diff samtools_idxstats.xml @ 1:88b8c2916784 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

--- 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>