diff macs2_bdgdiff.xml @ 0:fe62ba547975 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_bdgdiff.xml	Wed Feb 11 10:18:02 2015 -0500
@@ -0,0 +1,84 @@
+<tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.0">
+    <description>Differential peak detection based on paired four bedgraph files</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
+    <command>
+        macs2 bdgdiff
+            --t1 "${ infile_pileup_cond1 }"
+            --t2 "${ infile_pileup_cond2 }"
+            --c1 "${ infile_control_cond1 }"
+            --c2 "${ infile_control_cond2 }"
+            --cutoff "${ cutoff }"
+            --min-len "${ minlen }"
+            --depth1 "${ depth1 }"
+            --depth2 "${ depth2 }"
+            --max-gap "${ maxgap }"
+            --o-prefix MACS2
+
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile_pileup_cond1" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 1" />
+        <param name="infile_pileup_cond2" type="data" format="bedgraph" label="MACS pileup bedGraph for condition 2" />
+
+        <param name="infile_control_cond1" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 1" />
+        <param name="infile_control_cond2" type="data" format="bedgraph" label="MACS control lambda bedGraph for condition 2" />
+
+        <param name="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="Default: 1.0 (likelihood ratio=10) (--cutoff)"/>
+        <param name="minlen" type="integer" label="Minimum length of differential region" value="200"/>
+        <param name="depth1" type="integer" value="1" label="Sequence depth of condition 1 in million reads" help="default: 1 (--depth1)" />
+        <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="default: 1 (--depth2)" />
+        <param name="maxgap" type="integer" value="100" label="Maximum gap to merge nearby differential regions" help="Consider a wider gap for broad marks. Maximum gap should be smaller than minimum length. Default: 100 (-g)." />
+
+        <param name="outputs" type="select" display="checkboxes" multiple="True" label="Outputs">
+            <option value="--ofile-cond1">Unique regions in condition 1</option>
+            <option value="--ofile-cond2">Unique regions in condition 2</option>
+            <option value="--ofile-both-conditions" selected="true">Common regions in both conditions</option>
+            <validator type="no_options" message="Please select at least one output file." />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_cond1" format="bed" from_work_dir="MACS2_cond1.bed" label="${tool.name} on ${on_string} (cond 1)">
+            <filter>'--ofile-cond1' in outputs</filter>
+        </data>
+        <data name="output_cond2" format="bed" from_work_dir="MACS2_cond1.bed" label="${tool.name} on ${on_string} (cond 2)">
+            <filter>'--ofile-cond2' in outputs</filter>
+        </data>
+        <data name="output_both" format="bed" from_work_dir="MACS2_common.bed" label="${tool.name} on ${on_string} (both)">
+            <filter>'--ofile-both-conditions' in outputs</filter>
+        </data>
+    </outputs>
+    <tests>
+            <!-- we need a second condition here -->
+            <!--
+        <test>
+
+            <param name="infile_control_cond1" value="Control_200K.bed" ftype="bed"/>
+            <param name="infile_control_cond2" value="Control_200K.bed" ftype="bed"/>
+            <param name="infile_pileup_cond1" value="ChIP_200K.bed" ftype="bed"/>
+            <param name="infile_pileup_cond2" value="ChIP_200K.bed" ftype="bed"/>
+            <param name="cutoff" value="1.0"/>
+            <param name="minlen" value="200"/>
+            <param name="depth1" value="1"/>
+            <param name="depth2" value="1"/>
+            <param name="maxgap" value="100"/>
+            <param name="outputs" value="-ofile-cond1,-ofile-cond2,-ofile-both-conditions"/>
+            <output name="output_cond1" file=""/>
+            <output name="output_cond2" file=""/>
+            <output name="output_both" file=""/>
+        </test>
+            -->
+    </tests>
+    <help>
+**What it does**
+
+bdgdiff from macs2
+
+
+@citation@
+    </help>
+    <expand macro="citations" />
+</tool>