Mercurial > repos > devteam > clustalw
diff rgClustalw.xml @ 2:bed27b5c0f63 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit 31dd2ec1d105282421df5d6801c65cdcfd589f59
| author | devteam |
|---|---|
| date | Mon, 22 May 2017 21:02:31 -0400 |
| parents | ce785326df6e |
| children | fac9d3c091cb |
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--- a/rgClustalw.xml Tue Oct 13 12:14:40 2015 -0400 +++ b/rgClustalw.xml Mon May 22 21:02:31 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> -