# HG changeset patch
# User jbrayet
# Date 1448439718 18000
# Node ID 695b40cab89b158b7ba95864a1a3d0be0e408460
# Parent  fb7fc6b2e74c7f364bf2392d964331e582090e8d
Uploaded

diff -r fb7fc6b2e74c -r 695b40cab89b samtools_bedcov.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_bedcov.xml	Wed Nov 25 03:21:58 2015 -0500
@@ -0,0 +1,57 @@
+<tool id="samtools_bedcov" name="BedCov" version="2.0">
+  <description>calculate read depth for a set of genomic intervals</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+    <expand macro="stdio"></expand>
+    <expand macro="version_command"></expand>
+    <command><![CDATA[
+        for bamfile in 
+        #for dataset in $input_bams:
+            "${dataset}"
+        #end for
+        ; do
+            if [ ! -f \$bamfile.bai ] ; then
+                ln -s \$bamfile && samtools index `basename \$bamfile` ;
+            else
+                ln -s \$bamfile && ln -s \$bamfile.bai ;
+            fi ;
+        done ;
+        samtools bedcov "${input_bed}"
+        #for dataset in $input_bams:
+            `basename "${dataset}"`
+        #end for
+        > "${output}"
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_bed" type="data" format="bed" label="BED file" />
+        <param name="input_bams" type="data" format="bam" label="BAM file" multiple="true" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
+            <param name="input_bams" value="eboVir3.bam" ftype="bam" />
+            <output name="output" file="samtools_bedcov_out1.tab" />
+        </test>
+        <test>
+            <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
+            <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
+            <output name="output" file="samtools_bedcov_out2.tab" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::
+
+ samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]
+
+    </help>
+    <expand macro="citations"></expand>
+</tool>
+