# HG changeset patch
# User jbrayet
# Date 1448439759 18000
# Node ID fdf2125c9f02f908fb55c3023b7242f3bbf78c15
# Parent  4b56f6feb24867fd0cda3e6e2ebb9c55dc4a325e
Uploaded

diff -r 4b56f6feb248 -r fdf2125c9f02 samtools_idxstats.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_idxstats.xml	Wed Nov 25 03:22:39 2015 -0500
@@ -0,0 +1,72 @@
+<tool id="samtools_idxstats" name="IdxStats" version="2.0">
+    <description>tabulate mapping statistics for BAM dataset</description>
+    <macros>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"></expand>
+    <expand macro="stdio"></expand>
+    <expand macro="version_command"></expand>
+    <command><![CDATA[
+if [ ! -f "${input}.bai" ] ; then
+    ln -s "${input}" input.bam ;
+    samtools sort -o sorted.bam -O bam -T sts "${input}" ;
+    samtools index sorted.bam ;
+    samtools idxstats sorted.bam > "${output}" ;
+else
+    samtools idxstats "${input}" > "${output}" ;
+fi]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="bam" label="BAM file" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="phiX.bam" ftype="bam" />
+            <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Runs the ``samtools idxstats`` command. It retrieves and prints stats in the index file.
+
+Input is a sorted and indexed BAM file, the output is tabular with
+four columns (one row per reference sequence plus a final line for
+unmapped reads)::
+
+ Column Description
+ ------ -----------------------------
+      1 Reference sequence identifier
+      2 Reference sequence length
+      3 Number of mapped reads
+      4 Number of placed but unmapped reads
+           (typically unmapped partners of mapped reads)
+
+------
+
+**Example** output from a *de novo* assembly::
+
+ contig_1   170035  98397     0
+ contig_2   403835 199564     0
+ contig_3   553102 288189     0
+ ...           ...    ...   ...
+ contig_603    653     50     0
+ contig_604    214      6     0
+ \*              0      0 50320
+
+
+In this example there were 604 contigs, each with one line in the output table,
+plus the final row (labelled with an asterisk) representing 50320 unmapped reads.
+In this BAM file, the final column was otherwise zero.
+
+------
+
+Peter J.A. Cock (2013), `Galaxy wrapper <https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats>`_ for the samtools idxstats command
+]]>
+    </help>
+    <expand macro="citations"></expand>
+</tool>