| Previous changeset 8:89ab3b2973d8 (2020-05-07) Next changeset 10:7ec1d063fecd (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_extract.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 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 |
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| @@ -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> |
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| 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 |
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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 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 |
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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 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 |
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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 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 |
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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 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 |
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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 |