Mercurial > repos > yhoogstrate > segmentation_fold
changeset 13:63156f020cd3 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit fb0bbb26638c0185ef16efa2e0ac3952d671b711-dirty
| author | yhoogstrate |
|---|---|
| date | Thu, 19 May 2016 04:31:29 -0400 |
| parents | c690aa928d3d |
| children | 3d641127437e |
| files | macros.xml segmentation-fold.xml test-data/DBNFile.test_03.in.dbn test-data/DBNFile.test_03.out.l.dbn test-data/DBNFile.test_03.out.s.dbn test-data/SNORD114-4-revised.scan-for-segments.txt test-data/SNORD118-revised.scan-for-segments.txt test-data/SNORD13-revised.scan-for-segments.txt test-data/SNORD48-revised.scan-for-segments.txt test-data/segments_truncated.2.out.txt test-data/segments_truncated.out.txt tool_dependencies.xml utils_filter-by-energy.xml |
| diffstat | 13 files changed, 210 insertions(+), 56 deletions(-) [+] |
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--- a/macros.xml Fri May 06 06:08:36 2016 -0400 +++ b/macros.xml Thu May 19 04:31:29 2016 -0400 @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">smf-v1.6-4_utils-v1.0.3</token> + <token name="@VERSION@">smf-v1.6-5_utils-v1.0.3</token> <xml name="stdio"> <stdio> @@ -13,12 +13,14 @@ <token name="@REQUIREMENTS_UTILS@"><![CDATA[ + <requirement type="package" version="2.7.10">python</requirement> + <requirement type="package" version="1.9">numpy</requirement> + <requirement type="package" version="0.8.2.1">pysam</requirement> <requirement type="package" version="1.0.3">segmentation-fold-utils</requirement> - <requirement type="package" version="2.7.10">python</requirement> ]]></token> <token name="@REQUIREMENTS_SMF@"><![CDATA[ - <requirement type="package" version="1.6.3">segmentation-fold</requirement> + <requirement type="package" version="1.6.5">segmentation-fold</requirement> ]]></token>
--- a/segmentation-fold.xml Fri May 06 06:08:36 2016 -0400 +++ b/segmentation-fold.xml Thu May 19 04:31:29 2016 -0400 @@ -1,6 +1,6 @@ <tool id="segmentation_fold" name="segmentation-fold" version="@VERSION@-1"> <description>RNA-Folding including predefined segments including K-turns</description> - <macros> + <macros> <import>macros.xml</import> </macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DBNFile.test_03.in.dbn Thu May 19 04:31:29 2016 -0400 @@ -0,0 +1,42 @@ +>chr3.rna:5-35(+) x Kt-CD-box.CGU +TCTTGTGATGAGAAGTACTGGATCTGAAGT +>chr3.rna:5-35(+) x Kt-CD-box.UGU +TCTTGTGATGAGAAGTACTGGATCTGAAGT +(((.(((........))).)))........ .((...(((((...........))))))). -13.125 +>chr3.rna:5-80(+) x Kt-CD-box.CGU +TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA +>chr3.rna:5-80(+) x Kt-CD-box.UGU +TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA +(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))) (((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))) 0.0 +(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))) (((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))) 0.0 +>chr3.rna:50-80(+) x Kt-CD-box.CGU +ACTTGTGATGAAACACTCATGGTCTGAAGA +>chr3.rna:50-80(+) x Kt-CD-box.UGU +ACTTGTGATGAAACACTCATGGTCTGAAGA +..(..(((((...)).)))..)........ .((...(((((....(....).))))))). -13.125 +>chr4_SNORD118_revised:1-74(+) x Kt-CD-box.CGU +GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTG +...((............(((((.((.((((.....)))).))))))).((((((...........)))))))) ...((..((((((............))...)))).(((......))).((((((...........)))))))) 0.0 +>chr4_SNORD118_revised:1-74(+) x Kt-CD-box.UGU +GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTG +>chr4_SNORD118_revised:1-88(+) x Kt-CD-box.CGU +GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTGCTCCTGTCTGATTT +.........(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))...... ..(((..((((((............))...))))...........(((((((((...........)))))))))...)))....... 0.0 +>chr4_SNORD118_revised:1-88(+) x Kt-CD-box.UGU +GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTGCTCCTGTCTGATTT +>chr3.rna.RC:35-5(-) x Kt-CD-box.CGU +ACTTGTGATGAAACACTCATGGTCTGAAGA +>chr3.rna.RC:35-5(-) x Kt-CD-box.UGU +ACTTGTGATGAAACACTCATGGTCTGAAGA +..(..(((((...)).)))..)........ .((...(((((....(....).))))))). -13.125 +>chr3.rna.RC:80-5(-) x Kt-CD-box.CGU +TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA +>chr3.rna.RC:80-5(-) x Kt-CD-box.UGU +TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA +(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))) (((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))) 0.0 +(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))) (((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))) 0.0 +>chr3.rna.RC:80-50(-) x Kt-CD-box.CGU +TCTTGTGATGAGAAGTACTGGATCTGAAGT +>chr3.rna.RC:80-50(-) x Kt-CD-box.UGU +TCTTGTGATGAGAAGTACTGGATCTGAAGT +(((.(((........))).)))........ .((...(((((...........))))))). -13.125
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DBNFile.test_03.out.l.dbn Thu May 19 04:31:29 2016 -0400 @@ -0,0 +1,14 @@ +>chr3.rna:5-80(+) x Kt-CD-box.UGU +TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA +(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))) (((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))) 0.0 +(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))) (((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))) 0.0 +>chr4_SNORD118_revised:1-74(+) x Kt-CD-box.CGU +GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTG +...((............(((((.((.((((.....)))).))))))).((((((...........)))))))) ...((..((((((............))...)))).(((......))).((((((...........)))))))) 0.0 +>chr4_SNORD118_revised:1-88(+) x Kt-CD-box.CGU +GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTGCTCCTGTCTGATTT +.........(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))...... ..(((..((((((............))...))))...........(((((((((...........)))))))))...)))....... 0.0 +>chr3.rna.RC:80-5(-) x Kt-CD-box.UGU +TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA +(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))) (((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))) 0.0 +(((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).)))) (((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))) 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DBNFile.test_03.out.s.dbn Thu May 19 04:31:29 2016 -0400 @@ -0,0 +1,28 @@ +>chr3.rna:5-35(+) x Kt-CD-box.CGU +TCTTGTGATGAGAAGTACTGGATCTGAAGT +>chr3.rna:5-35(+) x Kt-CD-box.UGU +TCTTGTGATGAGAAGTACTGGATCTGAAGT +(((.(((........))).)))........ .((...(((((...........))))))). -13.125 +>chr3.rna:5-80(+) x Kt-CD-box.CGU +TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA +>chr3.rna:50-80(+) x Kt-CD-box.CGU +ACTTGTGATGAAACACTCATGGTCTGAAGA +>chr3.rna:50-80(+) x Kt-CD-box.UGU +ACTTGTGATGAAACACTCATGGTCTGAAGA +..(..(((((...)).)))..)........ .((...(((((....(....).))))))). -13.125 +>chr4_SNORD118_revised:1-74(+) x Kt-CD-box.UGU +GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTG +>chr4_SNORD118_revised:1-88(+) x Kt-CD-box.UGU +GAACATGATGATTGGAGATGCATGAAACGTGATTAACGTCTCTGCGTAATCAGGACTTGCAACACCCTGATTGCTCCTGTCTGATTT +>chr3.rna.RC:35-5(-) x Kt-CD-box.CGU +ACTTGTGATGAAACACTCATGGTCTGAAGA +>chr3.rna.RC:35-5(-) x Kt-CD-box.UGU +ACTTGTGATGAAACACTCATGGTCTGAAGA +..(..(((((...)).)))..)........ .((...(((((....(....).))))))). -13.125 +>chr3.rna.RC:80-5(-) x Kt-CD-box.CGU +TCTTGTGATGAGAAGTACTGGATCTGAAGTAGCCCTTTTTGGGCTACTTGTGATGAAACACTCATGGTCTGAAGA +>chr3.rna.RC:80-50(-) x Kt-CD-box.CGU +TCTTGTGATGAGAAGTACTGGATCTGAAGT +>chr3.rna.RC:80-50(-) x Kt-CD-box.UGU +TCTTGTGATGAGAAGTACTGGATCTGAAGT +(((.(((........))).)))........ .((...(((((...........))))))). -13.125
--- a/test-data/SNORD114-4-revised.scan-for-segments.txt Fri May 06 06:08:36 2016 -0400 +++ b/test-data/SNORD114-4-revised.scan-for-segments.txt Thu May 19 04:31:29 2016 -0400 @@ -1,12 +1,12 @@ ->SNORD114-4 revised x Kt-7 G2nA SAM riboswitch H. marismortui +>SNORD114-4 revised x Kt-7 G2nA SAM riboswitch (H. marismortui) CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-7 T. thermophilus +>SNORD114-4 revised x Kt-7 (T. thermophilus) CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-7 E. coli +>SNORD114-4 revised x Kt-7 (E. coli) CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-7 D. radiodurans +>SNORD114-4 revised x Kt-7 (D. radiodurans) CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-11 T. thermophilus +>SNORD114-4 revised x Kt-11 (T. thermophilus) CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA >SNORD114-4 revised x Kt-11.eco CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA @@ -53,5 +53,5 @@ CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA >SNORD114-4 revised x Kt-c-di-GMP-II.cac CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-G2nA-SAM-riboswitch T. tengcongensi +>SNORD114-4 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi) CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
--- a/test-data/SNORD118-revised.scan-for-segments.txt Fri May 06 06:08:36 2016 -0400 +++ b/test-data/SNORD118-revised.scan-for-segments.txt Thu May 19 04:31:29 2016 -0400 @@ -1,12 +1,12 @@ ->SNORD118 revised x Kt-7 G2nA SAM riboswitch H. marismortui +>SNORD118 revised x Kt-7 G2nA SAM riboswitch (H. marismortui) AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-7 T. thermophilus +>SNORD118 revised x Kt-7 (T. thermophilus) AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-7 E. coli +>SNORD118 revised x Kt-7 (E. coli) AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-7 D. radiodurans +>SNORD118 revised x Kt-7 (D. radiodurans) AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-11 T. thermophilus +>SNORD118 revised x Kt-11 (T. thermophilus) AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC >SNORD118 revised x Kt-11.eco AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC @@ -53,5 +53,5 @@ AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC >SNORD118 revised x Kt-c-di-GMP-II.cac AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-G2nA-SAM-riboswitch T. tengcongensi +>SNORD118 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi) AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
--- a/test-data/SNORD13-revised.scan-for-segments.txt Fri May 06 06:08:36 2016 -0400 +++ b/test-data/SNORD13-revised.scan-for-segments.txt Thu May 19 04:31:29 2016 -0400 @@ -1,12 +1,12 @@ ->SNORD13 revised x Kt-7 G2nA SAM riboswitch H. marismortui +>SNORD13 revised x Kt-7 G2nA SAM riboswitch (H. marismortui) GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-7 T. thermophilus +>SNORD13 revised x Kt-7 (T. thermophilus) GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-7 E. coli +>SNORD13 revised x Kt-7 (E. coli) GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-7 D. radiodurans +>SNORD13 revised x Kt-7 (D. radiodurans) GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-11 T. thermophilus +>SNORD13 revised x Kt-11 (T. thermophilus) GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC >SNORD13 revised x Kt-11.eco GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC @@ -53,5 +53,5 @@ GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC >SNORD13 revised x Kt-c-di-GMP-II.cac GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-G2nA-SAM-riboswitch T. tengcongensi +>SNORD13 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi) GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
--- a/test-data/SNORD48-revised.scan-for-segments.txt Fri May 06 06:08:36 2016 -0400 +++ b/test-data/SNORD48-revised.scan-for-segments.txt Thu May 19 04:31:29 2016 -0400 @@ -1,56 +1,56 @@ ->SNORD48 revised 2 extra bases on 5 end x Kt-7 G2nA SAM riboswitch H. marismortui +>SNORD48 revised (2 extra bases on 5' end) x Kt-7 G2nA SAM riboswitch (H. marismortui) GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-7 T. thermophilus +>SNORD48 revised (2 extra bases on 5' end) x Kt-7 (T. thermophilus) GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-7 E. coli +>SNORD48 revised (2 extra bases on 5' end) x Kt-7 (E. coli) GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-7 D. radiodurans +>SNORD48 revised (2 extra bases on 5' end) x Kt-7 (D. radiodurans) GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-11 T. thermophilus +>SNORD48 revised (2 extra bases on 5' end) x Kt-11 (T. thermophilus) GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-11.eco +>SNORD48 revised (2 extra bases on 5' end) x Kt-11.eco GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-15.hma +>SNORD48 revised (2 extra bases on 5' end) x Kt-15.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-23.tth +>SNORD48 revised (2 extra bases on 5' end) x Kt-23.tth GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-23.eco +>SNORD48 revised (2 extra bases on 5' end) x Kt-23.eco GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-38.hma +>SNORD48 revised (2 extra bases on 5' end) x Kt-38.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-42.hma +>SNORD48 revised (2 extra bases on 5' end) x Kt-42.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-42.tth +>SNORD48 revised (2 extra bases on 5' end) x Kt-42.tth GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-42.dra +>SNORD48 revised (2 extra bases on 5' end) x Kt-42.dra GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-42.eco +>SNORD48 revised (2 extra bases on 5' end) x Kt-42.eco GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-46.hma +>SNORD48 revised (2 extra bases on 5' end) x Kt-46.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-46.tth +>SNORD48 revised (2 extra bases on 5' end) x Kt-46.tth GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-46.dra +>SNORD48 revised (2 extra bases on 5' end) x Kt-46.dra GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-46.eco +>SNORD48 revised (2 extra bases on 5' end) x Kt-46.eco GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-58.hma +>SNORD48 revised (2 extra bases on 5' end) x Kt-58.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-U4a.hsa +>SNORD48 revised (2 extra bases on 5' end) x Kt-U4a.hsa GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-U4b.hsa +>SNORD48 revised (2 extra bases on 5' end) x Kt-U4b.hsa GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-CD-box.CGU +>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.CGU GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-CD-box.UGU +>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.UGU GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-L30e.sce +>SNORD48 revised (2 extra bases on 5' end) x Kt-L30e.sce GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-SAM-ribo.tte +>SNORD48 revised (2 extra bases on 5' end) x Kt-SAM-ribo.tte GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-T-box.bsu +>SNORD48 revised (2 extra bases on 5' end) x Kt-T-box.bsu GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-c-di-GMP-II.cac +>SNORD48 revised (2 extra bases on 5' end) x Kt-c-di-GMP-II.cac GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised 2 extra bases on 5 end x Kt-G2nA-SAM-riboswitch T. tengcongensi +>SNORD48 revised (2 extra bases on 5' end) x Kt-G2nA-SAM-riboswitch (T. tengcongensi) GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
--- a/test-data/segments_truncated.2.out.txt Fri May 06 06:08:36 2016 -0400 +++ b/test-data/segments_truncated.2.out.txt Thu May 19 04:31:29 2016 -0400 @@ -1,7 +1,7 @@ ->CD-box snoRNA x Kt-CD-box.CGU +>C/D-box snoRNA x Kt-CD-box.CGU GCUCUGACCGAAAGGCGUGAUGAGC ((((....((.....))....)))) (((((((((....))...))))))) 2.49938964844 ->Artificial double CD K-turn construct x Kt-CD-box.UGU +>Artificial double C/D K-turn construct x Kt-CD-box.UGU GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC ((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))))))) ((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))))))) -1.26037597656 ((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))))))) ((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))))))) -1.26037597656
--- a/test-data/segments_truncated.out.txt Fri May 06 06:08:36 2016 -0400 +++ b/test-data/segments_truncated.out.txt Thu May 19 04:31:29 2016 -0400 @@ -1,7 +1,7 @@ ->CD-box snoRNA x Kt-CD-box.CGU +>C/D-box snoRNA x Kt-CD-box.CGU GCUCUGACCGAAAGGCGUGAUGAGC ((((....((.....))....)))) (((((((((....))...))))))) 2.49938964844 ->Artificial double CD K-turn construct x Kt-CD-box.UGU +>Artificial double C/D K-turn construct x Kt-CD-box.UGU GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC ((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))))))) ((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))))))) -1.26037597656 ((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))))))) ((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))))))) -1.26037597656
--- a/tool_dependencies.xml Fri May 06 06:08:36 2016 -0400 +++ b/tool_dependencies.xml Thu May 19 04:31:29 2016 -0400 @@ -1,10 +1,16 @@ <?xml version="1.0"?> <tool_dependency> - <package name="segmentation-fold" version="1.6.3"> - <repository changeset_revision="97fc2a21b740" name="package_segmentation_fold_1_6_3" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="segmentation-fold" version="1.6.5"> + <repository changeset_revision="e3ef4c5b6f19" name="package_segmentation_fold_1_6_5" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="python" version="2.7.10"> <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> + <package name="numpy" version="1.9"> + <repository changeset_revision="fe0870696ca7" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="pysam" version="0.8.2.1"> + <repository changeset_revision="e6c1f548397a" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> </tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils_filter-by-energy.xml Thu May 19 04:31:29 2016 -0400 @@ -0,0 +1,62 @@ +<tool id="smf_utils_filter-by-energy" name="filter-by-energy" version="@VERSION@-0"> + <description>Split entries over two files based on the estimated energy</description> + + <macros> + <import>macros.xml</import> + </macros> + + <requirements> + @REQUIREMENTS_UTILS@ + </requirements> + <expand macro="stdio" /> + + <version_command>@VERSION_COMMAND_UTILS@</version_command> + + <command><![CDATA[ + segmentation-fold-utils + filter-by-energy + --energy ${energy} + '$dbn_input_file' + '$dbn_output_file_larger_or_equal' + '$dbn_output_file_smaller' + ]]></command> + + <inputs> + <param name="dbn_input_file" + type="data" + format="dbn,txt" + label="Input DBN file" + help="The 'fasta'-headers should contain the genomic position being used to find overlapping reads in the BAM file"/> + <param name="energy" + type="float" + value="0.0" + argument="--energy" + label="Energy value" + help="Entries with transitions with energy smaller than energy (< e) or without transitions will be put into DBN_OUTPUT_FILE_LARGER_OR_EQUAL and those larger or equal (>= e) to DBN_OUTPUT_FILE_SMALLER" /> + </inputs> + + <outputs> + <data name="dbn_output_file_larger_or_equal" + format="dbn" + label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name} - energy larger/equal than selected"/> + <data name="dbn_output_file_smaller" + format="dbn" + label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name} - energy smaller than selected"/> + </outputs> + + <tests> + <test> + <param name="dbn_input_file" value="DBNFile.test_03.in.dbn" ftype="dbn"/> + <param name="energy" value='0.0'/> + + <output name="dbn_output_file_larger_or_equal" file="DBNFile.test_03.out.l.dbn" /> + <output name="dbn_output_file_smaller" file="DBNFile.test_03.out.s.dbn" /> + </test> + </tests> + + <help><![CDATA[ +Filter based on whether the entries in the DBN file are already annotated or not + ]]></help> + + <expand macro="citations" /> +</tool>