# HG changeset patch
# User iuc
# Date 1590749848 14400
# Node ID e40017f9cff19a1fe923b67c3e0fa46968bdcdaf
# Parent  a1694947910f9a87a5344e4af639181f459ebe4f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"

diff -r a1694947910f -r e40017f9cff1 chira_quantify.xml
--- a/chira_quantify.xml	Thu May 07 03:35:45 2020 -0400
+++ b/chira_quantify.xml	Fri May 29 06:57:28 2020 -0400
@@ -20,7 +20,7 @@
         <param format="tabular" name="merged" type="data" label="Tabular file of merged alignments"/>
         <param name="crl_share" type="float" value="0.7" label="CRL locus fraction" min="0" max="1"
             help="Minimum fraction of reads of a locus that must overlap with all CRL loci inorder to merge itinto that CRL."/>
-        <param name="min_locus_size" type="integer" value="5" label="Minimum locus size" min="1"
+        <param name="min_locus_size" type="integer" value="10" label="Minimum locus size" min="1"
             help="Minimum number of reads a locus should have in order to participate in CRL creation.
                  Always set this value relative to your sequencing depth. Setting this to lower leads
                  CRLs of random multimappings Also consider setting the --crl_share option
@@ -38,6 +38,7 @@
         <test expect_num_outputs="1">
             <param name="segments" value="segments.bed"/>
             <param name="merged" value="merged.bed"/>
+            <param name="min_locus_size" value="5"/>
             <output name="loci" file="loci.counts"/>
         </test>
     </tests>
diff -r a1694947910f -r e40017f9cff1 macros.xml
--- a/macros.xml	Thu May 07 03:35:45 2020 -0400
+++ b/macros.xml	Fri May 29 06:57:28 2020 -0400
@@ -1,6 +1,6 @@
 <macros>
     <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token>
-    <token name="@TOOL_VERSION@">1.2.0</token>
+    <token name="@TOOL_VERSION@">1.3.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">chira</requirement>
diff -r a1694947910f -r e40017f9cff1 test-data/chimeras
--- a/test-data/chimeras	Thu May 07 03:35:45 2020 -0400
+++ b/test-data/chimeras	Fri May 29 06:57:28 2020 -0400
@@ -1,3 +1,3 @@
 tagid	txid1	txid2	geneid1	geneid2	symbol1	symbol2	region1	region2	tx_pos_start1	tx_pos_end1	tx_pos_strand1	length1	tx_pos_start2	tx_pos_end2	tx_pos_strand2	length2	read_info	genomic_pos1	genomic_pos2	locus1	locus2	groupid1	groupid2	tpm1	tpm2	score1	score2	score	sequences	hybrid	hybrid_pos	mfe
-4|1	mmu-miR-6979-3p	ENSMUST00000136025	NA	NA	NA	NA	NA	NA	2	12	+	21	32	46	+	188	30,39,2,15,54	mmu-miR-6979-3p:2:12:+	ENSMUST00000136025:32:46:+	mmu-miR-6979-3p:2:12:+	ENSMUST00000136025:32:46:+	7	1	165100.0	121100.0	1.0	1.0	2.0	GUGUCUGUCU&CAGGACUCUUGGCU	NA	NA	NA
-3|2	mmu-miR-20a-5p	ENSMUST00000136025	NA	NA	NA	NA	NA	NA	0	23	+	23	132	142	+	188	6,28,35,44,55	mmu-miR-20a-5p:0:23:+	ENSMUST00000136025:132:142:+	mmu-miR-20a-5p:0:23:+	ENSMUST00000136025:132:142:+	5	2	75660.0	165100.0	1.0	1.0	2.0	UAAAGUGCUUAUAGUGCAGGUAG&CUGCCUGCCU	((.((((((((&))))))))))	13&1	-10.88
+3|2	mmu-miR-20a-5p	ENSMUST00000136025	NA	NA	NA	NA	NA	NA	0	23	+	23	132	142	+	188	6,28,35,44,55	mmu-miR-20a-5p:0:23:+	ENSMUST00000136025:132:142:+	mmu-miR-20a-5p:0:23:+	ENSMUST00000136025:132:142:+	5	2	75660.00	165100.00	1.0	1.0	2.0	UAAAGUGCUUAUAGUGCAGGUAG&CUGCCUGCCU	((((((((((&)).))))))))	1&13	-13.7
+4|1	mmu-miR-6979-3p	ENSMUST00000136025	NA	NA	NA	NA	NA	NA	2	12	+	21	32	46	+	188	30,39,2,15,54	mmu-miR-6979-3p:2:12:+	ENSMUST00000136025:32:46:+	mmu-miR-6979-3p:2:12:+	ENSMUST00000136025:32:46:+	7	1	165100.00	121100.00	1.0	1.0	2.0	GUGUCUGUCU&CAGGACUCUUGGCU	((((.....((&))....))))	3&1	-4
diff -r a1694947910f -r e40017f9cff1 test-data/interactions
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/interactions	Fri May 29 06:57:28 2020 -0400
@@ -0,0 +1,2 @@
+mmu-miR-20a-5p:0:23:+	ENSMUST00000136025:132:142:+	1	UAAAGUGCUUAUAGUGCAGGUAG	CUGCCUGCCU	((((((((((&)).))))))))	1&13	-13.7	75660.00	165100.00	240760.0	1.0	1.0	2.0	NA	NA	mmu-miR-20a-5p	ENSMUST00000136025
+mmu-miR-6979-3p:2:12:+	ENSMUST00000136025:32:46:+	1	GUGUCUGUCU	CAGGACUCUUGGCU	((((.....((&))....))))	3&1	-4	165100.00	121100.00	286200.0	1.0	1.0	2.0	NA	NA	mmu-miR-6979-3p	ENSMUST00000136025
diff -r a1694947910f -r e40017f9cff1 test-data/loci.counts
--- a/test-data/loci.counts	Thu May 07 03:35:45 2020 -0400
+++ b/test-data/loci.counts	Fri May 29 06:57:28 2020 -0400
@@ -1,9 +1,9 @@
-6|1|1	ENSMUST00000182010	4	0	19	68	+	5S49M1S	ENSMUST00000182010:19:68:+	ENSMUST00000182010:19:74:+	1	1	6.485e+04
-7|9|1	ENSMUST00000182010	4	0	24	74	+	5S50M	ENSMUST00000182010:24:74:+	ENSMUST00000182010:19:74:+	1	1	6.485e+04
-4|1|2	ENSMUST00000136025	0	1	32	46	+	1S14M39S	ENSMUST00000136025:32:46:+	ENSMUST00000136025:32:46:+	1	1	1.211e+05
-3|2|2	ENSMUST00000136025	1	2	132	142	+	34S10M11S	ENSMUST00000136025:132:142:+	ENSMUST00000136025:132:142:+	1	1	1.651e+05
-2|2|2	ENSMUST00000137264	2	3	12	27	+	4S15M30S	ENSMUST00000137264:12:27:+	ENSMUST00000137264:12:27:+	1	1	1.135e+05
-6|1|4	ENSMUST00000160533	3	4	69	82	+	42S13M	ENSMUST00000160533:69:82:+	ENSMUST00000160533:69:82:+	1	1	1.297e+05
-3|2|1	mmu-miR-20a-5p	5	5	0	23	+	5S23M27S	mmu-miR-20a-5p:0:23:+	mmu-miR-20a-5p:0:23:+	1	1	7.566e+04
-2|2|1	mmu-miR-6898-5p	6	6	11	21	+	10M39S	mmu-miR-6898-5p:11:21:+	mmu-miR-6898-5p:11:21:+	1	1	1.651e+05
-4|1|1	mmu-miR-6979-3p	7	7	2	12	+	29S10M15S	mmu-miR-6979-3p:2:12:+	mmu-miR-6979-3p:2:12:+	1	1	1.651e+05
+2|2|1	mmu-miR-6898-5p	6	6	11	21	+	10M39S	mmu-miR-6898-5p:11:21:+	mmu-miR-6898-5p:11:21:+	1.00	1.00	1.651e+05
+2|2|2	ENSMUST00000137264	2	3	12	27	+	4S15M30S	ENSMUST00000137264:12:27:+	ENSMUST00000137264:12:27:+	1.00	1.00	1.135e+05
+3|2|1	mmu-miR-20a-5p	5	5	0	23	+	5S23M27S	mmu-miR-20a-5p:0:23:+	mmu-miR-20a-5p:0:23:+	1.00	1.00	7.566e+04
+3|2|2	ENSMUST00000136025	1	2	132	142	+	34S10M11S	ENSMUST00000136025:132:142:+	ENSMUST00000136025:132:142:+	1.00	1.00	1.651e+05
+4|1|1	mmu-miR-6979-3p	7	7	2	12	+	29S10M15S	mmu-miR-6979-3p:2:12:+	mmu-miR-6979-3p:2:12:+	1.00	1.00	1.651e+05
+4|1|2	ENSMUST00000136025	0	1	32	46	+	1S14M39S	ENSMUST00000136025:32:46:+	ENSMUST00000136025:32:46:+	1.00	1.00	1.211e+05
+6|1|1	ENSMUST00000182010	4	0	19	68	+	5S49M1S	ENSMUST00000182010:19:68:+	ENSMUST00000182010:19:74:+	1.00	1.00	6.485e+04
+6|1|4	ENSMUST00000160533	3	4	69	82	+	42S13M	ENSMUST00000160533:69:82:+	ENSMUST00000160533:69:82:+	1.00	1.00	1.297e+05
+7|9|1	ENSMUST00000182010	4	0	24	74	+	5S50M	ENSMUST00000182010:24:74:+	ENSMUST00000182010:19:74:+	1.00	1.00	6.485e+04
diff -r a1694947910f -r e40017f9cff1 test-data/singletons
--- a/test-data/singletons	Thu May 07 03:35:45 2020 -0400
+++ b/test-data/singletons	Fri May 29 06:57:28 2020 -0400
@@ -1,4 +1,4 @@
-tagid	txid	geneid	symbol	region	tx_pos_start	tx_pos_end	tx_pos_strand	length	read_info	genomic_pos	locus	groupid	tpm	score	score	sequences
-6|1	ENSMUST00000182010	NA	NA	NA	19	68	+	NA	6,54,55	ENSMUST00000182010:19:68:+	ENSMUST00000182010:19:74:+	0	64850.0	1.0	1.0	UCAUUAAUCAAGAACGAAAGUCGGAGUUUCGAAGACGAUCAGAUACCGUUGUAGU
-7|9	ENSMUST00000182010	NA	NA	NA	24	74	+	NA	6,55,55	ENSMUST00000182010:24:74:+	ENSMUST00000182010:19:74:+	0	64850.0	1.0	1.0	UCAUUAAUCAAGAACGAAAGUCGGAGUUUCGAAGACGAUCAGAUACCGUUGUAGU
-2|2	ENSMUST00000137264	NA	NA	NA	12	27	+	NA	5,19,49	ENSMUST00000137264:12:27:+	ENSMUST00000137264:12:27:+	3	113500.0	1.0	1.0	AGGGAGGACGAUGCG
+tagid	txid	geneid	symbol	region	tx_pos_start	tx_pos_end	tx_pos_strand	length	read_info	genomic_pos	locus	groupid	tpm	score
+2|2	mmu-miR-6898-5p	NA	NA	NA	11	21	+	NA	1,10,49	mmu-miR-6898-5p:11:21:+	mmu-miR-6898-5p:11:21:+	6	165100.00	1.00
+6|1	ENSMUST00000160533	NA	NA	NA	69	82	+	NA	43,55,55	ENSMUST00000160533:69:82:+	ENSMUST00000160533:69:82:+	4	129700.00	1.00
+7|9	ENSMUST00000182010	NA	NA	NA	24	74	+	NA	6,55,55	ENSMUST00000182010:24:74:+	ENSMUST00000182010:19:74:+	0	64850.00	1.00