# HG changeset patch
# User iuc
# Date 1590749821 14400
# Node ID 56b2d956a1a6b63be8447e34509a3bbb5de21ec1
# Parent  89ab3b2973d80d727eb34f5a8e596fdd38b25607
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"

diff -r 89ab3b2973d8 -r 56b2d956a1a6 chira_extract.xml
--- a/chira_extract.xml	Thu May 07 03:37:33 2020 -0400
+++ b/chira_extract.xml	Fri May 29 06:57:01 2020 -0400
@@ -31,6 +31,10 @@
             -f2 '$reference.ref_fasta2'
         #end if
         $hybridize
+        $seed_interaction
+        $summarize
+        -a '$accessibility'
+        -m '$intarna_mode'
         -p "\${GALAXY_SLOTS:-2}"
         -o ./
     ]]></command>
@@ -86,24 +90,42 @@
                        help="Reference fasta file"/>
             </when>
         </conditional>
-        <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" />
+        <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false"
+               label="Hybridize chimeric loci?"
+               help="Turning this option on increases the run time of the tool significantly."/>
+        <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--noSeed" checked="false"
+               label="Enforce seed interaction?"/>
+        <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"
+               label="Compute accessibility profiles for interacting sequences?"/>
+        <param name="intarna_mode" type="select">
+            <option value="H">Heuristic</option>
+            <option value="M">Exact</option>
+            <option value="S">Seed-only</option>
+        </param>
+        <param name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false"
+            label="Summarize interactions at loci level?"/>
     </inputs>
 
     <outputs>
         <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/>
         <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/>
+        <data format="tabular" name="interactions" from_work_dir="interactions" label="ChiRA interaction summary on ${on_string}">
+            <filter>summarize == True</filter>
+        </data>
     </outputs>
 
     <tests>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="3">
             <param name="loci" value="loci.counts"/>
             <param name="ref_type" value="split"/>
             <param name="ref_fasta1" value="ref1.fasta"/>
             <param name="ref_fasta2" value="ref2.fasta"/>
             <param name="annot_choice" value="no"/>
             <param name="hybridize" value="true" />
-            <output name="chimeras" file="chimeras" sort="True"/>
-            <output name="singletons" file="singletons" sort="True"/>
+            <param name="summarize" value="true" />
+            <output name="chimeras" file="chimeras"/>
+            <output name="singletons" file="singletons"/>
+            <output name="interactions" file="interactions"/>
         </test>
     </tests>
     <help>
diff -r 89ab3b2973d8 -r 56b2d956a1a6 macros.xml
--- a/macros.xml	Thu May 07 03:37:33 2020 -0400
+++ b/macros.xml	Fri May 29 06:57:01 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 89ab3b2973d8 -r 56b2d956a1a6 test-data/chimeras
--- a/test-data/chimeras	Thu May 07 03:37:33 2020 -0400
+++ b/test-data/chimeras	Fri May 29 06:57:01 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 89ab3b2973d8 -r 56b2d956a1a6 test-data/interactions
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/interactions	Fri May 29 06:57:01 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 89ab3b2973d8 -r 56b2d956a1a6 test-data/loci.counts
--- a/test-data/loci.counts	Thu May 07 03:37:33 2020 -0400
+++ b/test-data/loci.counts	Fri May 29 06:57:01 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 89ab3b2973d8 -r 56b2d956a1a6 test-data/singletons
--- a/test-data/singletons	Thu May 07 03:37:33 2020 -0400
+++ b/test-data/singletons	Fri May 29 06:57:01 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