diff bam_stat.xml @ 3:71ed55a3515a draft

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

--- a/bam_stat.xml	Thu Jul 18 11:01:08 2013 -0500
+++ b/bam_stat.xml	Tue Mar 14 10:22:57 2017 -0400
@@ -1,46 +1,58 @@
-<tool id="bam_stat" name="BAM/SAM Mapping Stats">
-	<description>
-		reads mapping statistics for a provided BAM or SAM file.
-	</description>
-	<requirements>
-		<requirement type="package" version="2.3.7">rseqc</requirement>
-	</requirements>s
-	<command interpreter="python">
-		bam_stat.py -i $input -q $mapqual &amp;> $output
-	</command>
-	<inputs>
-		<param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
-		<param label="Minimum mapping quality (default=30" type="integer" value="30" name="mapqual" />
-	</inputs>
-	<outputs>
-		<data format="txt" name="output" />
-	</outputs>
-	<tests>
-		<test>
-			<param name="input" value="Pairend_nonStrandSpecific_36mer_Human_hg19.bam" />
-			<output name="bamstatout.txt"
-		</test>
-	</tests>
-	<help>
-.. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
+<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>
+
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <expand macro="stdio" />
+
+    <version_command><![CDATA[bam_stat.py --version]]></version_command>
 
------
+    <command><![CDATA[
+        bam_stat.py -i '${input}' -q ${mapq} > '${output}'
+        ]]>
+    </command>
+
+    <inputs>
+        <expand macro="bam_param" />
+        <expand macro="mapq_param" />
+    </inputs>
 
-About RSeQC
+    <outputs>
+        <data format="txt" name="output" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
+            <output name="output" file="output.bamstats.txt" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+bam_stat.py
 +++++++++++
 
-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.
+This program is used to calculate reads mapping statistics from provided BAM
+file.  This script determines "uniquely mapped reads" from `mapping quality
+<http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores>`_,
+which quality the probability that a read is misplaced (Do NOT confused with
+sequence quality, sequence quality measures the probability that a base-calling
+was wrong) .
 
 Inputs
 ++++++++++++++
 
 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
 ++++++++++++++
@@ -50,6 +62,10 @@
 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads}
 
+@ABOUT@
 
-	</help>
-</tool>
\ No newline at end of file
+]]>
+    </help>
+
+    <expand macro="citations" />
+</tool>