diff read_distribution.xml @ 51:09846d5169fa draft

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

--- a/read_distribution.xml	Tue May 03 16:36:57 2016 -0400
+++ b/read_distribution.xml	Tue Mar 14 10:23:21 2017 -0400
@@ -1,27 +1,24 @@
-<tool id="rseqc_read_distribution" name="Read Distribution" version="2.4galaxy1">
+<tool id="rseqc_read_distribution" name="Read Distribution" version="@WRAPPER_VERSION@">
     <description>calculates how mapped reads were distributed over genome feature</description>
 
     <macros>
         <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[read_distribution.py --version]]></version_command>
 
     <command><![CDATA[
-        read_distribution.py -i $input -r $refgene > $output
+        read_distribution.py -i '${input}' -r '${refgene}' > '${output}'
         ]]>
     </command>
 
     <inputs>
-        <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
-        <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
+        <expand macro="bam_sam_param" />
+        <expand macro="refgene_param" />
     </inputs>
 
     <outputs>
@@ -89,18 +86,8 @@
 TES_down_10kb       140361190           896882              6.39
 ===============     ============        ===========         ===========
 
------
-
-About RSeQC
-+++++++++++
+@ABOUT@
 
-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/
 ]]>
     </help>