# HG changeset patch
# User lparsons
# Date 1436292844 14400
# Node ID cd2daa987b696d365752f6813af29da7cff8820b
# Parent  30612763595927dcedf982a63fedafd6cfc25ff9
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827

diff -r 306127635959 -r cd2daa987b69 bam_stat.xml
--- a/bam_stat.xml	Tue Jul 07 10:39:47 2015 -0400
+++ b/bam_stat.xml	Tue Jul 07 14:14:04 2015 -0400
@@ -17,13 +17,13 @@
     <version_command><![CDATA[bam_stat.py --version]]></version_command>
 
     <command><![CDATA[
-        bam_stat.py -i $input -q $mapqual 2> $output
+        bam_stat.py -i $input -q $mapq 2> $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" />
+        <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)" />
     </inputs>
 
     <outputs>
@@ -42,7 +42,8 @@
 +++++++++++
 
 This program is used to calculate reads mapping statistics from provided BAM
-file.  This script determines "uniquely mapped reads" from `mapping quality`_,
+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) .
@@ -54,7 +55,7 @@
 	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
 ++++++++++++++
diff -r 306127635959 -r cd2daa987b69 clipping_profile.xml
--- a/clipping_profile.xml	Tue Jul 07 10:39:47 2015 -0400
+++ b/clipping_profile.xml	Tue Jul 07 14:14:04 2015 -0400
@@ -23,7 +23,7 @@
     </command>
 
     <inputs>
-        <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
+        <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
     </inputs>
 
     <outputs>
diff -r 306127635959 -r cd2daa987b69 geneBody_coverage.xml
--- a/geneBody_coverage.xml	Tue Jul 07 10:39:47 2015 -0400
+++ b/geneBody_coverage.xml	Tue Jul 07 14:14:04 2015 -0400
@@ -36,12 +36,12 @@
     </command>
 
     <inputs>
-        <param name="input" type="data" label="Additional input .bam files" format="bam" />
-        <repeat name="additionalinputs" title="Input .bam file">
-            <param name="file" type="data" label="Input .bam file" format="bam" />
+        <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
+        <repeat name="additionalinputs" title="Additional input .bam files">
+            <param name="file" type="data" label="Additional input .bam file" format="bam" />
         </repeat>
-        <param name="refgene" type="data" label="Reference Genome" format="bed" />
-        <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length" help="Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100)." />
+        <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
+        <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length in bp (default: 100)" help="mRNA that are shorter than this value will be skipped (--minimum_length)." />
     </inputs>
 
     <outputs>