| Next changeset 1:876c70c6ecad (2019-02-08) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa commit c4bbc5b1d62a640a80681d7d467aee9eff4aa17f-dirty |
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added:
selectsequencesfrommsa.xml test-data/result.clustal test-data/result.selected |
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| diff -r 000000000000 -r 48fc2c21fe1c selectsequencesfrommsa.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/selectsequencesfrommsa.xml Sat Mar 11 16:59:55 2017 -0500 |
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| @@ -0,0 +1,62 @@ +<tool id="selectsequencesfrommsa" name="Select Sequences" version="1.0.2"> + <description> + Tool to select representative sequences from a multiple sequence alignment. + </description> + <requirements> + <requirement type="package" version="1.0.2">selectsequencesfrommsa</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + SelectSequencesFromMSA + -c '$input_clustal' + $x + -o `pwd` + -n $n + -i $i + -m $m + > warnings + ]]> + </command> + <inputs> + <param name="input_clustal" type="data" format="clustal" label="Input clustal alignment"/> + <param argument="-n" type="integer" value="6" min="1" label="Number of sequences in the output alignment." help=""/> + <param argument="-i" type="float" value="80" min="0.1" label="Optimize for this percentage of mean pairwise identity" help=""/> + <param argument="-m" type="float" value="95" min="0.1" label="Sequences with a higher percentage of pairwise identity will be removed." help=""/> + <param argument="-x" truevalue="-x" falsevalue="" checked="True" type="boolean" label="The first sequence (=reference sequence) is always present in the output alignment." help=""/> + </inputs> + <outputs> + <data format="clustal" name="clustal" from_work_dir="result.selected" label="Clustal alignment of selected sequences"/> + </outputs> + <tests> + <test> + <param name="input_clustal" value="result.clustal"/> + <output name="result.selected" file="result.selected"/> + </test> + </tests> + <help> + +<![CDATA[ + +**What it does** + +Tool to select representative sequences from a multiple sequence alignment in clustal format. +Useful before running RNAz, RNAcode, RNAalifold on alignments with many entries. + +**Input** +Multiple sequence alignment in clustal format + +**Options** +-n Number of sequences in the output alignment. (Default: 6) +-i Optimize for this percentage of mean pairwise identity (Default: 80) +-m Sequences with a higher percentage of pairwise identity will be removed (Default: 95) +-x The first sequence (=reference sequence) is always present in the output alignment per default. Default: True + +**Output** +Clustal alignment with selected sequences + +]]> + + </help> + <citations> + <citation type="doi">10.1093/nar/gkw558</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 48fc2c21fe1c test-data/result.clustal --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result.clustal Sat Mar 11 16:59:55 2017 -0500 |
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| b'@@ -0,0 +1,2797 @@\n+CLUSTAL 2.1 multiple sequence alignment\n+\n+AB001721.1/2735-2851 .CC.CGGUGACU..AU.AGA.GAG.A.GGG.CC.ACAC.CCGU..U.C.CCAUCCCGAAC\n+gb|CP006694.1|:152734-152851 uCC.CGGUGACU..AU.AGA.GAG.A.GGG.CC.ACAC.CCGU..U.C.CCAUCCCGAAC\n+gi|526641887:1-118 uCC.UGGUGAUU..AU.GGA.GAG.A.AGG.CC.AUAC.CCGU..U.C.CCAUUCCGAAC\n+gi|216762:421-538 uCC.UGGUGAUU..AU.GGA.GAG.A.AGG.CC.AUAC.CCGU..U.C.CCAUUCCGAAC\n+gi|452192414:1-117 .UC.UGUGCGCA..AU.AGA.GCA.A.GGG.UC.ACAC.CCGU..U.C.CCAUCCCGAAC\n+gi|216767:249-367 .UGcUGGCGCCA..AU.AGA.GAG.G.GUG.AU.ACAC.CUGU..U.C.CCAUCCCGAAC\n+gi|507148580:1-114 .CC.CGGUGGCC..AU.AGC.AGA.G.UGG.AU.AUAC.CCGU..U.C.CCAUCCCGAAC\n+gi|452192347:1-113 .CC.CGGUGGCC..AC.AGC.AGG.G.UGG.AC.ACAC.CCGU..U.C.CCAUCCCGAAC\n+gi|451991762:1-111 .CC.UGGUGGUU..AA.AGA.AAA.G.AGG.AA.ACAC.CUGU..U.A.UCAUUCCGAAC\n+gi|452192371:1-112 .CC.CGGUGGUC..AU.AGC.AGA.G.UGG.UC.AUAC.CCGU..U.C.CCAUCCCGAAC\n+gi|452192196:1-116 .CU.UGGUGACU..AU.AGU.GGA.G.GUG.UU.ACAC.CUGU..U.C.CCAUUCCGAAC\n+gi|452192221:1-115 .--.CGGUGACC..AU.AGA.GAA.A.GUG.AU.ACAC.CCGU..U.C.CCAUUCCGAAC\n+gi|507148498:1-116 .-U.CGGUGACC..AC.AGA.GAA.A.GUG.AU.ACAC.CCGU..U.C.CCAUUCCGAAC\n+gi|507148564:1-107 .--.-GGUGGUU..AA.AGA.AAA.G.AGG.AA.ACAC.CUGU..U.A.UCAUUCCGAAC\n+gb|KU291355.1|:36-147 .CC.UGGUGGUU..AA.AGA.AAA.G.AGG.AA.ACAC.CUGU..U.A.UCAUUCCGAAC\n+gb|CP002873.1|:2145056-2145173 uUU.CGGUGACC..AU.AGA.GAA.A.GUG.AU.ACAC.CCGU..U.C.CCAUUCCGAAC\n+gb|CP006647.2|:c434557-434446 .CC.UGGUGAUU..GA.AGA.AAA.G.AGG.AA.ACAC.CUGU..U.A.UCAUUCCGAAC\n+gi|507148596:1-116 .CC.UGGUGACA..AU.CGCgGAG.G.GGG.UC.CCAC.CCGU..U.C.CCAUUCCGAAC\n+gi|451992005:1-111 .CC.UGGUGAUU..AA.AGA.AAA.G.AGG.AA.ACAC.CUGU..U.A.UCAUUCCGAAC\n+gb|CP004267.1|:c439103-438992 .CC.UGGUGAUU..AA.AGA.AAA.G.AGG.AA.ACAC.CUGU..U.A.UCAUUCCGAAC\n+gb|CP007564.1|:466414-466525 .CC.UGGUGGUU..AA.AGA.AAA.G.AGG.AA.ACAC.CUGU..U.A.UCAUUCCGAAC\n+gi|452192501:1-108 .--.UGGUGGUU..AA.AGA.AAA.G.AGG.AA.ACAC.CUGU..U.A.UCAUUCCGAAC\n+gi|452192103:1-116 .-U.CGGUGACC..AU.AGA.GAA.A.GUG.AU.ACAC.CCGU..U.C.CCAUUCCGAAC\n+gi|451991616:1-110 .-C.AGGUGGCC..AU.AGU.GGA.G.AGG.UA.AUAC.CCGU..U.C.CCAUCCCGAAC\n+gb|CP005745.1|:c431115-431004 .CC.UGGUGAUU..CA.AGA.AAA.G.AGG.AA.ACAC.CUGU..C.A.UCAUUCCGAAC\n+gb|CP005829.1|:c428563-428452 .CC.UGGUGAUU..AA.AGA.AAA.G.AGG.AA.ACAC.CUGU..U.A.UCAUUCCGAAC\n+gb|CP000049.1|:c435752-435641 cCC.UGGUGAUU..AA.AGA.AAA.G.AGG.AA.ACAC.CUGU..U.A.UCAUUCCGAAC\n+gb|CP005851.1|:481735-481846 .CC.UGGUGAUU..GA.AGA.AAA.G.AGG.AA.ACAC.CUGU..U.A.UCAUUCCGAAC\n+gi|526641892:1-111 .CC.UGGUGGUU..AA.AGA.AAA.G.AGG.AA.ACAC.CUGU..U.A.UCAUUCCGAAC\n+gi|4468110:2-116 .CC.UGAUGACC..AU.AGC.GAG.U.UGG.UA.CCAC.CCCU..U.C.CCAUCCCGAAC\n+gb|CP015136.1|:656498-656615 .CC.CGGUGGCC..AU.AGG.GGA.G.GGG.UC.ACAC.CCGU..U.C.CCAUUCCGAAC\n+gb|CP013099.1|:3650031-3650144 .-C.UGGCGGCA..AU.AGC.GAG.U.UGG.AA.CCAC.CCGA..U.C.CCAUCCCGAAC\n+gb|CP013066.1|:1198376-1198490 .-C.UGGUGCCU..UU.AGC.GGC.G.GGG.UC.ACAC.CUGU..U.C.CCAUCUCGAAC\n+gb|CP011214.1|:386649-386764 .-U.UGGUGACU..UG.AGC.GCG.G.UGG.AA.CCAC.CUGA..U.U.CCAUUCCGAAC\n+gi|38938:2-120 .UA.CGGCGGUG..AU.AGC.GUG.G.GGG.AA.ACGC.CCGG..U.C.CCAUUCCGAAC\n+gb|CP009217.2|:1265876-1265989 .CU.UGGUGAUU..AU.AGC.ACA.G.GUG.AC.ACAC.CCGA..C.C.CCAUACCGAAC\n+gb|CP012154.1|:245759-245875 .CC.UGGUGGCA..AU.AGC.GGC.G.UGG.AA.CCAC.CCGA..C.C.CCAUCUCGAAC\n+gb|CP003801.1|:c1381757-1381640 .UG.UGGCGGUC..AU.AGC.GGA.G.UGA.AA.AAAC.CCGA..U.C.CCAUUUCGAAC\n+gi|662020025:1-116 .CC.UGGCGGCC..AU.AGC.GCG.G.UGG.UC.CCAC.CUGA..U.C.CCAUGCCGAAC\n+gb|CP011213.1|:c135211-135096 .-U.UGGUGCUU..-U.AAC.GUG.G.UGG.GU.ACAC.CUCU..U.C.CCAUUCCGAAC\n+gb|CP007706.1|:54289-54406 .CC.UGGUGGUU..AU.GGC.GGA.G.CGG.CU.GCAC.CCGA..U.C.CCAUUCCGAAC\n+gi|610510261:c2632714-2632599 .CU.CGGUGAUU..AU.UGC.GAG.G.AGC.CU.AAAC.CCGA..U.C.C'..b' CCCUGGGAGAGUAGG.UCGCUGCCAGGC\n+gi|451991914:2-119 ACGCGGGAGAGUAGG.UCGCUGCCAGGU\n+gi|451991913:2-119 ACGCGGGAGAGUAGG.UCGCUGCCAGGU\n+gi|451991605:2-118 CCAUGUGAGAGUAGG.UCAUCGUCAAGA\n+gb|DQ532441.1|:c9325-9209 CCAUGUGAGAGUAGG.UCAUCGUCAAGA\n+gi|451991936:1-114 CCAUGUGAGAGUAGG.UCAUCGUCAAGA\n+gb|ANOR01000024.1|:5607-5723 CCAUGUGAGAGUAGG.UCAUCGUCAAGA\n+gi|4468164:2-115 CCGUGUGAAAGUAGG.UCAUCGUCAGGC\n+gi|48257:4-119 CGCUGGGAGAGUAGG.UCGGUGCGGGGG\n+gi|224510780:2-119 GCCUGGGAGAGUAGG.UCGGUGCGGGGG\n+gi|451991880:1-115 ACGUGGGAGAGUAGG.UCACCGCCAGAC\n+gi|662019950:1-114 ACGUGGGAGAGUAGG.UCACCGCCAGAC\n+gb|CP009574.1|:c806523-806408 CCAGGUGAAAGUAGG.UAGUCGUCAGGA\n+gb|M33886.1|CYTRRAB:1-116 CCCUGUGAGAGUAGG.ACGUUGCCAGGC\n+gi|357428060:1522-1640 ACGUGGGAGAGUAGG.UCGCCGCCAGGU\n+gi|356882082:c402625-402507 ACGUGGGAGAGUAGG.UCGCCGCCAGGU\n+gb|CP012406.1|:664991-665109 ACGUGGGAGAGUAGG.UCGCCGCCAGGU\n+gi|451991726:1-113 UUGUGGGAAAGUAGG.ACGCUGCCG---\n+gi|452192559:1-115 ACCUGGGAGAGUAGG.UCGUCGCCAGGC\n+gb|M35166.1|PLLS5RRNAB:1-109 --GUGCGAAAGUAGG.U-AUCGCCGGA-\n+gb|CP011270.1|:4958369-4958477 AGGUGCGAAAGUAGG.UUAUUGCCGG--\n+gb|M35170.1|GEM5SRRNA:1-108 --GCGCGAGAGUAGG.-UAUCGCCGGCC\n+gi|452192403:1-110 ACUUGGAAAAGUAGG.UAGCCGCCA---\n+gi|452192413:1-112 ACCUGGGAGAGUAGG.UCGCCGCCUUCU\n+gb|M34775.1|ANCRRAA:1-116 ACCUGGGAGAGUAGG.UCGCUGCCAGGC\n+gb|M35569.1|LTTRR5S:3-117 GCGUGUGAAAGUAGG.UCAUCGUCAGGC\n+gi|452192547:1-114 ACGCGGGAGAGUAGG.UCGUUGCCAGGU\n+gi|40413:3-117 GCGCGGGAGAGUAGG.UCGCCGCCAGG-\n+gb|M35310.1|HESRRA:1-117 GCGCGGGAGAGUAGG.UCGCUGCCGGAU\n+gb|M35568.1|VITRR5SXX:1-115 CCGUGUGAAAGUAGG.ACAUCGUCAGGC\n+gi|451991653:1-112 UGGUGGGAGAGUAGG.ACGCCGCC----\n+gi|861061:1-118 CUGUGGGAGAGUAGG.ACGCCGCCAGCG\n+gi|860904:1-116 GCGCGGGAGAGUAGG.UCGCUGCCGGAU\n+gi|507148422:2-119 GCGUGGGAGAGUAGG.UCGCUGCCGGAU\n+gi|451991792:1-116 GCGCGGGAGAGUAGG.UCGCUGCCGGAU\n+gi|452192399:1-117 GCGCGGGAGAGUAGG.UCGCUGCCGGAU\n+gi|451991925:1-116 CCAUGUGAGAGUAGG.UCAUCGCCAAGC\n+gi|47140:2-118 CCAUGUGAGAGUAGG.UCAUUUCCAGGC\n+gi|451991802:1-112 AUGUGGGAAAGUAGG.UCGCCGCC----\n+gi|451992042:1-115 GGGUGGGAGAGUAGG.UCAUUGCCAG--\n+gi|452192373:1-117 GUGUGGGAGAGUAGG.ACGCCGCCGGAC\n+gi|451991686:3-118 ACGCGGGAGAGUAGG.UCGCUGCCAGGC\n+gi|328801247:21-136 CCAUGUGAGAGUAGG.UCAUCGUCAAGA\n+gb|KF901086.1|:6138-6252 GAGUGGGAAAAUAGG.UCACCGCCG---\n+gi|688725010:c1243-1130 CCGUGUGAAAGUAGG.UCAUCGUCAGGC\n+gb|AC167666.4|:1429-1542 CCGUGUGAAAGUAGG.UCAUCGUCAGGC\n+gi|690018164:461-574 CCGUGUGAAAGUAGG.UCAUCGUCAGGC\n+gi|451991889:1-113 CCGUGUGAAAGUAGG.UCAUCGUCAGGC\n+gi|688799711:426-535 CCGUGGGAGAGCAGG.UCGUCGCUA---\n+gi|307683286:c91863-91747 CUAUGGGAAAAUAGC.UCGGUGCCAGGA\n+gi|452192203:1-116 CUCUGGGAGAGCUGAuUCGCCGCC----\n+gi|765338145:1-113 GUGCGUGAAAGUAGG.UCAUCGUCAGAC\n+gb|CP006885.2|:13738-13857 CUCUGGGAAACGCGGuUCGCCGCC----\n+gi|689936939:3579-3693 GUGUGGGAGAGUAAG.ACGCUGCCG---\n+gi|841942794:7818-7933 CCAUGCGAGAGUAGG.GAACUGCCAGGC\n+gi|156148669:c114797-114685 ACGCGGGAGAGUAGG.UCGCUGCCA---\n+gi|687058084:c326-216 AUGUGGGAGAGUAGG.AGGCCGCC----\n+gi|687836183:c2166-2052 CCAUGCGAGAGUAGG.UCAUCGCCAGGG\n+gi|49258838:3-122 CUCUGGGAAACCCGGuUCGCCGCC----\n+gi|20609:4653-4769 UUUUGGGAAAGUAGC.UCAGUGCCAAGG\n+gi|451991654:1-118 CUCUGGGAAAUCCGGuUCGCCGCC----\n+gb|CP007060.1|:196416-196534 CUCUGGGAAAUUCGGuUCGCCGCC----\n+gi|37927900:1-119 CUCUGGGAAACCCGGuUCGCCGCC----\n+gi|526641914:1-118 CUCUGGGAAAUCCGGuUCGCCGCC----\n+ * * \n' |
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| diff -r 000000000000 -r 48fc2c21fe1c test-data/result.selected --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result.selected Sat Mar 11 16:59:55 2017 -0500 |
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| @@ -0,0 +1,19 @@ +CLUSTAL W (1.8) multiple sequence alignment + + +AB001721-1-2735-2851 CCCGGUGACUAUAGAGAGAGGGCCACACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCU +gi-258590833-c1582130-1582011 CCUGGUGGCCAUAGCGGAGGGGAAACACCCGUUCCCAUUCCGAACACGGAAGUGAAGCCC +gb-M29856-1-BTTDNA-1-115 UCUGGUGACCAUAGCGGAGGGGAUCCACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCC +gi-452192175-1-116 --CGGUGGUCAUAGCGGAGGGGACACACCCGUUCCCAUUCCGAACACGGAAGUUAAGCCC +gb-AF116563-1--6176-6294 UUCGGUGGUUAUAGCGGUGGGGAAACACCCGGUCCCAUUCCGAACCCGGUAGUUAAGCCC +gb-CP012370-1--152653-152770 UCUGGUGGUAAUAGCGGAGGGGAAACACCCGUUCCCAUCCCGAACACGGCAGUUAAGCCC + + +AB001721-1-2735-2851 CUCAUCGCUGAUGGUACUAUGUGGUUCGCUGCAUGGGAGAGUAGGACGUUGCCGGGU +gi-258590833-c1582130-1582011 UCCAGCGCCGAUGGUACUGCGUGGGCAACUGCGCGGGAGAGUAGGUCGCCGCCAGGA +gb-M29856-1-BTTDNA-1-115 UCCAGCGCCGAUGGUACUUGGGGA--UGACCCCUGGGAGAGUAGGUCGUUGCCAGGC +gi-452192175-1-116 UCCAGCGCCGAUGGUACUGCCCUGGCGACGGGGCGGGAGAGUAGGUCGCUGCCGGGG +gb-AF116563-1--6176-6294 GCCAGCGCCGAUGGUACUGCACUGGUGACGGUGUGGGAGAGUAGGUCGCCGCCGGAC +gb-CP012370-1--152653-152770 UCCAGCGCCGAUGGUACUGGGGAG--UAUUCCCCGGGAGAGUAGGACACCGCCAGGA + + |