Mercurial > repos > devteam > clustalw
diff rgClustalw.xml @ 4:d9c2b2fde6a3 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
| author | devteam |
|---|---|
| date | Thu, 15 Sep 2022 12:12:51 +0000 |
| parents | d6694932c5e0 |
| children | 83e828f8ba26 |
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--- a/rgClustalw.xml Mon May 22 21:02:45 2017 -0400 +++ b/rgClustalw.xml Thu Sep 15 12:12:51 2022 +0000 @@ -1,11 +1,12 @@ -<tool id="clustalw" name="ClustalW" version="2.1"> +<tool id="clustalw" name="ClustalW" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>multiple sequence alignment program for DNA or proteins</description> - <requirements> - <requirement type="package" version="2.1">clustalw</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '$input' input.fasta && -clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$dnarna +clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$type_conditional.dnarna #if $outcontrol.outform == "clustal" -OUTPUT=CLUSTAL #if $outcontrol.out_seqnos == "ON" @@ -21,13 +22,62 @@ #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" /> - <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="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> @@ -69,18 +119,92 @@ <test> <param name="input" value="rgClustal_testin.fasta" /> <param name="outform" value="fasta" /> - <param name="dnarna" value="DNA" /> + <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_ using the default options. - +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 @@ -92,11 +216,13 @@ ---- +.. 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. +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_.