diff macs2_bdgbroadcall.xml @ 2:bfe57d6e0c4c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74

--- a/macs2_bdgbroadcall.xml	Thu Feb 12 10:40:25 2015 -0500
+++ b/macs2_bdgbroadcall.xml	Mon Oct 12 11:24:39 2015 -0400
@@ -1,12 +1,13 @@
 <tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@VERSION_STRING@.0">
     <description>Call broad peaks from bedGraph output</description>
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
     <expand macro="requirements">
         <requirement type="package" version="4.1.0">gnu_awk</requirement>
     </expand>
+    <expand macro="stdio" />
     <expand macro="version_command" />
-    <macros>
-        <import>macs2_macros.xml</import>
-    </macros>
     <command>
         macs2 bdgbroadcall
             --ifile "${ infile }"
@@ -19,18 +20,17 @@
         &amp;&amp;
         awk '!/^track name/' "macs2_bdgbroadcall.bdg" > "${ outfile }"
     </command>
-    <expand macro="stdio" />
     <inputs>
         <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
-        <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" 
+        <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0"
             help="Cutoff for peaks depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 2 means qvalue 0.01. default: 2.0 (--cutoff-peak)"/>
-        <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0" 
+        <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0"
             help=" Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. default: 1 (--cutoff-link)"/>
-        <param name="minlen" type="integer" label="Minimum length of peak" value="200" 
+        <param name="minlen" type="integer" label="Minimum length of peak" value="200"
             help="It is recommended to set it as d value." />
-        <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30" 
+        <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30"
             help="It is recommended to set it to tag size" />
-        <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800" 
+        <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800"
             help="It is recommended to set it to 4 times of d value" />
     </inputs>
     <outputs>