Mercurial > repos > rnateam > mlocarna
changeset 0:59055c49a112 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
| author | rnateam |
|---|---|
| date | Tue, 06 Dec 2016 11:39:14 -0500 |
| parents | |
| children | |
| files | macros.xml mlocarna.xml test-data/archaea-default.stdout test-data/archaea-probabilistic.aln test-data/archaea.fa test-data/haca.snoRNA-default.stdout test-data/haca.snoRNA.fa test-data/tRNA_5.fa |
| diffstat | 8 files changed, 419 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Dec 06 11:39:14 2016 -0500 @@ -0,0 +1,125 @@ +<macros> + <token name="@VERSION@">1.8.12</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">locarna</requirement> + </requirements> + </xml> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + </stdio> + </xml> + + <xml name="version"> + <version_command> + <![CDATA[ + mlocarna --version + ]]> + </version_command> + </xml> + + <xml name="common_scoring_parameters"> + <param name="struct_weight" argument="struct-weight" + label="Structure weight" type="integer" + value="200" min="0" max="800" /> + <param name="indel_opening" argument="indel-opening" + label="Indel opening score" type="integer" + value="-500" max="0" min="-1500" /> + <param argument="indel" label="Indel score" type="integer" + value="-350" min="-1000" max="0" /> + <param argument="tau" type="integer" value="50" + min="0" max="200" + label="Sequence contribution at structure match in percent"/> + + <conditional name="sequence_score"> + <param name="sequence_score_selector" type="select" label="Type of sequence score contribution"> + <option value="ribofit">Use ribofit</option> + <option value="ribosum">Use RIBOSUM85_60</option> + <option value="match">Simple match/mismatch costs</option> + </param> + <when value="ribofit" /> + <when value="ribosum" /> + <when value="match"> + <param name="match" type="integer" value="50" + min="0" max="400" + label="Match score" /> + <param name="mismatch" type="integer" value="0" + min="-400" max="0" + label="Mismatch score" /> + </when> + </conditional> + </xml> + + <xml name="common_folding_parameters"> + <param name="plfold_span" argument="--plfold-span" + type="integer" value="150" min="-1" max="400" + label="Maximum basepair span (local folding); -1 for global folding" /> + + <param name="plfold_winsize" argument="--plfold-winsize" + type="integer" value="300" min="-1" max="800" + label="Window size for local folding" /> + + <param name="rnafold_temperature" argument="rnafold-temperature" + type="float" value="37.0" min="10" max="50" + label="Temperature for RNAfold (RNAfold's -T option)" /> + </xml> + + <xml name="common_heuristic_parameters"> + <param name="min_prob" argument="min-prob" type="float" value="0.0005" + min="0.0" max="0.2" + label="Minimal / cutoff probability" /> + + <param name="max_diff_am" argument="max-diff-am" + type="integer" value="30" + min="-1" max="300" + label="Maximal difference for sizes of matched arcs (-1=off)" /> + <param name="max_diff" argument="max-diff" type="integer" + value="60" min="-1" max="300" + label="Maximal difference for alignment traces (-1=off)" /> + + <param name="max_diff_at_am" argument="max-diff-am" type="integer" + value="-1" min="-1" max="300" + label="Maximal difference for alignment traces, only at arc match positions" /> + + <param name="max_bps_length_ratio" argument="max-bps-length-ratio" + type="float" value="0.0" min="0.0" max="1.0" + label="Maximal ratio of #base pairs divided by sequence length (default: no effect)" /> + + <param name="alifold_consensus_dp" argument="alifold-consensus-dp" + type="boolean" checked="false" + truevalue="--alifold-consensus-dp" falsevalue="" + label="Compute consensus dot plot by alifold" /> + </xml> + + <xml name="common_other_parameters"> + </xml> + + <xml name="common_outputs"> + <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}"> + <filter>stdout_verbosity != '--quiet'</filter> + </data> + <data format="clustal" name="clustal" from_work_dir="outdir/results/result.aln" + label="${tool.name} alignment (clustal) on ${on_string}"> + <filter>'clustal' in outputs</filter> + </data> + <data format="stockholm" name="stockholm" from_work_dir="outdir/results/result.stk" + label="${tool.name} alignment (stockholm) on ${on_string}"> + <filter>'stockholm' in outputs</filter> + </data> + </xml> + + <xml name="citations"> + <citations> + <citation + type="doi">10.1371/journal.pcbi.0030065</citation> + <citation type="doi">10.1261/rna.029041.111</citation> + </citations> + </xml> + + + +</macros> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mlocarna.xml Tue Dec 06 11:39:14 2016 -0500 @@ -0,0 +1,195 @@ +<tool id="mlocarna" name="LocARNA" version="@VERSION@.0"> + <description> + Multiple Alignment and Folding of RNAs + </description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements" /> + + <expand macro="stdio" /> + + <expand macro="version" /> + + <command><![CDATA[ + mlocarna + + '$input_data' + #if 'stockholm' in str($outputs).split(","): + --stockholm + #end if + + --tgtdir 'outdir' + + ## -------------------- alignment mode and specific options + + #if str($alignment_mode.alignment_mode_selector) == "global_locarna" + $alignment_mode.free_endgaps + #else if str($alignment_mode.alignment_mode_selector) == "local_locarna" + --sequ-local on + #else if str($alignment_mode.alignment_mode_selector) == "probabilistic" + --probabilistic + $alignment_mode.consistency_transformation + + #if str($alignment_mode.iterate) == "true" + --iterate + --iterations $alignment_mode.iterations + #end if + #else if str($alignment_mode.alignment_mode_selector) == "sparse" + --sparse + #end if + + ## -------------------- scoring parameters + + --indel $Scoring.indel + --indel-opening $Scoring.indel_opening + --struct-weight $Scoring.struct_weight + --tau $Scoring.tau + + #if str($Scoring.sequence_score.sequence_score_selector) == "match" + --match $Scoring.sequence_score.match + --mismatch $Scoring.sequence_score.mismatch + #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum" + --use-ribosum true + #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit" + --ribofit true + #end if + + ## -------------------- folding parameters + + #if $Folding.plfold_span>=0 + --plfold-span $Folding.plfold_span + --plfold-winsize $Folding.plfold_winsize + #end if + + --rnafold-temperature $Folding.rnafold_temperature + + ## -------------------- heuristic parameters + + -p $Heuristics.min_prob + --max-diff-am $Heuristics.max_diff_am + --max-diff $Heuristics.max_diff + --max-diff-at-am $Heuristics.max_diff_at_am + --max-bps-length-ratio $Heuristics.max_bps_length_ratio + + $Heuristics.alifold_consensus_dp + + ## -------------------- other parameters + + $Other.lonely_pairs + + $stdout_verbosity + + #if str($stdout_verbosity) != "--quiet": + > '$stdout' + #end if + ]]></command> + + <inputs> + <param name="input_data" type="data" format="text,fasta" label="Sequence input" + help="Sequence input in fasta format, optionally with locarna-specific extensions" + /> + + <conditional name="alignment_mode"> + <param name="alignment_mode_selector" type="select" label="Alignment mode"> + <option value="global_locarna">Global alignment (LocARNA)</option> + <option value="local_locarna">Local alignment (LocARNA)</option> + <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option> + <option value="sparse">Global alignment (SPARSE)</option> + </param> + <when value="global_locarna"> + <param name="free_endgaps" type="select" label="Free endgaps"> + <option value="">No free endgaps</option> + <option value="--free-endgaps">Free endgaps</option> + <option value="--free-endgaps-5">Free endgaps, only 5'</option> + <option value="--free-endgaps-3">Free endgaps, only 3'</option> + </param> + </when> + <when value="local_locarna" /> + <when value="probabilistic"> + <param name="consistency_transformation" type="boolean" + truevalue="--consistency-transformation" falsevalue="" + checked="true" label="Consistency transformation" + help="--consistency-transformation" /> + <param name="iterate" type="boolean" + truevalue="true" falsevalue="false" + checked="false" label="Iterative refinement" + help="--iterate" /> + <param name="iterations" type="integer" + value="1" label="Number of refinement iterations" + help="--iterations num" /> + </when> + <when value="sparse" /> + </conditional> + + <param name="outputs" type="select" display="checkboxes" multiple="True" + label="Output options"> + <option value="clustal" selected="True">Output alignment + in Clustalw format</option> + <option value="stockholm" selected="False">Output + alignment in Stockholm format</option> + </param> + + <param name="stdout_verbosity" type="select" label="Standard output verbosity"> + <option value="--quiet">Don't report standard + output</option> + <option value="">Non verbose</option> + <option value="--verbose">Verbose</option> + <option value="--moreverbose">More verbose</option> + </param> + + + <section name="Scoring" title="Scoring parameters"> + <expand macro="common_scoring_parameters" /> + </section> + + <section name="Folding" title="RNA folding parameters"> + <expand macro="common_folding_parameters" /> + </section> + + <section name="Heuristics" title="Heuristic parameters"> + <expand macro="common_heuristic_parameters" /> + </section> + + <section name="Other" title="Other parameters"> + <expand macro="common_other_parameters" /> + <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" + checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" /> + </section> + </inputs> + + <outputs> + <expand macro="common_outputs" /> + </outputs> + + <tests> + <test> + <param name="input_data" value="archaea.fa" /> + <param name="stdout_verbosity" value="" /> + <output name="stdout" file="archaea-default.stdout" /> + </test> + <test> + <param name="input_data" value="haca.snoRNA.fa" /> + <param name="stdout_verbosity" value="" /> + <output name="stdout" file="haca.snoRNA-default.stdout" /> + </test> + <test> + <param name="input_data" value="archaea.fa" /> + <param name="stdout_verbosity" value="" /> + <param name="outputs" value="clustal" /> + <param name="alignment_mode_selector" value="probabilistic" /> + <output name="clustal" file="archaea-probabilistic.aln" /> + </test> + </tests> + + <help><![CDATA[ **Multiple alignment of RNAs** + +For more information, see +.. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/ + ]]></help> + + <expand macro="citations" /> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea-default.stdout Tue Dec 06 11:39:14 2016 -0500 @@ -0,0 +1,18 @@ +mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.8.12 +Copyright Sebastian Will + +Compute pair probs ... +Compute pairwise alignments ... +Perform progressive alignment ... + + + +vhuU AG-CUCACAACCGAACCC-AU------------UUGGGAGGUUGUGAGCU- +fwdB AU-GUUGGAGGGGAACCC-GU------------AAGGGACCCUCCAAGAU- +selD UUACGAUGUGCCGAACCCUUU------------AAGGGAGGCACAUCGAAA +hdrA GG--CACCACUCGAAGGC--U------------AAGCCAAAGUGGUG-CU- +vhuD GU--UCUCUCGGGAACCCGUC------------AAGGGACCGAGAGA-AC- +fruA ---CCUCGAGGGGAACCC-GA------------AAGGGACCCGAGAGG--- +fdhA CG-CCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGGCG- + +alifold ((.(((((((((...(((.................))).))))))))))). (-31.59 = -20.01 + -11.58)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea-probabilistic.aln Tue Dec 06 11:39:14 2016 -0500 @@ -0,0 +1,11 @@ +CLUSTAL W --- LocARNA 1.8.12 + + + +selD UUACGAUGUGCCGAACCCUU------------UAAGGGAGGCACAUCGAAA +vhuU AGC-UCACAACCGAACCCAU-------------UUGGGAGGUUGUGAG-CU +fwdB AUG-UUGGAGGGGAACCCGU-------------AAGGGACCCUCCAAG-AU +hdrA GGC-ACC-ACUCGAAGGCU--------------AAGCCAAAGU-GGUG-CU +vhuD GUU-CUC-UCGGGAACCCGU------------CAAGGGACCGA-GAGA-AC +fdhA CGC-CACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGG-CG +fruA CC-UCG--AGGGGAACCCGA-------------AAGGGACCC--GAGA-GG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea.fa Tue Dec 06 11:39:14 2016 -0500 @@ -0,0 +1,14 @@ +>fruA +CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG +>fdhA +CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG +>vhuU +AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU +>hdrA +GGCACCACUCGAAGGCUAAGCCAAAGUGGUGCU +>vhuD +GUUCUCUCGGGAACCCGUCAAGGGACCGAGAGAAC +>selD +UUACGAUGUGCCGAACCCUUUAAGGGAGGCACAUCGAAA +>fwdB +AUGUUGGAGGGGAACCCGUAAGGGACCCUCCAAGAU
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA-default.stdout Tue Dec 06 11:39:14 2016 -0500 @@ -0,0 +1,25 @@ +mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.8.12 +Copyright Sebastian Will + +Compute pair probs ... +Compute pairwise alignments ... +Perform progressive alignment ... + + + +ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUUCGGAA-AGGGAGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG +ACA30 UGGCACUUUCACAG--UUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG +ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAA--GGCUGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG +ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUGGGUGAC--CCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA +#A1 ................................................................AAAAAA.................................................. +#A2 ................................................................123456.................................................. + +ACA7 AUUGGA--AGA---CACU-CUGCG-----ACA +ACA30 CAACUG--UCA---CUCA-AUGGG-----ACA +ACA5 GGAUAA--AUU---UGGU-UACAG-----ACA +ACA59 ACAAUACUUACUCUCGUUGGUGAUAAGGAACA +#A1 .............................BBB +#A2 .............................123 + +alifold .((((((((........((((.(((((((......))))))).))))......))..)))))).............((((((.....((.....((((((((((((.....))))))))) + )))......)).....)).))))......... (-61.69 = -33.85 + -27.84)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA.fa Tue Dec 06 11:39:14 2016 -0500 @@ -0,0 +1,21 @@ +>ACA59 +GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGGCCCAUGGGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACA +.............................................................xxxxxx...............................................................................xxx #S +.............................................................AAAAAA...............................................................................BBB #1 +.............................................................123456...............................................................................123 #2 + +>ACA7 +ACCUCCUGGGAUCGCAUCUGGAGAGUGCCUAGUAUUCUGCCAGCUUCGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCGAUUGGAAGACACUCUGCGACA +...........................................................xxxxxx...................................................................xxx #S +...........................................................AAAAAA...................................................................BBB #1 +...........................................................123456...................................................................123 #2 +>ACA5 +UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAAGGCUGCCACAGAAACACUGUGACUCAUGGGCCCUGUUCCUGUGUCCCAGGCUCAGGGAUAAAUUUGGUUACAGACA +..............................................................xxxxxx............................................................xxx #S +..............................................................AAAAAA............................................................BBB #1 +..............................................................123456............................................................123 #2 +>ACA30 +UGGCACUUUCACAGUUCCUUCCCCAGGCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAACCCUUGAUUGUAUUCUUGCCCUGGGAUUAUACCAGUGGCAACUGUCACUCAAUGGGACA +..........................................................xxxxxx..........................................................xxx #S +..........................................................AAAAAA..........................................................BBB #1 +..........................................................123456..........................................................123 #2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_5.fa Tue Dec 06 11:39:14 2016 -0500 @@ -0,0 +1,10 @@ +>D10744 +GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG +>AF008220 +GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA +>Z11880 +GCCUUCCUAGCUCAGUGGUAGAGCGCACGGCUUUUAACCGUGUGGUCGUGGGUUCGAUCCCCACGGAAGGCG +>X02172 +GCCUUUAUAGCUUAGUGGUAAAGCGAUAAACUGAAGAUUUAUUUACAUGUAGUUCGAUUCUCAUUAAGGGCA +>M68929 +GCGGAUAUAACUUAGGGGUUAAAGUUGCAGAUUGUGGCUCUGAAAACACGGGUUCGAAUCCCGUUAUUCGCC