# HG changeset patch
# User iuc
# Date 1528927345 14400
# Node ID 5873cd7afb67cc3a57b66eb38621e792be83f51c
# Parent  080fd5739bb4a0445bc6b7073f6b4f5c71f4f1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 62a9135bf04aec398d3172d17ccd60f5242d8e82

diff -r 080fd5739bb4 -r 5873cd7afb67 FPKM_count.xml
--- a/FPKM_count.xml	Tue Mar 20 05:37:48 2018 -0400
+++ b/FPKM_count.xml	Wed Jun 13 18:02:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_FPKM_count" name="FPKM Count" version="@WRAPPER_VERSION@">
+<tool id="rseqc_FPKM_count" name="FPKM Count" version="@WRAPPER_VERSION@.1">
     <description>calculates raw read count, FPM, and FPKM for each gene</description>
 
     <macros>
diff -r 080fd5739bb4 -r 5873cd7afb67 RNA_fragment_size.xml
--- a/RNA_fragment_size.xml	Tue Mar 20 05:37:48 2018 -0400
+++ b/RNA_fragment_size.xml	Wed Jun 13 18:02:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@WRAPPER_VERSION@">
+<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@WRAPPER_VERSION@.1">
     <description>
      calculates the fragment size for each gene/transcript
     </description>
@@ -35,7 +35,18 @@
         <test>
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
             <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
-            <output name="output" file="output.RNA_fragment_size.txt" />
+            <output name="output">
+                <assert_contents>
+                    <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$" />
+                    <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$" />
+                    <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$" />
+                    <has_line_matching expression="^chr1\t17368\t17436\tNR_106918\t0\t0\t0\t0$" />
+                    <has_line_matching expression="^chr1\t17368\t17436\tNR_107062\t0\t0\t0\t0$" />
+                    <has_line_matching expression="^chr1\t34610\t36081\tNR_026818\t0\t0\t0\t0$" />
+                    <has_line_matching expression="^chr1\t34610\t36081\tNR_026820\t0\t0\t0\t0$" />
+                    <has_line_matching expression="^chr1\t69090\t70008\tNM_001005484\t0\t0\t0\t0$" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
 
diff -r 080fd5739bb4 -r 5873cd7afb67 RPKM_saturation.xml
--- a/RPKM_saturation.xml	Tue Mar 20 05:37:48 2018 -0400
+++ b/RPKM_saturation.xml	Wed Jun 13 18:02:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@WRAPPER_VERSION@">
+<tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@WRAPPER_VERSION@.1">
     <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description>
 
     <macros>
diff -r 080fd5739bb4 -r 5873cd7afb67 geneBody_coverage.xml
--- a/geneBody_coverage.xml	Tue Mar 20 05:37:48 2018 -0400
+++ b/geneBody_coverage.xml	Wed Jun 13 18:02:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="@WRAPPER_VERSION@.1">
+<tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="@WRAPPER_VERSION@.2">
   <description>
     Read coverage over gene body.
   </description>
diff -r 080fd5739bb4 -r 5873cd7afb67 geneBody_coverage2.xml
--- a/geneBody_coverage2.xml	Tue Mar 20 05:37:48 2018 -0400
+++ b/geneBody_coverage2.xml	Wed Jun 13 18:02:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_geneBody_coverage2" name="Gene Body Converage (Bigwig)" version="@WRAPPER_VERSION@">
+<tool id="rseqc_geneBody_coverage2" name="Gene Body Converage (Bigwig)" version="@WRAPPER_VERSION@.1">
     <description>
         Read coverage over gene body
     </description>
diff -r 080fd5739bb4 -r 5873cd7afb67 infer_experiment.xml
--- a/infer_experiment.xml	Tue Mar 20 05:37:48 2018 -0400
+++ b/infer_experiment.xml	Wed Jun 13 18:02:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_infer_experiment" name="Infer Experiment" version="@WRAPPER_VERSION@">
+<tool id="rseqc_infer_experiment" name="Infer Experiment" version="@WRAPPER_VERSION@.1">
     <description>speculates how RNA-seq were configured</description>
 
     <macros>
diff -r 080fd5739bb4 -r 5873cd7afb67 inner_distance.xml
--- a/inner_distance.xml	Tue Mar 20 05:37:48 2018 -0400
+++ b/inner_distance.xml	Wed Jun 13 18:02:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_inner_distance" name="Inner Distance" version="@WRAPPER_VERSION@">
+<tool id="rseqc_inner_distance" name="Inner Distance" version="@WRAPPER_VERSION@.1">
     <description>calculate the inner distance (or insert size) between two paired RNA reads</description>
 
     <macros>
diff -r 080fd5739bb4 -r 5873cd7afb67 junction_annotation.xml
--- a/junction_annotation.xml	Tue Mar 20 05:37:48 2018 -0400
+++ b/junction_annotation.xml	Wed Jun 13 18:02:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_junction_annotation" name="Junction Annotation" version="@WRAPPER_VERSION@">
+<tool id="rseqc_junction_annotation" name="Junction Annotation" version="@WRAPPER_VERSION@.1">
     <description>compares detected splice junctions to reference gene model</description>
 
     <macros>
diff -r 080fd5739bb4 -r 5873cd7afb67 junction_saturation.xml
--- a/junction_saturation.xml	Tue Mar 20 05:37:48 2018 -0400
+++ b/junction_saturation.xml	Wed Jun 13 18:02:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_junction_saturation" name="Junction Saturation" version="@WRAPPER_VERSION@">
+<tool id="rseqc_junction_saturation" name="Junction Saturation" version="@WRAPPER_VERSION@.1">
     <description>detects splice junctions from each subset and compares them to reference gene model</description>
 
     <macros>
diff -r 080fd5739bb4 -r 5873cd7afb67 read_distribution.xml
--- a/read_distribution.xml	Tue Mar 20 05:37:48 2018 -0400
+++ b/read_distribution.xml	Wed Jun 13 18:02:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_read_distribution" name="Read Distribution" version="@WRAPPER_VERSION@">
+<tool id="rseqc_read_distribution" name="Read Distribution" version="@WRAPPER_VERSION@.1">
     <description>calculates how mapped reads were distributed over genome feature</description>
 
     <macros>
diff -r 080fd5739bb4 -r 5873cd7afb67 rseqc_macros.xml
--- a/rseqc_macros.xml	Tue Mar 20 05:37:48 2018 -0400
+++ b/rseqc_macros.xml	Wed Jun 13 18:02:25 2018 -0400
@@ -26,7 +26,7 @@
     </xml>
 
     <xml name="refgene_param">
-        <param name="refgene" type="data" format="bed" label="Reference gene model" help="(--refgene)"/>
+        <param name="refgene" type="data" format="bed12" label="Reference gene model" help="(--refgene)"/>
     </xml>
 
     <xml name="mapq_param">
diff -r 080fd5739bb4 -r 5873cd7afb67 test-data/output.RNA_fragment_size.txt
--- a/test-data/output.RNA_fragment_size.txt	Tue Mar 20 05:37:48 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-chrom	tx_start	tx_end	symbol	frag_count	frag_mean	frag_median	frag_std
-chr1	11873	14409	NR_046018	1	0	0	0
-chr1	14361	29370	NR_024540	14	66.5	51.0	41.119599080869314
-chr1	17368	17436	NR_106918	0	0	0	0
-chr1	17368	17436	NR_107062	0	0	0	0
-chr1	34610	36081	NR_026818	0	0	0	0
-chr1	34610	36081	NR_026820	0	0	0	0
-chr1	69090	70008	NM_001005484	0	0	0	0
diff -r 080fd5739bb4 -r 5873cd7afb67 test-data/output.tin.summary.txt
--- a/test-data/output.tin.summary.txt	Tue Mar 20 05:37:48 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-Bam_file	TIN(mean)	TIN(median)	TIN(stdev)
-input.bam	8.870967741935486	8.870967741935486	0.0
diff -r 080fd5739bb4 -r 5873cd7afb67 tin.xml
--- a/tin.xml	Tue Mar 20 05:37:48 2018 -0400
+++ b/tin.xml	Wed Jun 13 18:02:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="rseqc_tin" name="Transcript Integrity Number" version="@WRAPPER_VERSION@">
+<tool id="rseqc_tin" name="Transcript Integrity Number" version="@WRAPPER_VERSION@.1">
     <description>
         evaluates RNA integrity at a transcript level
     </description>
@@ -50,7 +50,12 @@
         <test>
             <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
             <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
-            <output name="outputsummary" file="output.tin.summary.txt"/>
+            <output name="outputsummary">
+                <assert_contents>
+                    <has_line_matching expression="^Bam_file\tTIN\(mean\)\tTIN\(median\)\tTIN\(stdev\)$" />
+                    <has_line_matching expression="^input\.bam\t8\.8709677419\d+\t8\.8709677419\d+\t0\.0$" />
+                </assert_contents>
+            </output>
             <output name="outputxls" file="output.tin.xls"/>
         </test>
     </tests>