Mercurial > repos > devteam > clustalw
changeset 3:d6694932c5e0 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit 31dd2ec1d105282421df5d6801c65cdcfd589f59
| author | devteam |
|---|---|
| date | Mon, 22 May 2017 21:02:45 -0400 |
| parents | f8aad74cc8c1 |
| children | d9c2b2fde6a3 |
| files | rgClustalw.py rgClustalw.xml test-data/rgClustal_testin.dnd test-data/rgClustal_testout.log tool_dependencies.xml |
| diffstat | 5 files changed, 119 insertions(+), 321 deletions(-) [+] |
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--- a/rgClustalw.py Fri Oct 09 15:45:22 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -""" -rgclustalw.py -wrapper for clustalw necessitated by bad choice of output path for .dnd file based on input file. Naughty. -Copyright ross lazarus march 2011 -All rights reserved -Licensed under the LGPL -""" - -import sys,optparse,os,subprocess,tempfile,shutil - -class Clustrunner: - """ - """ - def __init__(self,opts=None): - self.opts = opts - self.iname = 'infile_copy' - shutil.copy(self.opts.input,self.iname) - - def run(self): - tlf = open(self.opts.outlog,'w') - cl = ['clustalw2 -INFILE=%s -OUTFILE=%s -OUTORDER=%s -TYPE=%s -OUTPUT=%s' % (self.iname,self.opts.output,self.opts.out_order,self.opts.dnarna,self.opts.outform)] - if self.opts.seq_range_end <> None and self.opts.seq_range_start <> None: - cl.append('-RANGE=%s,%s' % (self.opts.seq_range_start,self.opts.seq_range_end)) - if self.opts.outform=='CLUSTAL' and self.opts.outseqnos <> None: - cl.append('-SEQNOS=ON') - process = subprocess.Popen(' '.join(cl), shell=True, stderr=tlf, stdout=tlf) - rval = process.wait() - dndf = '%s.dnd' % self.iname - if os.path.exists(dndf): - tlf.write('\nClustal created the following dnd file for your information:\n') - dnds = open('%s.dnd' % self.iname,'r').readlines() - for row in dnds: - tlf.write(row) - tlf.write('\n') - tlf.close() - os.unlink(self.iname) - - - -if __name__ == "__main__": - op = optparse.OptionParser() - op.add_option('-i', '--input', default=None) - op.add_option('-o', '--output', default=None) - op.add_option('-t', '--outname', default="rgClustal") - op.add_option('-s', '--out_order', default='ALIGNMENT') - op.add_option('-f', '--outform', default='CLUSTAL') - op.add_option('-e', '--seq_range_end',default=None) - op.add_option('-b', '--seq_range_start',default=None) - op.add_option('-l','--outlog',default='rgClustalw.log') - op.add_option('-q', '--outseqnos',default=None) - op.add_option('-d', '--dnarna',default='DNA') - - opts, args = op.parse_args() - assert opts.input <> None - assert os.path.isfile(opts.input) - c = Clustrunner(opts) - c.run() - - -
--- a/rgClustalw.xml Fri Oct 09 15:45:22 2015 -0400 +++ b/rgClustalw.xml Mon May 22 21:02:45 2017 -0400 @@ -1,133 +1,110 @@ -<tool id="clustalw" name="ClustalW" version="0.1"> - <requirements> - <requirement type="package" version="2.1">clustalw2</requirement> - </requirements> - <description>multiple sequence alignment program for DNA or proteins</description> - <command interpreter="python"> - rgClustalw.py -i "$input" -o "$output" -s "$out_order" -l "$outlog" -t "$outname" -d "$dnarna" - #if ($range.mode=="part") --b "$range.seq_range_start" -e "$range.seq_range_end" - #end if - #if ($outcontrol.outform=="clustal") --f "CLUSTAL" - #if ($outcontrol.out_seqnos=="ON") --q "ON" - #end if - #end if - #if ($outcontrol.outform=="phylip") --f "PHYLIP" - #end if - #if ($outcontrol.outform=="fasta") --f "FASTA" +<tool id="clustalw" name="ClustalW" version="2.1"> + <description>multiple sequence alignment program for DNA or proteins</description> + <requirements> + <requirement type="package" version="2.1">clustalw</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +ln -s '$input' input.fasta && +clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$dnarna +#if $outcontrol.outform == "clustal" + -OUTPUT=CLUSTAL + #if $outcontrol.out_seqnos == "ON" + -SEQNOS=ON #end if - </command> - <inputs> - <page> - <param format="fasta" name="input" type="data" label="Fasta File" /> - <param name="outname" label="Name for output files to make it easy to remember what you did" type="text" value="Clustal_run" /> - <param name="dnarna" type="select" label="Data Type"> - <option value="DNA" selected="True">DNA nucleotide sequences</option> - <option value="PROTEIN">Protein sequences</option> - </param> - <conditional name="outcontrol"> - <param name="outform" type="select" label="Output alignment format"> - <option value="clustal" selected="True">Native Clustal output format</option> - <option value="phylip">Phylip format</option> - <option value="fasta">Fasta format</option> - </param> - <when value="fasta" /> - <when value="phylip" /> - <when value="clustal"> - <param name="out_seqnos" type="select" label="Show residue numbers in clustal format output"> - <option value="ON">yes</option> - <option value="OFF" selected="true">no</option> - </param> - </when> - </conditional> - <param name="out_order" type="select" label="Output Order"> - <option value="ALIGNED">aligned</option> - <option value="INPUT">same order as input file</option> - </param> - - <conditional name="range"> - <param name="mode" type="select" label="Output complete alignment (or specify part to output)"> - <option value="complete">complete alignment</option> - <option value="part">only part of the alignment</option> +#end if +#if $outcontrol.outform == "phylip" + -OUTPUT=PHYLIP +#end if +#if $outcontrol.outform == "fasta" + -OUTPUT=FASTA +#end if +#if $range.mode == "part" + -RANGE=${range.seq_range_start},${range.seq_range_end} +#end if + ]]></command> + <inputs> + <param name="input" type="data" format="fasta" label="FASTA file" /> + <param name="dnarna" type="select" label="Data type"> + <option value="DNA" selected="True">DNA nucleotide sequences</option> + <option value="PROTEIN">Protein sequences</option> + </param> + <conditional name="outcontrol"> + <param name="outform" type="select" label="Output alignment format"> + <option value="clustal" selected="True">Native Clustal output format</option> + <option value="phylip">PHYLIP format</option> + <option value="fasta">FASTA format</option> + </param> + <when value="fasta" /> + <when value="phylip" /> + <when value="clustal"> + <param name="out_seqnos" type="boolean" truevalue="ON" falsevalue="OFF" label="Show residue numbers in clustal format output" /> + </when> + </conditional> + <param name="out_order" type="select" label="Output order"> + <option value="ALIGNED">Aligned</option> + <option value="INPUT">Same order as input file</option> </param> - <when value="complete"> - </when> - <when value="part"> - <param name="seq_range_start" type="integer" value="1" label="start point" help="sequence range to write"> - </param> - <param name="seq_range_end" type="integer" value="99999" label="end point" > - </param> - </when> - </conditional> - </page> - </inputs> - <outputs> - <data format="clustal" name="output" label="${outname}_output.${outcontrol.outform}"> - <change_format> - <when input="outcontrol.outform" value="phylip" format="phylip" /> - <when input="outcontrol.outform" value="fasta" format="fasta" /> - </change_format> - </data> - <data format="txt" name="outlog" label="${outname}_clustal_log.txt"/> - </outputs> - <tests> - <test> - <param name="input" value="rgClustal_testin.fasta" /> - <param name="outname" value="" /> - <param name="outform" value="fasta" /> - <param name="dnarna" value="DNA" /> - <param name="mode" value="complete" /> - <param name="out_order" value="ALIGNED" /> - <output name="output" file="rgClustal_testout.fasta" ftype="fasta" /> - <output name="outlog" file="rgClustal_testout.log" ftype="txt" lines_diff="5" /> - </test> - </tests> - <help> - + <conditional name="range"> + <param name="mode" type="select" label="Output complete alignment (or specify part to output)"> + <option value="complete">Complete alignment</option> + <option value="part">Only part of the alignment</option> + </param> + <when value="complete" /> + <when value="part"> + <param name="seq_range_start" type="integer" value="1" label="Start point" help="Sequence range to write" /> + <param name="seq_range_end" type="integer" value="99999" label="End point" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" format="clustal" label="${tool.name} on ${on_string}: ${outcontrol.outform}"> + <change_format> + <when input="outcontrol.outform" value="phylip" format="phylip" /> + <when input="outcontrol.outform" value="fasta" format="fasta" /> + </change_format> + </data> + <data name="dnd" format="nhx" label="${tool.name} on ${on_string}: dnd" from_work_dir="input.dnd" /> + </outputs> + <tests> + <test> + <param name="input" value="rgClustal_testin.fasta" /> + <param name="outform" value="fasta" /> + <param name="dnarna" value="DNA" /> + <param name="mode" value="complete" /> + <param name="out_order" value="ALIGNED" /> + <output name="output" file="rgClustal_testout.fasta" ftype="fasta" /> + <output name="dnd" file="rgClustal_testin.dnd" ftype="nhx" /> + </test> + </tests> + <help><![CDATA[ **Note** -This tool allows you to run a multiple sequence alignment with ClustalW2 (see Clustsrc_) using the default options. - -For a tutorial introduction, see ClustalW2_ +This tool allows you to run a multiple sequence alignment with ClustalW_ using the default options. -You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a fasta file +You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a FASTA file. -A log will be output to your history showing the output Clustal would normally write to standard output. - -The alignments will appear as a clustal format file or optionally, as phylip or fasta format files in your history. If you choose fasta as +The alignments will appear as a clustal format file or optionally, as PHYLIP or FASTA format files in your history. If you choose FASTA as the output format, you can create a 'Logo' image using the Sequence Logo tool. -If Clustal format is chosen, you have the option of adding basepair counts to the output +If Clustal format is chosen, you have the option of adding basepair counts to the output. -A subsequence of the alignment can be output by setting the Output complete parameter to "Partial" and defining the offset and end of the subsequence to be output +A subsequence of the alignment can be output by setting the Output complete parameter to "Partial" and defining the offset and end of the subsequence to be output. ---- **Attribution** -Clustal attribution and associated documentation are available at Clustsrc_ - -The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz - see Clustfirst_ +The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz. -It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added - -This wrapper is released licensed under the LGPL_ +It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added. -.. _ClustalW2: http://www.ebi.ac.uk/2can/tutorials/protein/clustalw.html - -.. _Clustsrc: http://www.clustal.org +This wrapper is released licensed under the LGPL_. -.. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html +.. _ClustalW: http://www.clustal.org/clustal2/ -.. _LGPL: http://www.gnu.org/copyleft/lesser.html - - </help> +.. _LGPL: https://www.gnu.org/copyleft/lesser.html + ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btm404</citation> </citations> </tool> -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rgClustal_testin.dnd Mon May 22 21:02:45 2017 -0400 @@ -0,0 +1,31 @@ +( +( +c_briggsae-chrII_+_/43862-46313:0.07349, +c_brenneri-Cbre_Contig60_+_/627772-630087:0.04317) +:0.02387, +( +c_remanei-Crem_Contig172_-_/123228-124941:0.06114, +c_elegans-II_+_/9706834-9708803:0.07219) +:0.01779, +( +( +( +c_briggsae-chrIfooI_+_/43862-46313:0.10368, +c_brenneri-Cbre_Contig60gak_+_/627772-630087:0.06298) +:0.01654, +( +c_remanei-Crem_Contig172foo_-_/123228-124941:0.05765, +c_elegans-II_+_more/9706834-9708803:0.05902) +:0.06262) +:0.31533, +( +( +c_briggsae-chrII_+_bar/43862-46313:0.02327, +c_brenneri-Cbre_Contig60fee_+_/627772-630087:0.13463) +:0.05016, +( +c_remanei-Crem_Contig172zot_-_/123228-124941:0.11667, +c_elegans-II_+_meh/9706834-9708803:0.11737) +:0.12013) +:0.20951) +:0.30133);
--- a/test-data/rgClustal_testout.log Fri Oct 09 15:45:22 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,144 +0,0 @@ - - - - CLUSTAL 2.1 Multiple Sequence Alignments - - -Sequence type explicitly set to DNA -Sequence format is Pearson -Sequence 1: c_briggsae-chrII_+_/43862-46313 60 bp -Sequence 2: c_remanei-Crem_Contig172_-_/123228-124941 60 bp -Sequence 3: c_brenneri-Cbre_Contig60_+_/627772-630087 60 bp -Sequence 4: c_elegans-II_+_/9706834-9708803 60 bp -Sequence 5: c_briggsae-chrIfooI_+_/43862-46313 60 bp -Sequence 6: c_remanei-Crem_Contig172foo_-_/123228-124941 60 bp -Sequence 7: c_brenneri-Cbre_Contig60gak_+_/627772-630087 60 bp -Sequence 8: c_elegans-II_+_more/9706834-9708803 60 bp -Sequence 9: c_briggsae-chrII_+_bar/43862-46313 60 bp -Sequence 10: c_remanei-Crem_Contig172zot_-_/123228-124941 60 bp -Sequence 11: c_brenneri-Cbre_Contig60fee_+_/627772-630087 60 bp -Sequence 12: c_elegans-II_+_meh/9706834-9708803 60 bp -Start of Pairwise alignments -Aligning... - -Sequences (1:2) Aligned. Score: 80 -Sequences (1:3) Aligned. Score: 88 -Sequences (1:4) Aligned. Score: 83 -Sequences (1:5) Aligned. Score: 21 -Sequences (1:6) Aligned. Score: 20 -Sequences (1:7) Aligned. Score: 23 -Sequences (1:8) Aligned. Score: 18 -Sequences (1:9) Aligned. Score: 21 -Sequences (1:10) Aligned. Score: 16 -Sequences (1:11) Aligned. Score: 25 -Sequences (1:12) Aligned. Score: 10 -Sequences (2:3) Aligned. Score: 85 -Sequences (2:4) Aligned. Score: 86 -Sequences (2:5) Aligned. Score: 21 -Sequences (2:6) Aligned. Score: 20 -Sequences (2:7) Aligned. Score: 25 -Sequences (2:8) Aligned. Score: 20 -Sequences (2:9) Aligned. Score: 36 -Sequences (2:10) Aligned. Score: 16 -Sequences (2:11) Aligned. Score: 22 -Sequences (2:12) Aligned. Score: 17 -Sequences (3:4) Aligned. Score: 85 -Sequences (3:5) Aligned. Score: 13 -Sequences (3:6) Aligned. Score: 20 -Sequences (3:7) Aligned. Score: 25 -Sequences (3:8) Aligned. Score: 20 -Sequences (3:9) Aligned. Score: 36 -Sequences (3:10) Aligned. Score: 16 -Sequences (3:11) Aligned. Score: 18 -Sequences (3:12) Aligned. Score: 25 -Sequences (4:5) Aligned. Score: 13 -Sequences (4:6) Aligned. Score: 11 -Sequences (4:7) Aligned. Score: 20 -Sequences (4:8) Aligned. Score: 10 -Sequences (4:9) Aligned. Score: 31 -Sequences (4:10) Aligned. Score: 17 -Sequences (4:11) Aligned. Score: 29 -Sequences (4:12) Aligned. Score: 14 -Sequences (5:6) Aligned. Score: 73 -Sequences (5:7) Aligned. Score: 83 -Sequences (5:8) Aligned. Score: 80 -Sequences (5:9) Aligned. Score: 31 -Sequences (5:10) Aligned. Score: 14 -Sequences (5:11) Aligned. Score: 14 -Sequences (5:12) Aligned. Score: 12 -Sequences (6:7) Aligned. Score: 80 -Sequences (6:8) Aligned. Score: 88 -Sequences (6:9) Aligned. Score: 26 -Sequences (6:10) Aligned. Score: 16 -Sequences (6:11) Aligned. Score: 25 -Sequences (6:12) Aligned. Score: 12 -Sequences (7:8) Aligned. Score: 78 -Sequences (7:9) Aligned. Score: 31 -Sequences (7:10) Aligned. Score: 10 -Sequences (7:11) Aligned. Score: 12 -Sequences (7:12) Aligned. Score: 12 -Sequences (8:9) Aligned. Score: 31 -Sequences (8:10) Aligned. Score: 10 -Sequences (8:11) Aligned. Score: 14 -Sequences (8:12) Aligned. Score: 12 -Sequences (9:10) Aligned. Score: 63 -Sequences (9:11) Aligned. Score: 84 -Sequences (9:12) Aligned. Score: 78 -Sequences (10:11) Aligned. Score: 64 -Sequences (10:12) Aligned. Score: 76 -Sequences (11:12) Aligned. Score: 46 -Guide tree file created: [infile_copy.dnd] - -There are 11 groups -Start of Multiple Alignment - -Aligning... -Group 1: Sequences: 2 Score:1045 -Group 2: Sequences: 2 Score:1016 -Group 3: Sequences: 4 Score:1001 -Group 4: Sequences: 2 Score:313 -Group 5: Sequences: 2 Score:731 -Group 6: Sequences: 4 Score:516 -Group 7: Sequences: 8 Score:344 -Group 8: Sequences: 2 Score:1016 -Group 9: Sequences: 2 Score:1054 -Group 10: Sequences: 4 Score:945 -Group 11: Sequences: 12 Score:380 -Alignment Score 6283 - -CLUSTAL-Alignment file created [/share/shared/galaxy/database/files/002/dataset_2801.dat] - - -Clustal created the following dnd file for your information: -( -( -c_briggsae-chrII_+_/43862-46313:0.07349, -c_brenneri-Cbre_Contig60_+_/627772-630087:0.04317) -:0.02387, -( -c_remanei-Crem_Contig172_-_/123228-124941:0.06114, -c_elegans-II_+_/9706834-9708803:0.07219) -:0.01779, -( -( -( -c_briggsae-chrIfooI_+_/43862-46313:0.10368, -c_brenneri-Cbre_Contig60gak_+_/627772-630087:0.06298) -:0.01654, -( -c_remanei-Crem_Contig172foo_-_/123228-124941:0.05765, -c_elegans-II_+_more/9706834-9708803:0.05902) -:0.06262) -:0.31533, -( -( -c_briggsae-chrII_+_bar/43862-46313:0.02327, -c_brenneri-Cbre_Contig60fee_+_/627772-630087:0.13463) -:0.05016, -( -c_remanei-Crem_Contig172zot_-_/123228-124941:0.11667, -c_elegans-II_+_meh/9706834-9708803:0.11737) -:0.12013) -:0.20951) -:0.30133); -
--- a/tool_dependencies.xml Fri Oct 09 15:45:22 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="clustalw2" version="2.1"> - <repository changeset_revision="09243d89e7a4" name="package_clustalw_2_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>