diff multiCov.xml @ 8:0d3aa592ce27 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/multiCov.xml	Tue Apr 28 22:56:34 2015 -0400
@@ -0,0 +1,75 @@
+<tool id="bedtools_multicovtbed" name="MultiCovBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        #for $i, $bam in enumerate( $bams ):
+            ln -s -f $bam ${i}.bam &&
+            ln -s -f $bam.metadata.bam_index ${i}.bam.bai &&
+        #end for
+
+        bedtools multicov
+            -bed $input
+            -bams
+            #for $i, $bam in enumerate( $bams ):
+                ${i}.bam
+            #end for
+            $strand
+            -f $overlap
+            $reciprocal
+            $split
+            -q $q
+            $duplicate
+            $failed
+            $proper
+            > $output
+]]>
+    </command>
+    <inputs>
+        <param name="input" format="bed" type="data" label="Sorted BED file" />
+        <!-- Additional files, if the user needs more -->
+        <param name="bams" format="bam" type="data" multiple="True" label="BAM file" />
+
+        <expand macro="strand2" />
+        <expand macro="overlap" />
+        <expand macro="reciprocal" />
+        <expand macro="split" />
+        <param name="q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" help="(-q)" />
+        <param name="duplicate" type="boolean" checked="False" truevalue="-D" falsevalue=""
+            label="Include duplicate reads"
+            help="Default counts non-duplicates only. (-D)" />
+        <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue=""
+            label="Include failed-QC reads" 
+            help="Default counts pass-QC reads only (-F)"/>
+        <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue=""
+            label="Only count proper pairs"
+            help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field. (-p)" />
+    </inputs>
+    <outputs>
+        <data name="output" metadata_source="input" format_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="multiCov1.bed" ftype="bed" />
+            <param name="bams" value="srma_in3.bam,srma_in3.bam" ftpye="bam"/>
+            <param name="q" value="1"/>
+            <param name="split" value="False"/>
+            <output name="output" file="multiCovBed_result1.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file.
+
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>