Mercurial > repos > iuc > chira_map

changeset 7:f11619faed12 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
author iuc
date Fri, 29 May 2020 10:53:29 +0000
parents 2032d4ab9cbd
children 3ba6fe6e7e82
files chira_map.xml macros.xml test-data/chimeras test-data/interactions test-data/loci.counts test-data/singletons
diffstat 6 files changed, 22 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/chira_map.xml	Thu May 07 07:34:13 2020 +0000
+++ b/chira_map.xml	Fri May 29 10:53:29 2020 +0000
@@ -113,6 +113,10 @@
     <tests>
         <!-- Test: Map with BWA-mem -->
         <test expect_num_outputs="2">
+            <param name="seed_length1" value="12"/>
+            <param name="seed_length2" value="6"/>
+            <param name="align_score1" value="18"/>
+            <param name="align_score2" value="10"/>
             <param name="aligner" value="bwa"/>
             <param name="query" value="reads.fasta"/>
             <param name="ref_type" value="split"/>
--- a/macros.xml	Thu May 07 07:34:13 2020 +0000
+++ b/macros.xml	Fri May 29 10:53:29 2020 +0000
@@ -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>
--- a/test-data/chimeras	Thu May 07 07:34:13 2020 +0000
+++ b/test-data/chimeras	Fri May 29 10:53:29 2020 +0000
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/interactions	Fri May 29 10:53:29 2020 +0000
@@ -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
--- a/test-data/loci.counts	Thu May 07 07:34:13 2020 +0000
+++ b/test-data/loci.counts	Fri May 29 10:53:29 2020 +0000
@@ -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
--- a/test-data/singletons	Thu May 07 07:34:13 2020 +0000
+++ b/test-data/singletons	Fri May 29 10:53:29 2020 +0000
@@ -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