| Previous changeset 7:a1694947910f (2020-05-07) Next changeset 9:96ed25eb39f0 (2020-06-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688" |
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modified:
chira_quantify.xml macros.xml test-data/chimeras test-data/loci.counts test-data/singletons |
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added:
test-data/interactions |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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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 -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 |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |