# HG changeset patch
# User iuc
# Date 1494343142 14400
# Node ID 88b8c2916784edd480105d6f3a4f30b18a14df21
# Parent  87398ae795c7b49263b856bfa79e2b9faa5ade4f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

diff -r 87398ae795c7 -r 88b8c2916784 macros.xml
--- a/macros.xml	Tue Apr 21 16:00:31 2015 -0400
+++ b/macros.xml	Tue May 09 11:19:02 2017 -0400
@@ -1,16 +1,17 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.2">samtools</requirement>
+            <requirement type="package" version="1.3.1">samtools</requirement>
             <yield/>
         </requirements>
     </xml>
+    <token name="@TOOL_VERSION@">1.3.1</token>
     <xml name="citations">
         <citations>
             <citation type="bibtex">
                 @misc{SAM_def,
                 title={Definition of SAM/BAM format},
-                url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+                url = {https://samtools.github.io/hts-specs/},}
             </citation>
             <citation type="doi">10.1093/bioinformatics/btp352</citation>
             <citation type="doi">10.1093/bioinformatics/btr076</citation>
@@ -41,7 +42,7 @@
         </citations>
     </xml>
     <xml name="version_command">
-        <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
     </xml>
     <xml name="stdio">
         <stdio>
@@ -64,7 +65,5 @@
 5. Click **Save**
 
 The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
-
     </token>
-
 </macros>
diff -r 87398ae795c7 -r 88b8c2916784 samtools_idxstats.xml
--- a/samtools_idxstats.xml	Tue Apr 21 16:00:31 2015 -0400
+++ b/samtools_idxstats.xml	Tue May 09 11:19:02 2017 -0400
@@ -1,21 +1,16 @@
-<tool id="samtools_idxstats" name="IdxStats" version="2.0">
-    <description>tabulate mapping statistics for BAM dataset</description>
+<tool id="samtools_idxstats" name="IdxStats" version="2.0.1">
+    <description>reports stats of the BAM index file</description>
     <macros>
-      <import>macros.xml</import>
+        <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"></expand>
-    <expand macro="stdio"></expand>
-    <expand macro="version_command"></expand>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
     <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>
+        ln -f -s '${input.metadata.bam_index}' '${input}.bai' &&
+
+        samtools idxstats '${input}' > '${output}'
+    ]]></command>
     <inputs>
         <param name="input" type="data" format="bam" label="BAM file" />
     </inputs>
@@ -28,8 +23,7 @@
             <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Runs the ``samtools idxstats`` command. It retrieves and prints stats in the index file.
@@ -58,7 +52,6 @@
  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.
@@ -66,7 +59,6 @@
 ------
 
 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>
+    ]]></help>
+    <expand macro="citations"/>
 </tool>
diff -r 87398ae795c7 -r 88b8c2916784 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 21 16:00:31 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="samtools" version="1.2">
-        <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>