Repository 'chira_collapse'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse

Changeset 9:f1dee212ab70 (2020-06-14)
Previous changeset 8:872c99389c69 (2020-06-06) Next changeset 10:5ba5704a8105 (2020-06-17)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 51f68a6d51d9e87f8e54021ce760b1506a3589b8"
modified:
macros.xml
test-data/chimeras
test-data/interactions
removed:
test-data/singletons
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diff -r 872c99389c69 -r f1dee212ab70 macros.xml
--- a/macros.xml Sat Jun 06 08:16:36 2020 -0400
+++ b/macros.xml Sun Jun 14 17:38:00 2020 -0400
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@@ -1,6 +1,6 @@
 <macros>
     <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token>
-    <token name="@TOOL_VERSION@">1.3.3</token>
+    <token name="@TOOL_VERSION@">1.3.4</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">chira</requirement>
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diff -r 872c99389c69 -r f1dee212ab70 test-data/chimeras
--- a/test-data/chimeras Sat Jun 06 08:16:36 2020 -0400
+++ b/test-data/chimeras Sun Jun 14 17:38:00 2020 -0400
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@@ -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
-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
+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 ............((.((((((((&)))))))))) 13&1 -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 NA NA NA
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diff -r 872c99389c69 -r f1dee212ab70 test-data/interactions
--- a/test-data/interactions Sat Jun 06 08:16:36 2020 -0400
+++ b/test-data/interactions Sun Jun 14 17:38:00 2020 -0400
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@@ -1,2 +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
+1 mmu-miR-20a-5p 0 23 + ENSMUST00000136025 132 142 + UAAAGUGCUUAUAGUGCAGGUAG CUGCCUGCCU ............((.((((((((&)))))))))) -13.7 AGUGCAGGUAG CUGCCUGCCU 13&1 mmu-miR-20a-5p 12 23 + ENSMUST00000136025 132 142 + 75660.00 165100.00 240760.0 1.0 1.0 2.0 NA NA mmu-miR-20a-5p ENSMUST00000136025
+1 mmu-miR-6979-3p 2 12 + ENSMUST00000136025 32 46 + GUGUCUGUCU CAGGACUCUUGGCU NA NA NA NA NA mmu-miR-6979-3p 2 12 + ENSMUST00000136025 32 46 + 165100.00 121100.00 286200.0 1.0 1.0 2.0 NA NA mmu-miR-6979-3p ENSMUST00000136025
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diff -r 872c99389c69 -r f1dee212ab70 test-data/singletons
--- a/test-data/singletons Sat Jun 06 08:16:36 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -1,4 +0,0 @@
-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