diff macs2_bdgbroadcall.xml @ 0:fe62ba547975 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_bdgbroadcall.xml	Wed Feb 11 10:18:02 2015 -0500
@@ -0,0 +1,59 @@
+<tool id="macs2_bdgbroadcall" name="MACS2 bdgbroadcall" version="@VERSION_STRING@.0">
+    <description>Call broad peaks from bedGraph output</description>
+    <expand macro="requirements">
+        <requirement type="package" version="4.1.0">gnu_awk</requirement>
+    </expand>
+    <expand macro="version_command" />
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
+    <command>
+        macs2 bdgbroadcall
+            --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" > "${ outfile }"
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
+        <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" 
+            help="Cutoff for peaks depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 2 means qvalue 0.01. default: 2.0 (--cutoff-peak)"/>
+        <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0" 
+            help=" Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. default: 1 (--cutoff-link)"/>
+        <param name="minlen" type="integer" label="Minimum length of peak" value="200" 
+            help="It is recommended to set it as d value." />
+        <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30" 
+            help="It is recommended to set it to tag size" />
+        <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800" 
+            help="It is recommended to set it to 4 times of d value" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="callpeak_treatment_part.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"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Call broad peaks from bedGraph output.
+bdgbroadcall from macs2
+
+@citation@
+    </help>
+    <expand macro="citations" />
+</tool>