# HG changeset patch
# User ieguinoa
# Date 1570649901 14400
# Node ID 2f5e9c0fe3676074aa78280b7900e07cd41a9b45

"planemo upload for repository https://github.com/ieguinoa/tximport-galaxy-wrapper commit 2bb25471c1320fb1206afa2c4daf536b6d6e275f-dirty"

diff -r 000000000000 -r 2f5e9c0fe367 README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Wed Oct 09 15:38:21 2019 -0400
@@ -0,0 +1,2 @@
+## tximport-galaxy-wrapper
+Wrapper for the package [tximport](https://bioconductor.org/packages/release/bioc/html/tximport.html)
diff -r 000000000000 -r 2f5e9c0fe367 test-data/Araport11_subset.gff3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Araport11_subset.gff3	Wed Oct 09 15:38:21 2019 -0400
@@ -0,0 +1,106 @@
+Chr1	Araport11	gene	3631	5899	.	+	.	ID=AT1G01010;Alias=ANAC001,NAC domain containing protein 1;symbol=NAC001;tid=AT1G01010.1;Name=AT1G01010;gene_id=AT1G01010
+Chr1	Araport11	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;gene_id=AT1G01010
+Chr1	Araport11	exon	3631	3913	.	+	.	ID=AT1G01010.1:exon:1;Parent=AT1G01010.1;Name=AT1G01010;gene_id=AT1G01010
+Chr1	Araport11	five_prime_UTR	3631	3759	.	+	.	ID=AT1G01010.1:five_prime_UTR;Parent=AT1G01010.1;Name=AT1G01010;gene_id=AT1G01010
+Chr1	Araport11	exon	3996	4276	.	+	.	ID=AT1G01010.1:exon:2;Parent=AT1G01010.1;Name=AT1G01010;gene_id=AT1G01010
+Chr1	Araport11	exon	4486	4605	.	+	.	ID=AT1G01010.1:exon:3;Parent=AT1G01010.1;Name=AT1G01010;gene_id=AT1G01010
+Chr1	Araport11	exon	4706	5095	.	+	.	ID=AT1G01010.1:exon:4;Parent=AT1G01010.1;Name=AT1G01010;gene_id=AT1G01010
+Chr1	Araport11	exon	5174	5326	.	+	.	ID=AT1G01010.1:exon:5;Parent=AT1G01010.1;Name=AT1G01010;gene_id=AT1G01010
+Chr1	Araport11	exon	5439	5899	.	+	.	ID=AT1G01010.1:exon:6;Parent=AT1G01010.1;Name=AT1G01010;gene_id=AT1G01010
+Chr1	Araport11	five_prime_UTR	3759	5439	.	+	.	ID=AT1G01010.1:five_prime_UTR;Parent=AT1G01010.1;Name=AT1G01010;gene_id=AT1G01010
+Chr1	Araport11	three_prime_UTR	5631	5899	.	+	.	ID=AT1G01010.1:three_prime_UTR;Parent=AT1G01010.1;Name=AT1G01010;gene_id=AT1G01010
+Chr1	Araport11	gene	6788	9130	.	-	.	ID=AT1G01020;symbol=ARV1;tid=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	mRNA	6788	9130	.	-	.	ID=AT1G01020.5;Parent=AT1G01020;Name=AT1G01020.5;gene_id=AT1G01020
+Chr1	Araport11	exon	6788	7069	.	-	.	ID=AT1G01020.5:exon:1;Parent=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	6788	6914	.	-	.	ID=AT1G01020.5:five_prime_UTR;Parent=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7157	7232	.	-	.	ID=AT1G01020.5:exon:2;Parent=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7384	7450	.	-	.	ID=AT1G01020.5:exon:3;Parent=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7564	7649	.	-	.	ID=AT1G01020.5:exon:4;Parent=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7762	7835	.	-	.	ID=AT1G01020.5:exon:5;Parent=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7942	7987	.	-	.	ID=AT1G01020.5:exon:6;Parent=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8236	8325	.	-	.	ID=AT1G01020.5:exon:7;Parent=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8417	8464	.	-	.	ID=AT1G01020.5:exon:8;Parent=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	6914	8417	.	-	.	ID=AT1G01020.5:five_prime_UTR;Parent=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	three_prime_UTR	8420	8464	.	-	.	ID=AT1G01020.5:three_prime_UTR;Parent=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8594	9130	.	-	.	ID=AT1G01020.5:exon:9;Parent=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	three_prime_UTR	8594	9130	.	-	.	ID=AT1G01020.5:three_prime_UTR;Parent=AT1G01020.5;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	mRNA	6788	9130	.	-	.	ID=AT1G01020.4;Parent=AT1G01020;Name=AT1G01020.4;gene_id=AT1G01020
+Chr1	Araport11	exon	6788	7069	.	-	.	ID=AT1G01020.4:exon:1;Parent=AT1G01020.4;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	6788	6914	.	-	.	ID=AT1G01020.4:five_prime_UTR;Parent=AT1G01020.4;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7157	7232	.	-	.	ID=AT1G01020.4:exon:2;Parent=AT1G01020.4;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7384	7450	.	-	.	ID=AT1G01020.4:exon:3;Parent=AT1G01020.4;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7564	7649	.	-	.	ID=AT1G01020.4:exon:4;Parent=AT1G01020.4;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7762	7835	.	-	.	ID=AT1G01020.4:exon:5;Parent=AT1G01020.4;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7942	7987	.	-	.	ID=AT1G01020.4:exon:6;Parent=AT1G01020.4;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8236	8464	.	-	.	ID=AT1G01020.4:exon:7;Parent=AT1G01020.4;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	6914	8236	.	-	.	ID=AT1G01020.4:five_prime_UTR;Parent=AT1G01020.4;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	three_prime_UTR	8443	8464	.	-	.	ID=AT1G01020.4:three_prime_UTR;Parent=AT1G01020.4;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8594	9130	.	-	.	ID=AT1G01020.4:exon:8;Parent=AT1G01020.4;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	three_prime_UTR	8594	9130	.	-	.	ID=AT1G01020.4:three_prime_UTR;Parent=AT1G01020.4;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	mRNA	6788	9130	.	-	.	ID=AT1G01020.3;Parent=AT1G01020;Name=AT1G01020.3;gene_id=AT1G01020
+Chr1	Araport11	exon	6788	7069	.	-	.	ID=AT1G01020.3:exon:1;Parent=AT1G01020.3;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	6788	6914	.	-	.	ID=AT1G01020.3:five_prime_UTR;Parent=AT1G01020.3;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7157	7232	.	-	.	ID=AT1G01020.3:exon:2;Parent=AT1G01020.3;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7384	7450	.	-	.	ID=AT1G01020.3:exon:3;Parent=AT1G01020.3;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7564	7649	.	-	.	ID=AT1G01020.3:exon:4;Parent=AT1G01020.3;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7762	7835	.	-	.	ID=AT1G01020.3:exon:5;Parent=AT1G01020.3;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7942	7987	.	-	.	ID=AT1G01020.3:exon:6;Parent=AT1G01020.3;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8236	8464	.	-	.	ID=AT1G01020.3:exon:7;Parent=AT1G01020.3;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	6914	8236	.	-	.	ID=AT1G01020.3:five_prime_UTR;Parent=AT1G01020.3;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	three_prime_UTR	8443	8464	.	-	.	ID=AT1G01020.3:three_prime_UTR;Parent=AT1G01020.3;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8571	9130	.	-	.	ID=AT1G01020.3:exon:8;Parent=AT1G01020.3;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	three_prime_UTR	8571	9130	.	-	.	ID=AT1G01020.3:three_prime_UTR;Parent=AT1G01020.3;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	mRNA	6788	9130	.	-	.	ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;gene_id=AT1G01020
+Chr1	Araport11	exon	6788	7069	.	-	.	ID=AT1G01020.1:exon:1;Parent=AT1G01020.1;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	6788	6914	.	-	.	ID=AT1G01020.1:five_prime_UTR;Parent=AT1G01020.1;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7157	7232	.	-	.	ID=AT1G01020.1:exon:2;Parent=AT1G01020.1;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7384	7450	.	-	.	ID=AT1G01020.1:exon:3;Parent=AT1G01020.1;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7564	7649	.	-	.	ID=AT1G01020.1:exon:4;Parent=AT1G01020.1;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7762	7835	.	-	.	ID=AT1G01020.1:exon:5;Parent=AT1G01020.1;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7942	7987	.	-	.	ID=AT1G01020.1:exon:6;Parent=AT1G01020.1;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8236	8325	.	-	.	ID=AT1G01020.1:exon:7;Parent=AT1G01020.1;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8417	8464	.	-	.	ID=AT1G01020.1:exon:8;Parent=AT1G01020.1;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8571	9130	.	-	.	ID=AT1G01020.1:exon:9;Parent=AT1G01020.1;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	6914	8571	.	-	.	ID=AT1G01020.1:five_prime_UTR;Parent=AT1G01020.1;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	three_prime_UTR	8667	9130	.	-	.	ID=AT1G01020.1:three_prime_UTR;Parent=AT1G01020.1;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	mRNA	6788	8737	.	-	.	ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;gene_id=AT1G01020
+Chr1	Araport11	exon	6788	7069	.	-	.	ID=AT1G01020.2:exon:1;Parent=AT1G01020.2;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	6788	7069	.	-	.	ID=AT1G01020.2:five_prime_UTR;Parent=AT1G01020.2;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7157	7450	.	-	.	ID=AT1G01020.2:exon:2;Parent=AT1G01020.2;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	7157	7314	.	-	.	ID=AT1G01020.2:five_prime_UTR;Parent=AT1G01020.2;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7564	7649	.	-	.	ID=AT1G01020.2:exon:3;Parent=AT1G01020.2;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7762	7835	.	-	.	ID=AT1G01020.2:exon:4;Parent=AT1G01020.2;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7942	7987	.	-	.	ID=AT1G01020.2:exon:5;Parent=AT1G01020.2;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8236	8325	.	-	.	ID=AT1G01020.2:exon:6;Parent=AT1G01020.2;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8417	8464	.	-	.	ID=AT1G01020.2:exon:7;Parent=AT1G01020.2;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8571	8737	.	-	.	ID=AT1G01020.2:exon:8;Parent=AT1G01020.2;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	7314	8571	.	-	.	ID=AT1G01020.2:five_prime_UTR;Parent=AT1G01020.2;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	three_prime_UTR	8667	8737	.	-	.	ID=AT1G01020.2:three_prime_UTR;Parent=AT1G01020.2;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	mRNA	6788	8737	.	-	.	ID=AT1G01020.6;Parent=AT1G01020;Name=AT1G01020.6;gene_id=AT1G01020
+Chr1	Araport11	exon	6788	7069	.	-	.	ID=AT1G01020.6:exon:1;Parent=AT1G01020.6;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	6788	7069	.	-	.	ID=AT1G01020.6:five_prime_UTR;Parent=AT1G01020.6;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7157	7450	.	-	.	ID=AT1G01020.6:exon:2;Parent=AT1G01020.6;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	7157	7314	.	-	.	ID=AT1G01020.6:five_prime_UTR;Parent=AT1G01020.6;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	7564	7649	.	-	.	ID=AT1G01020.6:exon:3;Parent=AT1G01020.6;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8236	8325	.	-	.	ID=AT1G01020.6:exon:4;Parent=AT1G01020.6;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8417	8464	.	-	.	ID=AT1G01020.6:exon:5;Parent=AT1G01020.6;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	five_prime_UTR	7314	8417	.	-	.	ID=AT1G01020.6:five_prime_UTR;Parent=AT1G01020.6;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	three_prime_UTR	8420	8464	.	-	.	ID=AT1G01020.6:three_prime_UTR;Parent=AT1G01020.6;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	exon	8594	8737	.	-	.	ID=AT1G01020.6:exon:6;Parent=AT1G01020.6;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	three_prime_UTR	8594	8737	.	-	.	ID=AT1G01020.6:three_prime_UTR;Parent=AT1G01020.6;Name=AT1G01020;gene_id=AT1G01020
+Chr1	Araport11	gene	11649	13714	.	-	.	ID=AT1G01030;symbol=NGA3;full_name=NGATHA3;tid=AT1G01030.1;Name=AT1G01030;gene_id=AT1G01030
+Chr1	Araport11	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;gene_id=AT1G01030
+Chr1	Araport11	exon	11649	13173	.	-	.	ID=AT1G01030.1:exon:1;Parent=AT1G01030.1;Name=AT1G01030;gene_id=AT1G01030
+Chr1	Araport11	five_prime_UTR	11649	11863	.	-	.	ID=AT1G01030.1:five_prime_UTR;Parent=AT1G01030.1;Name=AT1G01030;gene_id=AT1G01030
+Chr1	Araport11	three_prime_UTR	12941	13173	.	-	.	ID=AT1G01030.1:three_prime_UTR;Parent=AT1G01030.1;Name=AT1G01030;gene_id=AT1G01030
+Chr1	Araport11	exon	13335	13714	.	-	.	ID=AT1G01030.1:exon:2;Parent=AT1G01030.1;Name=AT1G01030;gene_id=AT1G01030
+Chr1	Araport11	three_prime_UTR	13335	13714	.	-	.	ID=AT1G01030.1:three_prime_UTR;Parent=AT1G01030.1;Name=AT1G01030;gene_id=AT1G01030
+Chr1	Araport11	mRNA	11649	13714	.	-	.	ID=AT1G01030.2;Parent=AT1G01030;Name=AT1G01030.2;gene_id=AT1G01030
+Chr1	Araport11	exon	11649	12354	.	-	.	ID=AT1G01030.2:exon:1;Parent=AT1G01030.2;Name=AT1G01030;gene_id=AT1G01030
+Chr1	Araport11	five_prime_UTR	11649	11863	.	-	.	ID=AT1G01030.2:five_prime_UTR;Parent=AT1G01030.2;Name=AT1G01030;gene_id=AT1G01030
+Chr1	Araport11	exon	12424	13173	.	-	.	ID=AT1G01030.2:exon:2;Parent=AT1G01030.2;Name=AT1G01030;gene_id=AT1G01030
+Chr1	Araport11	five_prime_UTR	11863	12424	.	-	.	ID=AT1G01030.2:five_prime_UTR;Parent=AT1G01030.2;Name=AT1G01030;gene_id=AT1G01030
+Chr1	Araport11	three_prime_UTR	12941	13173	.	-	.	ID=AT1G01030.2:three_prime_UTR;Parent=AT1G01030.2;Name=AT1G01030;gene_id=AT1G01030
+Chr1	Araport11	exon	13335	13714	.	-	.	ID=AT1G01030.2:exon:3;Parent=AT1G01030.2;Name=AT1G01030;gene_id=AT1G01030
+Chr1	Araport11	three_prime_UTR	13335	13714	.	-	.	ID=AT1G01030.2:three_prime_UTR;Parent=AT1G01030.2;Name=AT1G01030;gene_id=AT1G01030
+
diff -r 000000000000 -r 2f5e9c0fe367 test-data/cached_locally/tx2gene.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/tx2gene.loc	Wed Oct 09 15:38:21 2019 -0400
@@ -0,0 +1,5 @@
+#The tx2gene.loc file has this format:
+#
+#<unique_build_id>	<dbkey>	<display_name>	<path_to_tx2gene_file>
+
+Ath_Araport11_subset	Ath	Arabidopsis thaliana - Araport11 - subset	${__HERE__}/../tx2gene.tab
diff -r 000000000000 -r 2f5e9c0fe367 test-data/custom_sample.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_sample.tab	Wed Oct 09 15:38:21 2019 -0400
@@ -0,0 +1,14 @@
+Transcript_id_here	Here_goes_the_length	Extra_useless_column_1	Abundance_goes_here	Extra_useless_column_2	Here_goes_the_counts
+AT1G01010.1	1688	1487.57	4.6817	1	156
+AT1G01020.3	1420	1219.57	1.68167	2	45.9399
+AT1G01020.4	711	510.567	6.65521	3	76.113
+AT1G01020.1	738	537.567	18.1462	4	218.506
+AT1G01020.5	1179	978.567	0.491433	5	10.7721
+AT1G01020.6	617	416.567	0.607591	6	5.66944
+AT1G01020.2	647	446.567	2.63345e-08	7	2.63425e-07
+AT1G03987.1	272	97.3356	0	8	0
+AT1G01030.2	1456	1255.57	0.519509	9	14.6109
+AT1G01030.1	1905	1704.57	0.298284	10	11.3891
+AT1G01040.1	6276	6075.57	1.56643	11	213.178
+AT1G03993.1	788	587.567	0	12	0
+AT1G01040.2	5877	5676.57	4.30834	13	547.822
diff -r 000000000000 -r 2f5e9c0fe367 test-data/salmon_sample1.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/salmon_sample1.tab	Wed Oct 09 15:38:21 2019 -0400
@@ -0,0 +1,14 @@
+Name	Length	EffectiveLength	TPM	NumReads
+AT1G01010.1	1688	1487.57	4.6817	156
+AT1G01020.3	1420	1219.57	1.68167	45.9399
+AT1G01020.4	711	510.567	6.65521	76.113
+AT1G01020.1	738	537.567	18.1462	218.506
+AT1G01020.5	1179	978.567	0.491433	10.7721
+AT1G01020.6	617	416.567	0.607591	5.66944
+AT1G01020.2	647	446.567	2.63345e-08	2.63425e-07
+AT1G03987.1	272	97.3356	0	0
+AT1G01030.2	1456	1255.57	0.519509	14.6109
+AT1G01030.1	1905	1704.57	0.298284	11.3891
+AT1G01040.1	6276	6075.57	1.56643	213.178
+AT1G03993.1	788	587.567	0	0
+AT1G01040.2	5877	5676.57	4.30834	547.822
diff -r 000000000000 -r 2f5e9c0fe367 test-data/salmon_sample2.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/salmon_sample2.tab	Wed Oct 09 15:38:21 2019 -0400
@@ -0,0 +1,14 @@
+Name	Length	EffectiveLength	TPM	NumReads
+AT1G01010.1	1688	1487.57	4.6817	156
+AT1G01020.3	1420	1219.57	1.68167	45.9399
+AT1G01020.4	711	510.567	6.65521	76.113
+AT1G01020.1	738	537.567	18.1462	218.506
+AT1G01020.5	1179	978.567	0.491433	10.7721
+AT1G01020.6	617	416.567	0.607591	5.66944
+AT1G01020.2	647	446.567	2.63345e-08	2.63425e-07
+AT1G03987.1	272	97.3356	0	0
+AT1G01030.2	1456	1255.57	0.519509	14.6109
+AT1G01030.1	1905	1704.57	0.298284	11.3891
+AT1G01040.1	6276	6075.57	1.56643	213.178
+AT1G03993.1	788	587.567	0	0
+AT1G01040.2	5877	5676.57	4.30834	547.822
diff -r 000000000000 -r 2f5e9c0fe367 test-data/tx2gene.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tx2gene.tab	Wed Oct 09 15:38:21 2019 -0400
@@ -0,0 +1,14 @@
+Transcript	Gene
+AT1G01010.1	AT1G01010
+AT1G01020.3	AT1G01020
+AT1G01020.4	AT1G01020
+AT1G01020.1	AT1G01020
+AT1G01020.5	AT1G01020
+AT1G01020.6	AT1G01020
+AT1G01020.2	AT1G01020
+AT1G03987.1	AT1G03987
+AT1G01030.2	AT1G01030
+AT1G01030.1	AT1G01030
+AT1G01040.1	AT1G01040
+AT1G03993.1	AT1G03993
+AT1G01040.2	AT1G01040
diff -r 000000000000 -r 2f5e9c0fe367 tool-data/tx2gene.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tx2gene.loc.sample	Wed Oct 09 15:38:21 2019 -0400
@@ -0,0 +1,1 @@
+#value, dbkey, name, path
diff -r 000000000000 -r 2f5e9c0fe367 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Oct 09 15:38:21 2019 -0400
@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<tables>
+        <table name="tx2gene_table" comment_char="#" allow_duplicate_entries="False">
+            <columns>value, dbkey, name, path</columns>
+            <file path="tool-data/tx2gene.loc" />
+        </table>
+</tables>
diff -r 000000000000 -r 2f5e9c0fe367 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Wed Oct 09 15:38:21 2019 -0400
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+        <table name="tx2gene_table" comment_char="#" allow_duplicate_entries="False">
+            <columns>value, dbkey, name, path</columns>
+            <file path="${__HERE__}/test-data/cached_locally/tx2gene.loc" />
+        </table>
+</tables>
+
diff -r 000000000000 -r 2f5e9c0fe367 tximport-galaxy-wrapper.tar
Binary file tximport-galaxy-wrapper.tar has changed
diff -r 000000000000 -r 2f5e9c0fe367 tximport.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tximport.R	Wed Oct 09 15:38:21 2019 -0400
@@ -0,0 +1,119 @@
+# setup R error handling to go to stderr
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+library("getopt")
+#library("tools")
+options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
+args <- commandArgs(trailingOnly = TRUE)
+
+# get options, using the spec as defined by the enclosed list.
+# we read the options from the default: commandArgs(TRUE).
+spec <- matrix(c(
+  "help", "h", 0, "logical",
+  "base_dir", "w", 1, "character",
+  "out_file", "o", 1, "character",
+  "countsFiles", "n", 1, "character",
+  "countsFromAbundance", "r", 1, "character",
+  "format", "v", 1, "character",
+  "gff_file", "H", 0, "character",
+  "tx2gene", "f", 0, "character",
+  "geneIdCol", "l", 0, "character",
+  "txIdCol" , "p", 1, "character",
+  "abundanceCol", "i", 0, "character",
+  "countsCol", "y", 1, "character",
+  "lengthCol", "x", 1, "character"),
+  byrow=TRUE, ncol=4)
+
+opt <- getopt(spec)
+
+
+
+
+# if help was asked for print a friendly message
+# and exit with a non-zero error code
+if (!is.null(opt$help)) {
+  cat(getopt(spec, usage=TRUE))
+  q(status=1)
+}
+	
+if (is.null(opt$gff_file) & is.null(opt$tx2gene)) {
+  cat("A GFF/GTF file or a tx2gene table is required\n")
+  q(status=1)
+}
+
+if (opt$format == 'none'){  #custom format
+    if (is.null(opt$txIdCol) | is.null(opt$abundanceCol) | is.null(opt$countsCol) | is.null(opt$lengthCol)) {
+        cat("If you select a custom format for the input files you need to specify the column names\n")
+        q(status=1)
+   }
+}
+
+if (is.null(opt$countsFiles)) {
+  cat("'countsFiles' is required\n")
+  q(status=1)
+}
+
+## parse counts files
+library(rjson)
+dat <- fromJSON(opt$countsFiles)
+samples_df <- lapply(dat, function(samples) # Loop through each "sample"
+{
+  # Convert each group to a data frame.
+  # This assumes you have 6 elements each time
+  data.frame(matrix(unlist(samples), ncol=2, byrow=T))
+})
+samples_df <- do.call(rbind, samples_df)
+colnames(samples_df) <- c("path","id")
+rownames(samples_df) <- NULL
+
+# Prepare char vector with files and sample names 
+files <- file.path(samples_df[,"path"])
+names(files) <- samples_df[,"id"]
+#files
+#all(file.exists(files))
+
+
+
+library(tximport)
+
+
+
+
+### if the input is a gff/gtf file first need to create the tx2gene table
+if (!is.null(opt$gff_file)) {
+    suppressPackageStartupMessages({
+        library("GenomicFeatures")
+    })
+    txdb <- makeTxDbFromGFF(opt$gff_file)
+    k <- keys(txdb, keytype = "TXNAME")
+    tx2gene <- select(txdb, keys=k, columns="GENEID", keytype="TXNAME")
+    # Remove 'transcript:' from transcript IDs (when gffFile is a GFF3 from Ensembl and the transcript does not have a Name)
+    tx2gene$TXNAME <- sub('^transcript:', '', tx2gene$TXNAME)
+
+} else {
+        tx2gene <- read.table(opt$tx2gene,header=FALSE)
+    }
+
+
+
+##
+if (is.null(opt$geneIdCol)) { ## there is a tx2gene table
+    if (opt$format == 'none'){  #predefined format 
+        cat("here i am too\n")  
+        txi_out <- tximport(files, type="none",txIdCol=opt$txIdCol,abundanceCol=opt$abundanceCol,countsCol=opt$countsCol,lengthCol=opt$lengthCol,tx2gene=tx2gene,countsFromAbundance=opt$countsFromAbundance)
+    } else {
+        txi_out <- tximport(files, type=opt$format, tx2gene=tx2gene,countsFromAbundance=opt$countsFromAbundance)
+    }
+} else {  # the gene_ID is a column in the counts table
+    if (opt$format == 'none'){  #predefined format
+        txi_out <- tximport(files, type="none",geneIdCol=opt$geneIdCol,txIdCol=opt$txIdCol,abundanceCol=opt$abundanceCol,countsCol=opt$countsCol,lengthCol=opt$lengthCol,tx2gene=tx2gene,countsFromAbundance=opt$countsFromAbundance)
+    } else {
+        txi_out <- tximport(files, type=opt$format, geneIdCol=opt$geneIdCol,countsFromAbundance=opt$countsFromAbundance)
+    }
+
+}
+# write count as table
+write.table(txi_out$counts, file=opt$out_file, row.names = TRUE, col.names = TRUE, quote = FALSE, sep = "\t")
diff -r 000000000000 -r 2f5e9c0fe367 tximport.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tximport.xml	Wed Oct 09 15:38:21 2019 -0400
@@ -0,0 +1,228 @@
+<tool name="tximport" id="tximport" version="0.1">
+    <description> Summarize transcript-level estimates for gene-level analysis </description>
+    <requirements>
+        <requirement type="package">bioconductor-tximport</requirement>
+        <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
+        <requirement type="package" version="1.20.2">r-getopt</requirement>
+        <requirement type="package" version="0.2.20">r-rjson</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error code returned" />
+        <regex match="is not TRUE"
+           source="both"
+           level="fatal"
+           description="Execution halted." />
+    </stdio>
+
+<command>
+ <![CDATA[
+#import json
+#if $gene_name_source_selector.gene_name_source == 'external_file':
+    #if $gene_name_source_selector.gff_source_selector.gff_source == 'history':
+        #if $gene_name_source_selector.gff_source_selector.gff_tx2gene_selector.mapping_file_option == 'gff_gtf':
+            ln -s '$gene_name_source_selector.gff_source_selector.gff_tx2gene_selector.own_gff' mapping.gff &&
+        #else:
+            ln -s '$gene_name_source_selector.gff_source_selector.gff_tx2gene_selector.own_tx2gene' mapping.tab &&
+        #end if
+    #end if
+#end if
+
+Rscript '${__tool_directory__}/tximport.R'
+    --base_dir $__tool_directory__
+    --format $input_source_selector.input_source
+    #if $input_source_selector.input_source == 'none':
+        --txIdCol $input_source_selector.tx_id_col
+        --abundanceCol $input_source_selector.abundance_col
+        --countsCol $input_source_selector.counts_col
+        --lengthCol $input_source_selector.length_col
+    #end if
+    #if $gene_name_source_selector.gene_name_source == 'gene_name_column_option':
+        --geneIdCol $gene_name_source_selector.gene_id_col
+    #else
+        #if $gene_name_source_selector.gff_source_selector.gff_source == "history":
+            #if $gene_name_source_selector.gff_source_selector.gff_tx2gene_selector.mapping_file_option == 'tx2gene':
+                    --tx2gene mapping.tab
+                #else
+                    --gff_file mapping.gff
+                #end if
+        #else:
+	--tx2gene $gene_name_source_selector.gff_source_selector.tx2gene.fields.path
+        #end if
+    #end if
+
+    --countsFromAbundance $counts_from_abundance 
+    #set $count_files = list()
+    #for $file in $counts_file:
+        #set $filename_to_element_identifiers = {}
+        $filename_to_element_identifiers.__setitem__('id',str($file.element_identifier))
+        $filename_to_element_identifiers.__setitem__('path',str($file))
+        $count_files.append(filename_to_element_identifiers)
+    #end for
+    #set $samples_dict = {}
+    $samples_dict.__setitem__('samples',$count_files)
+    --countsFiles '#echo json.dumps(samples_dict)#'
+    --out_file '${gene_level_values}' 
+
+]]></command>
+
+
+
+<inputs>
+    <conditional name="input_source_selector">
+        <param name="input_source" type ="select" label="Select the source of the quantification file">
+           <option value="salmon" selected="True">Salmon</option>
+            <option value="sailfish">Sailfish</option>
+            <option value="alevin">Alevin</option>
+            <option value="kallisto">Kallisto</option>
+            <option value="rsem">RSEM</option>
+            <option value="stringtie">Stringtie</option>
+            <option value="none">Custom format (specify the columns)</option>
+        </param>
+        <when value="none"> 
+            <param name="tx_id_col" type="text" label="Name of the txID columns"/>
+            <param name="abundance_col" type="text" label="Name of the abundance column"/>
+            <param name="counts_col" type="text" label="Name of the counts column"/>
+            <param name="length_col" type="text" label="Name of the length column"/>
+        </when>
+        <when value="salmon"/>
+        <when value="sailfish"/>
+        <when value="alevin"/>
+        <when value="kallisto"/>
+        <when value="rsem"/>
+         <when value="stringtie"/>
+    </conditional> 
+    <conditional name="gene_name_source_selector" >
+        <param name="gene_name_source" type="select" label="Is the gene name part of the counts file or will be obtained from an external file?">
+            <option value="external_file" selected="True">Use an external file to map transcript to gene names</option>
+            <option value="gene_name_column_option">Gene name is a column of the input file</option>
+        </param>
+        <when value="gene_name_column_option"> 
+            <param name="gene_name_column" type="text" label="Name of the column containing the geneID"/>
+        </when>
+        <when value="external_file">
+            <conditional name="gff_source_selector">
+                <param name="gff_source" type="select" label="Select a GFF from your history or use a built-in file?">
+                    <option value="built-in" selected="True">Use a built-in file</option>
+                    <option value="history" >Use one from the history</option>
+                </param>
+                <when value="built-in">
+                    <param name="tx2gene" type="select" label="Select an annotation version" help="If the build of your interest is not listed contact your Galaxy admin">
+                        <options from_data_table="tx2gene_table">
+                            <filter type="sort_by" column="1"/>
+                            <validator type="no_options" message="No files are available for the selected input dataset"/>
+                          </options>
+                    </param>
+                </when>  
+                <when value="history"> 
+                    <conditional name="gff_tx2gene_selector">
+                        <param name="mapping_file_option" type="select" label="Will you provide a tx2gene or a GFF/GTF file?">
+                            <option value="tx2gene" selected="True">TranscriptID to GeneID table</option>
+                            <option value="gff_gtf">GTF/GFF file</option>
+                        </param>
+                        <when value="gff_gtf">
+                            <param name="own_gff" type="data" format="gff" label="Select your GFF file"/>
+                        </when>
+                        <when value="tx2gene">
+                            <param name="own_tx2gene" type="data" format="tabular" label="Select your TranscriptID to GeneID table file"/>
+                        </when>  
+                    </conditional>
+                 </when> 
+            </conditional>
+         </when>  
+    </conditional>
+    <param name="counts_from_abundance" type="select" label="Summarization using the abundance (TPM) values?">    
+        <option value="no">No</option>
+        <option value="scaled_TPM">Scaled up to library size</option>
+        <option value="length_scaled_TPM">Scaled using the avg. transcript legth over samples and then the library size</option>
+        <option value="dtu_scaled_TPM">Scaled using the median transcript length among isoforms of a gene, and then the library size</option>
+    </param>
+    <param name="counts_file" type="data" format="tabular" multiple="true" label="Counts file(s)"/>   
+</inputs>
+
+
+<outputs>
+    <data format="tabular" name="gene_level_values" label="Gene level summarization on ${on_string}"/>
+</outputs>
+
+
+<tests>
+        <test>
+            <param name="input_source" value="salmon"/>
+            <param name="gene_name_source" value="external_file"/>
+            <param name="counts_from_abundance" value="no"/>
+            <param name="gff_source" value="history"/>
+            <param name="mapping_file_option" value="tx2gene"/>
+            <param name="own_tx2gene" value="tx2gene.tab"/>
+            <param name="counts_file" value="salmon_sample2.tab,salmon_sample1.tab" />
+            <output name="gene_level_values">
+                 <assert_contents>
+                    <has_text_matching expression="salmon_sample2.tab\tsalmon_sample1.tab" />
+                    <has_text_matching expression="AT1G01010\t156\t156" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_source" value="salmon"/>
+            <param name="gene_name_source" value="external_file"/>
+            <param name="counts_from_abundance" value="no"/>
+            <param name="gff_source" value="history"/>
+            <param name="mapping_file_option" value="gff_gtf"/>
+            <param name="own_gff" value="Araport11_subset.gff3"/>
+            <param name="counts_file" value="salmon_sample2.tab,salmon_sample1.tab" />
+            <output name="gene_level_values">
+                <assert_contents>
+                    <has_text_matching expression="salmon_sample2.tab\tsalmon_sample1.tab" />
+                    <has_text_matching expression="AT1G01010\t156\t156" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_source" value="salmon"/>
+            <param name="gene_name_source" value="external_file"/>
+            <param name="counts_from_abundance" value="no"/>
+            <param name="gff_source" value="built-in"/>
+            <param name="tx2gene" value="Ath_Araport11_subset"/>
+            <param name="counts_file" value="salmon_sample2.tab,salmon_sample1.tab" />
+            <output name="gene_level_values">
+                 <assert_contents>
+                    <has_text_matching expression="salmon_sample2.tab\tsalmon_sample1.tab" />
+                    <has_text_matching expression="AT1G01010\t156\t156" />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test input with custom format -->
+	<test>
+	    <param name="input_source" value="none"/>	
+            <param name="tx_id_col" value="Transcript_id_here"/>
+            <param name="abundance_col" value="Abundance_goes_here"/>
+            <param name="counts_col" value="Here_goes_the_counts"/>
+	    <param name="length_col" value="Here_goes_the_length"/>
+            <param name="counts_from_abundance" value="no"/>
+            <param name="gff_source" value="built-in"/>
+            <param name="tx2gene" value="Ath_Araport11_subset"/>
+            <param name="counts_file" value="custom_sample.tab" />
+            <output name="gene_level_values">
+                 <assert_contents>
+                    <has_text_matching expression="custom_sample.tab" />
+                    <has_text_matching expression="AT1G01010\t156" />
+                </assert_contents>
+            </output>
+
+        </test>
+
+</tests>
+    <help>
+
+.. class:: infomark
+
+Current version only works in 'merge' mode: A single table of gene summarizations is generated with one column for each sample file.
+Take into account that DEseq2 package in Galaxy requires one table per sample. 
+    </help>
+    
+    <citations>
+        <citation type="doi">doi:10.18129/B9.bioc.tximport</citation>
+    </citations>
+
+</tool>
+