diff macs2_bdgbroadcall.xml @ 5:beb902da6e5f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b

--- a/macs2_bdgbroadcall.xml	Mon Feb 06 02:30:37 2017 -0500
+++ b/macs2_bdgbroadcall.xml	Sat Apr 08 08:28:57 2017 -0400
@@ -9,49 +9,53 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command>
+         <![CDATA[
         macs2 bdgbroadcall
-            --ifile "${ infile }"
-            --cutoff-peak "${ cutoffpeak }"
-            --cutoff-link "${ cutofflink }"
-            --min-length "${ minlen }"
-            --lvl1-max-gap "${ LVL1MAXGAP }"
-            --lvl2-max-gap "${ LVL2MAXGAP }"
+            --ifile '${ infile }'
+            --cutoff-peak '${ cutoffpeak }'
+            --cutoff-link '${ cutofflink }'
+            --min-length '${ minlen }'
+            --lvl1-max-gap '${ LVL1MAXGAP }'
+            --lvl2-max-gap '${ LVL2MAXGAP }'
             --ofile "macs2_bdgbroadcall.bdg"
-        &amp;&amp;
-        awk '!/^track name/' "macs2_bdgbroadcall.bdg" > "${ outfile }"
+        &&
+        awk '!/^track name/' "macs2_bdgbroadcall.bdg" > '${ outfile }'
+        ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
+        <param name="infile" type="data" format="bedgraph" label="bedGraph generated MACS" />
         <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)"/>
+            help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. Default=5 (--cutoff)"/>
         <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)"/>
+            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"
-            help="It is recommended to set it as d value." />
+            help="It is recommended to set it as d value. Default=200 (--min-length)" />
         <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30"
-            help="It is recommended to set it to tag size" />
+            help="It is recommended to set it to tag size. Default=30 (--lvl1-max-gap)" />
         <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" />
+            help="It is recommended to set it to 4 times of d value. Default=800 (--lvl2-max-gap)" />
     </inputs>
     <outputs>
-        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+        <data name="outfile" format="interval" label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="callpeak_treatment_part.bdg" ftype="bedgraph" />
+            <param name="infile" value="bdgbroadcall_input.bdg" ftype="bedgraph" />
             <param name="cutoffpeak" value="2.0"/>
             <param name="cutofflink" value="1.0"/>
             <param name="minlen" value="200"/>
             <param name="LVL1MAXGAP" value="30"/>
             <param name="LVL2MAXGAP" value="800"/>
-            <output name="outfile" file="bdgbroadcall_on_callpeak_treatment.tabular"/>
+            <output name="outfile" file="bdgbroadcall_output.bdg"/>
         </test>
     </tests>
     <help>
 **What it does**
 
-Call broad peaks from bedGraph output.
-bdgbroadcall from macs2
+This is **bdgbroadcall** utility from the MACS2_ Package. It is designed to call broad peaks (e.g., histone) from bedGraph datasets generated with MACS2.
+
+.. _MACS2: https://github.com/taoliu/MACS
+
 
 @citation@
     </help>