# HG changeset patch
# User iuc
# Date 1582140420 18000
# Node ID a1f0b3f4b78144ed7b046b6705dab66fd3a9208f
# Parent  9ffcddf6f9c00a2daf7f82ad6f392f346c0913ac
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 11b94d7cd69b919f16feb10bd4b830a963334ab8"

diff -r 9ffcddf6f9c0 -r a1f0b3f4b781 picard_CollectRnaSeqMetrics.xml
--- a/picard_CollectRnaSeqMetrics.xml	Mon Feb 17 10:24:29 2020 -0500
+++ b/picard_CollectRnaSeqMetrics.xml	Wed Feb 19 14:27:00 2020 -0500
@@ -2,7 +2,7 @@
     <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description>
     <macros>
         <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@WRAPPER_VERSION@">2</token>
     </macros>
     <expand macro="requirements">
         <requirement type="package" version="3.4.1">r-base</requirement>
@@ -22,18 +22,16 @@
       ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format
 
       #if str($gene_reference_source.gene_reference_source_selector) == "gtf"
-        #if $gene_reference_source.refFlat.ext != 'gff3'
-            gtfToGenePred -genePredExt '${gene_reference_source.refFlat}' refFlat.tab.raw &&
+        #if $gene_reference_source.refFlat.ext == 'gff3'
+            gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
         #else
-            gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
+            gtfToGenePred -genePredExt '${gene_reference_source.refFlat}' refFlat.tab.raw &&
         #end if
-
         grep -v '^#' refFlat.tab.raw | awk '{print $12"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab &&
       #else
-        grep -v '^#' ${refFlat} | awk '{print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab &&
+        grep -v '^#' ${refFlat} | awk '{if ($3 == "+" || $3 == "-") print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10; else print}' > refFlat.tab &&
       #end if
 
-
       ## Start picard command
 
       @java_options@
@@ -145,6 +143,20 @@
       <param name="rrna_fragment_percentage" value="0.8" />
       <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
     </test>
+   <test>
+      <param name="reference_source_selector" value="history"/>
+      <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
+      <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
+      <param name="assume_sorted" value="true" />
+
+      <param name="gene_reference_source_selector" value="refflat" />
+      <param name="refFlat" value="picard_CollectRnaSeqMetrics.ucsc_output" />
+      <param name="metric_accumulation_level" value="ALL_READS" />
+      <param name="minimum_length" value="500" />
+      <param name="strand_specificity" value="NONE" />
+      <param name="rrna_fragment_percentage" value="0.8" />
+      <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
+    </test>
 
     <test>
       <param name="reference_source_selector" value="history"/>
diff -r 9ffcddf6f9c0 -r a1f0b3f4b781 test-data/picard_CollectRnaSeqMetrics.refFlat
--- a/test-data/picard_CollectRnaSeqMetrics.refFlat	Mon Feb 17 10:24:29 2020 -0500
+++ b/test-data/picard_CollectRnaSeqMetrics.refFlat	Wed Feb 19 14:27:00 2020 -0500
@@ -1,21 +1,21 @@
-#hg19.knownGene.name	hg19.knownGene.chrom	hg19.knownGene.strand	hg19.knownGene.txStart	hg19.knownGene.txEnd	hg19.knownGene.cdsStart	hg19.knownGene.cdsEnd	hg19.knownGene.exonCount	hg19.knownGene.exonStarts	hg19.knownGene.exonEnds	hg19.kgXref.kgID
-uc004coq.4	chrM	-	235	368	235	235	1	235,	368,	uc004coq.4
-uc022bqo.2	chrM	+	650	674	650	650	1	650,	674,	uc022bqo.2
-uc004cor.1	chrM	+	1603	1634	1603	1603	1	1603,	1634,	uc004cor.1
-uc004cos.5	chrM	+	1843	4264	1843	1843	1	1843,	4264,	uc004cos.5
-uc022bqp.1	chrM	-	5543	5566	5543	5543	1	5543,	5566,	uc022bqp.1
-uc022bqq.1	chrM	-	5585	5606	5585	5585	1	5585,	5606,	uc022bqq.1
-uc022bqr.1	chrM	-	5690	5714	5690	5690	1	5690,	5714,	uc022bqr.1
-uc031tga.1	chrM	+	5904	7439	5904	5904	1	5904,	7439,	uc031tga.1
-uc022bqs.1	chrM	-	7586	15888	7586	7586	2	7586,15503,	7982,15888,	uc022bqs.1
-uc011mfi.2	chrM	+	7586	9208	7586	7586	1	7586,	9208,	uc011mfi.2
-uc022bqt.1	chrM	-	8366	14149	8366	8366	2	8366,13449,	8472,14149,	uc022bqt.1
-uc022bqu.2	chrM	+	10059	10404	10059	10059	1	10059,	10404,	uc022bqu.2
-uc004cov.5	chrM	+	10470	12138	10470	10470	1	10470,	12138,	uc004cov.5
-uc031tgb.1	chrM	-	10760	14149	10760	10760	2	10760,13978,	11231,14149,	uc031tgb.1
-uc004cow.2	chrM	+	12207	12264	12207	12207	1	12207,	12264,	uc004cow.2
-uc004cox.4	chrM	+	12907	14149	12907	12907	1	12907,	14149,	uc004cox.4
-uc022bqv.1	chrM	-	14674	14698	14674	14674	1	14674,	14698,	uc022bqv.1
-uc022bqw.1	chrM	+	14856	15888	14856	14856	1	14856,	15888,	uc022bqw.1
-uc022bqx.1	chrM	-	15959	16024	15959	15959	1	15959,	16024,	uc022bqx.1
-uc004coz.1	chrM	+	15998	16571	15998	15998	1	15998,	16571,	uc004coz.1
+#hg19.kgXref.kgID	hg19.knownGene.name	hg19.knownGene.chrom	hg19.knownGene.strand	hg19.knownGene.txStart	hg19.knownGene.txEnd	hg19.knownGene.cdsStart	hg19.knownGene.cdsEnd	hg19.knownGene.exonCount	hg19.knownGene.exonStarts	hg19.knownGene.exonEnds
+uc004coq.4	uc004coq.4	chrM	-	235	368	235	235	1	235,	368,
+uc022bqo.2	uc022bqo.2	chrM	+	650	674	650	650	1	650,	674,
+uc004cor.1	uc004cor.1	chrM	+	1603	1634	1603	1603	1	1603,	1634,
+uc004cos.5	uc004cos.5	chrM	+	1843	4264	1843	1843	1	1843,	4264,
+uc022bqp.1	uc022bqp.1	chrM	-	5543	5566	5543	5543	1	5543,	5566,
+uc022bqq.1	uc022bqq.1	chrM	-	5585	5606	5585	5585	1	5585,	5606,
+uc022bqr.1	uc022bqr.1	chrM	-	5690	5714	5690	5690	1	5690,	5714,
+uc031tga.1	uc031tga.1	chrM	+	5904	7439	5904	5904	1	5904,	7439,
+uc022bqs.1	uc022bqs.1	chrM	-	7586	15888	7586	7586	2	7586,15503,	7982,15888,
+uc011mfi.2	uc011mfi.2	chrM	+	7586	9208	7586	7586	1	7586,	9208,
+uc022bqt.1	uc022bqt.1	chrM	-	8366	14149	8366	8366	2	8366,13449,	8472,14149,
+uc022bqu.2	uc022bqu.2	chrM	+	10059	10404	10059	10059	1	10059,	10404,
+uc004cov.5	uc004cov.5	chrM	+	10470	12138	10470	10470	1	10470,	12138,
+uc031tgb.1	uc031tgb.1	chrM	-	10760	14149	10760	10760	2	10760,13978,	11231,14149,
+uc004cow.2	uc004cow.2	chrM	+	12207	12264	12207	12207	1	12207,	12264,
+uc004cox.4	uc004cox.4	chrM	+	12907	14149	12907	12907	1	12907,	14149,
+uc022bqv.1	uc022bqv.1	chrM	-	14674	14698	14674	14674	1	14674,	14698,
+uc022bqw.1	uc022bqw.1	chrM	+	14856	15888	14856	14856	1	14856,	15888,
+uc022bqx.1	uc022bqx.1	chrM	-	15959	16024	15959	15959	1	15959,	16024,
+uc004coz.1	uc004coz.1	chrM	+	15998	16571	15998	15998	1	15998,	16571,
diff -r 9ffcddf6f9c0 -r a1f0b3f4b781 test-data/picard_CollectRnaSeqMetrics.ucsc_output
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/picard_CollectRnaSeqMetrics.ucsc_output	Wed Feb 19 14:27:00 2020 -0500
@@ -0,0 +1,21 @@
+#hg19.knownGene.name	hg19.knownGene.chrom	hg19.knownGene.strand	hg19.knownGene.txStart	hg19.knownGene.txEnd	hg19.knownGene.cdsStart	hg19.knownGene.cdsEnd	hg19.knownGene.exonCount	hg19.knownGene.exonStarts	hg19.knownGene.exonEnds	hg19.kgXref.kgID
+uc004coq.4	chrM	-	235	368	235	235	1	235,	368,	uc004coq.4
+uc022bqo.2	chrM	+	650	674	650	650	1	650,	674,	uc022bqo.2
+uc004cor.1	chrM	+	1603	1634	1603	1603	1	1603,	1634,	uc004cor.1
+uc004cos.5	chrM	+	1843	4264	1843	1843	1	1843,	4264,	uc004cos.5
+uc022bqp.1	chrM	-	5543	5566	5543	5543	1	5543,	5566,	uc022bqp.1
+uc022bqq.1	chrM	-	5585	5606	5585	5585	1	5585,	5606,	uc022bqq.1
+uc022bqr.1	chrM	-	5690	5714	5690	5690	1	5690,	5714,	uc022bqr.1
+uc031tga.1	chrM	+	5904	7439	5904	5904	1	5904,	7439,	uc031tga.1
+uc022bqs.1	chrM	-	7586	15888	7586	7586	2	7586,15503,	7982,15888,	uc022bqs.1
+uc011mfi.2	chrM	+	7586	9208	7586	7586	1	7586,	9208,	uc011mfi.2
+uc022bqt.1	chrM	-	8366	14149	8366	8366	2	8366,13449,	8472,14149,	uc022bqt.1
+uc022bqu.2	chrM	+	10059	10404	10059	10059	1	10059,	10404,	uc022bqu.2
+uc004cov.5	chrM	+	10470	12138	10470	10470	1	10470,	12138,	uc004cov.5
+uc031tgb.1	chrM	-	10760	14149	10760	10760	2	10760,13978,	11231,14149,	uc031tgb.1
+uc004cow.2	chrM	+	12207	12264	12207	12207	1	12207,	12264,	uc004cow.2
+uc004cox.4	chrM	+	12907	14149	12907	12907	1	12907,	14149,	uc004cox.4
+uc022bqv.1	chrM	-	14674	14698	14674	14674	1	14674,	14698,	uc022bqv.1
+uc022bqw.1	chrM	+	14856	15888	14856	14856	1	14856,	15888,	uc022bqw.1
+uc022bqx.1	chrM	-	15959	16024	15959	15959	1	15959,	16024,	uc022bqx.1
+uc004coz.1	chrM	+	15998	16571	15998	15998	1	15998,	16571,	uc004coz.1