diff macs2_predictd.xml @ 0:fe62ba547975 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_predictd.xml	Wed Feb 11 10:18:02 2015 -0500
@@ -0,0 +1,71 @@
+<tool id="macs2_predictd" name="MACS2 predictd" version="@VERSION_STRING@.0">
+    <description>Predict 'd' or fragment size from alignment results</description>
+    <expand macro="requirements">
+        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
+        <requirement type="package" version="4.1.0">gnu_awk</requirement>
+    </expand>
+    <expand macro="version_command" />
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
+    <command>
+        macs2 predictd
+            -i ${ ' '.join( map( lambda x:'"%s"' % ( x ), $infiles ) ) }
+            @tag_size@
+            @effective_genome_size@
+            --bw "${ band_width }"
+            --mfold "${ mfoldlo }" "${ mfoldhi }"
+
+            ## remove the timepoint and strip the output
+            2>&amp;1 | awk -F: '{print $4}' | awk '{$1=$1}1'
+
+            &gt; "${ outfile }"
+            
+        &amp;&amp;
+
+        Rscript predictd
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infiles" type="data" format="bam,sam,bed" multiple="True" label="ChIP-seq alignment file" help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
+        <expand macro="conditional_effective_genome_size" />
+        <expand macro="tag_size" />
+        <expand macro="band_width" />
+
+        <param name="mfoldlo" type="integer" label="Fold-enrichment lower limit" value="5"
+            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
+        <param name="mfoldhi" type="integer" label="Fold-enrichment upper-limit" value="50"
+            help="Select the regions with MFOLD high-confidence enrichment ratio against background to build model (--mfold)"/>
+
+    </inputs>
+
+    <outputs>
+        <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
+        <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" />
+            <param name="effective_genome_size_options_selector" value="user_defined" />
+            <param name="gsize" value="3300000000" />
+            <param name="tsize" value="-1.0"/>
+            <param name="band_width" value="300"/>
+            <param name="mfoldlo" value="5"/>
+            <param name="mfoldhi" value="50"/>
+            <output name="outfile" file="predictd_on_ChIP_200K_and_Control_200K.txt"/>
+            <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+predictd from macs2
+
+
+Note that pair-end data is not supposed to work with this command.
+
+
+@citation@
+    </help>
+    <expand macro="citations" />
+</tool>