
                 <param  name="input_gff" type="data" format="gff" multiple="True" label="Predict peaks on" />
@@ -64,8 +64,8 @@
             </output_collection>
         </test>
         <test>
-            <param name="input_ssccidx" value="genetrack_input3.ssccidx" ftype="ssccidx" />
-            <param name="input_format" value="ssccidx" />
+            <param name="input_scidx" value="genetrack_input3.scidx" ftype="scidx" />
+            <param name="input_format" value="scidx" />
             <param name="sigma" value="5" />
             <param name="exclusion" value="20" />
             <param name="up_width" value="10" />
@@ -98,6 +98,8 @@
 reads from surrounding reads.  Finally, it ensures each peak is above a threshold and that two peaks are not
 too close to each other.
 
+-----
+
 **Options**
 
 * **Sigma to use when smoothing reads** - Sigma to use when smoothing reads to call peaks.