Repository 'mlocarna'
hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/mlocarna

Changeset 0:59055c49a112 (2016-12-06)
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mlocarna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
added:
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
b
diff -r 000000000000 -r 59055c49a112 macros.xml
--- /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 ${on_string}">
+            <filter>'stockholm' in outputs</filter>
+        </data>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation
+            type="doi">10.1371/journal.pcbi.0030065</citation>
+            <citation type="doi">10.1261/rna.029041.111</citation>
+        </citations>
+    </xml>
+
+
+
+</macros>
+
b
diff -r 000000000000 -r 59055c49a112 mlocarna.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mlocarna.xml Tue Dec 06 11:39:14 2016 -0500
[
@@ -0,0 +1,195 @@
+<tool id="mlocarna" name="LocARNA" version="@VERSION@.0">
+    <description>
+        Multiple Alignment and Folding of RNAs
+    </description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements" />
+
+    <expand macro="stdio" />
+    
+    <expand macro="version" />
+    
+    <command><![CDATA[
+    mlocarna
+    
+    '$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>
b
diff -r 000000000000 -r 59055c49a112 test-data/archaea-default.stdout
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-default.stdout Tue Dec 06 11:39:14 2016 -0500
b
@@ -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)
b
diff -r 000000000000 -r 59055c49a112 test-data/archaea-probabilistic.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-probabilistic.aln Tue Dec 06 11:39:14 2016 -0500
b
@@ -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
b
diff -r 000000000000 -r 59055c49a112 test-data/archaea.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea.fa Tue Dec 06 11:39:14 2016 -0500
b
@@ -0,0 +1,14 @@
+>fruA
+CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG
+>fdhA
+CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG
+>vhuU
+AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU
+>hdrA
+GGCACCACUCGAAGGCUAAGCCAAAGUGGUGCU
+>vhuD
+GUUCUCUCGGGAACCCGUCAAGGGACCGAGAGAAC
+>selD
+UUACGAUGUGCCGAACCCUUUAAGGGAGGCACAUCGAAA
+>fwdB
+AUGUUGGAGGGGAACCCGUAAGGGACCCUCCAAGAU
b
diff -r 000000000000 -r 59055c49a112 test-data/haca.snoRNA-default.stdout
--- /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
b
@@ -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)
b
diff -r 000000000000 -r 59055c49a112 test-data/haca.snoRNA.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA.fa Tue Dec 06 11:39:14 2016 -0500
b
@@ -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
b
diff -r 000000000000 -r 59055c49a112 test-data/tRNA_5.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_5.fa Tue Dec 06 11:39:14 2016 -0500
b
@@ -0,0 +1,10 @@
+>D10744
+GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
+>AF008220
+GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA
+>Z11880
+GCCUUCCUAGCUCAGUGGUAGAGCGCACGGCUUUUAACCGUGUGGUCGUGGGUUCGAUCCCCACGGAAGGCG
+>X02172
+GCCUUUAUAGCUUAGUGGUAAAGCGAUAAACUGAAGAUUUAUUUACAUGUAGUUCGAUUCUCAUUAAGGGCA
+>M68929
+GCGGAUAUAACUUAGGGGUUAAAGUUGCAGAUUGUGGCUCUGAAAACACGGGUUCGAAUCCCGUUAUUCGCC