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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw commit 4048394d36408ccfeca401a84c4909a6c023e30e
author | iuc |
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date | Thu, 02 Nov 2023 10:44:37 +0000 |
parents | 83e828f8ba26 |
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<tool id="clustalw" name="ClustalW" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>multiple sequence alignment program for DNA or proteins</description> <macros> <import>macros.xml</import> </macros> <expand macro="biotools" /> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '$input' input.fasta && clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$type_conditional.dnarna #if $outcontrol.outform == "clustal" -OUTPUT=CLUSTAL #if $outcontrol.out_seqnos == "ON" -SEQNOS=ON #end if #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 #if $type_conditional.dnarna == 'PROTEIN' #if $type_conditional.algorithm_conditional.selector == '' -PWMATRIX=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWMATRIX @SLOW_PAIRWISE_ALIGNMENTS@ #else @FAST_PAIRWISE_ALIGNMENTS@ #end if -MATRIX=$type_conditional.multiple_alignments.MATRIX @MULTIPLE_ALIGNMENTS@ #else #if $type_conditional.algorithm_conditional.selector == '' -PWDNAMATRIX=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWDNAMATRIX @SLOW_PAIRWISE_ALIGNMENTS@ #else @FAST_PAIRWISE_ALIGNMENTS@ #end if -DNAMATRIX=$type_conditional.multiple_alignments.DNAMATRIX @MULTIPLE_ALIGNMENTS@ #end if -OUTPUTTREE=$tree_calculation.OUTPUTTREE $tree_calculation.KIMURA $tree_calculation.TOSSGAPS ]]></command> <inputs> <param name="input" type="data" format="fasta" label="FASTA file" /> <conditional name="type_conditional"> <param name="dnarna" type="select" label="Data type"> <option value="DNA" selected="True">DNA nucleotide sequences</option> <option value="PROTEIN">Protein sequences</option> </param> <when value="DNA"> <expand macro="macro_options" algorithm="PWDNAMATRIX" multiple="DNAMATRIX" label="DNA" default="IUB"> <option value="IUB" selected="true">IUB</option> <option value="CLUSTALW">CLUSTALW</option> </expand> </when> <when value="PROTEIN"> <expand macro="macro_options" algorithm="PWMATRIX" multiple="MATRIX" label="Protein" default="GONNET"> <option value="BLOSUM">BLOSUM</option> <option value="PAM">PAM</option> <option value="GONNET" selected="true">GONNET</option> <option value="ID">ID</option> </expand> </when> </conditional> <section name="tree_calculation" title="Tree calculation/BOOTSTRAP options"> <param argument="-OUTPUTTREE" type="select" label="Output tree/distance forma" help="Specify the output format. Default: phylip"> <option value="PHYLIP">PHYLIP</option> <option value="DIST">DIST</option> <option value="NJ">NJ</option> <option value="NEXUS">NEXUS</option> </param> <param argument="-KIMURA" type="boolean" truevalue="-KIMURA" falsevalue="" checked="false" label="Use Kimura correction" help="For small divergence (say inferior 10%) this option makes no difference. For greater divergence, this option corrects for the fact that observed distances underestimate actual evolutionary distances." /> <param argument="-TOSSGAPS" type="boolean" truevalue="-TOSSGAPS" falsevalue="" checked="false" label="Ignore positions with gaps" help="Default: No" /> </section> <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> <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" /> <conditional name="type_conditional"> <param name="dnarna" value="DNA"/> </conditional> <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> <!-- Test DNA options--> <test expect_num_outputs="2"> <param name="input" value="rgClustal_testin.fasta"/> <param name="out_order" value="ALIGNED"/> <section name="tree_calculation"> <param name="OUTPUTTREE" value="PHYLIP"/> <param name="KIMURA" value="true"/> <param name="TOSSGAPS" value="true"/> </section> <conditional name="type_conditional"> <param name="dnarna" value="DNA"/> <section name="multiple_alignments"> <param name="DNAMATRIX" value="IUB"/> <param name="GAPOPEN" value="2"/> <param name="GAPEXT" value="1"/> <param name="ENDGAPS" value="true"/> <param name="GAPDIST" value="1"/> <param name="NOPGAP" value="true"/> <param name="NOHGAP" value="true"/> <param name="MAXDIV" value="1"/> <param name="NEGATIVE" value="true"/> <param name="TRANSWEIGHT" value="1"/> </section> <conditional name="algorithm_conditional"> <param name="selector" value=""/> <section name="slow_pairwise_alignments"> <param name="PWGAPOPEN" value="2"/> <param name="PWGAPEXT" value="1"/> </section> </conditional> </conditional> <output name="output" file="rgClustal_testout02.aln" ftype="clustal"/> <output name="dnd" file="rgClustal_testout02.dnd" ftype="nhx"/> </test> <!-- Test protein options and fast algorithm--> <test expect_num_outputs="2"> <param name="input" value="rgClustal_testin_prot.fasta"/> <param name="out_order" value="ALIGNED"/> <section name="tree_calculation"> <param name="OUTPUTTREE" value="PHYLIP"/> <param name="KIMURA" value="false"/> <param name="TOSSGAPS" value="false"/> </section> <conditional name="type_conditional"> <param name="dnarna" value="PROTEIN"/> <section name="multiple_alignments"> <param name="MATRIX" value="BLOSUM"/> <param name="GAPOPEN" value="3"/> <param name="GAPEXT" value="1"/> <param name="ENDGAPS" value="true"/> <param name="GAPDIST" value="2"/> <param name="NOPGAP" value="true"/> <param name="NOHGAP" value="true"/> <param name="MAXDIV" value="1"/> <param name="NEGATIVE" value="true"/> <param name="TRANSWEIGHT" value="1"/> </section> <conditional name="algorithm_conditional"> <param name="selector" value="-QUICKTREE"/> <section name="fast_pairwise_alignments"> <param name="KTUPLE" value="1"/> <param name="TOPDIAGS" value="1"/> <param name="WINDOW" value="2"/> <param name="PAIRGAP" value="2"/> <param name="SCORE" value="PERCENT"/> </section> </conditional> </conditional> <output name="output" file="rgClustal_testout03.aln" ftype="clustal"/> <output name="dnd" file="rgClustal_testout03.dnd" ftype="nhx"/> </test> </tests> <help><![CDATA[ .. class:: infomark **Note** This tool allows you to run a multiple sequence alignment with ClustalW_. You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a FASTA file. 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. 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. ---- .. class:: infomark **Attribution** 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. Cristóbal Gallardo included the remaining parameters. This wrapper is released licensed under the LGPL_. .. _ClustalW: http://www.clustal.org/clustal2/ .. _LGPL: https://www.gnu.org/copyleft/lesser.html ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btm404</citation> </citations> </tool>