diff bam_stat.xml @ 51:09846d5169fa draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83

--- a/bam_stat.xml	Tue May 03 16:36:57 2016 -0400
+++ b/bam_stat.xml	Tue Mar 14 10:23:21 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="2.4galaxy1">
+<tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="@WRAPPER_VERSION@">
     <description>
         reads mapping statistics for a provided BAM or SAM file.
     </description>
@@ -7,23 +7,20 @@
         <import>rseqc_macros.xml</import>
     </macros>
 
-    <requirements>
-        <expand macro="requirement_package_numpy" />
-        <expand macro="requirement_package_rseqc" />
-    </requirements>
+    <expand macro="requirements" />
 
     <expand macro="stdio" />
 
     <version_command><![CDATA[bam_stat.py --version]]></version_command>
 
     <command><![CDATA[
-        bam_stat.py -i $input -q $mapq 2> $output
+        bam_stat.py -i '${input}' -q ${mapq} > '${output}'
         ]]>
     </command>
 
     <inputs>
-        <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
-        <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" />
+        <expand macro="bam_param" />
+        <expand macro="mapq_param" />
     </inputs>
 
     <outputs>
@@ -32,8 +29,8 @@
 
     <tests>
         <test>
-            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
-            <output name="output" file="bamstats.txt"/>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
+            <output name="output" file="output.bamstats.txt" />
         </test>
     </tests>
 
@@ -52,10 +49,10 @@
 ++++++++++++++
 
 Input BAM/SAM file
-	Alignment file in BAM/SAM format.
+    Alignment file in BAM/SAM format.
 
 Minimum mapping quality
-	Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30)
+    Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30)
 
 Output
 ++++++++++++++
@@ -65,19 +62,7 @@
 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads}
 
------
-
-About RSeQC
-+++++++++++
-
-
-The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
-
-The RSeQC package is licensed under the GNU GPL v3 license.
-
-.. image:: http://rseqc.sourceforge.net/_static/logo.png
-
-.. _RSeQC: http://rseqc.sourceforge.net/
+@ABOUT@
 
 ]]>
     </help>