| Previous changeset 15:bf28a8cff401 (2024-03-20) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 3d98df472498e1273369d23822d10db14f337443 |
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modified:
macros.xml mafft-add.xml mafft.xml |
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| diff -r bf28a8cff401 -r 8e649f27aa0d macros.xml --- a/macros.xml Wed Mar 20 07:34:52 2024 +0000 +++ b/macros.xml Thu Aug 22 19:20:24 2024 +0000 |
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| @@ -1,6 +1,5 @@ -<?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">7.520</token> + <token name="@TOOL_VERSION@">7.526</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.01</token> <!-- currently, the fasta3 executable is named according to its major version @@ -18,15 +17,15 @@ </requirements> </xml> <xml name="weighti_param"> - <param argument="--weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments."/> + <param argument="--weighti" type="float" min="1" max="100" value="2.7" label="Weighting factor for the consistency term calculated from pairwise alignments."/> </xml> <xml name="parttree_parameters"> - <param argument="--retree" type="integer" value="2" min="1" max="3" label="Guide tree is built this number of times in the progressive stage."/> - <param argument="--partsize" type="integer" value="50" min="0" max="1000" label="Number of partitions in the PartTree algorithm."/> - <param argument="--groupsize" type="integer" value="-1" min="-1" label="Group size" help="Do not make alignment larger than this number of sequences. The default of -1 means set the value automatically to the number of input sequences."/> + <param argument="--retree" type="integer" min="1" max="3" value="2" label="Guide tree is built this number of times in the progressive stage."/> + <param argument="--partsize" type="integer" min="0" max="1000" value="50" label="Number of partitions in the PartTree algorithm."/> + <param argument="--groupsize" type="integer" min="-1" value="-1" label="Group size" help="Do not make alignment larger than this number of sequences. The default of -1 means set the value automatically to the number of input sequences."/> </xml> <xml name="misc_scoring_scheme"> - <param argument="--fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition into the scoring matrix?" /> + <param argument="--fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition into the scoring matrix?"/> <conditional name="gap_costs"> <param name="use_defaults" type="select" label="Configure gap costs"> <option value="yes">Use default values</option> @@ -42,7 +41,7 @@ <xml name="global_align_options"> <section name="treat_unrelated_segments" title="Handling of unrelated segments in global alignments" expanded="true"> <param argument="--unalignlevel" type="float" min="0" max="0.8" value="0" label="Over-alignment correction factor" help="The higher this factor the more likely will unrelated sequence stretches in globally related sequences be left unaligned. The default of 0 turns over-alignment correction off, turning it on increases run time."/> - <param argument="--leavegappyregion" type="boolean" truevalue="--leavegappyregion" falsevalue="" label="Leave gappy region" help="Older option for preventing over-alignment by not trying to force gap-rich regions into an alignment. Can be used alone or in combination with the over-alignment correction factor, but has a much higher impact on run time and becomes less effective with more sequences. Not recommended for > ~1000 sequences."/> + <param argument="--leavegappyregion" type="boolean" truevalue="--leavegappyregion" falsevalue="" label="Leave gappy region" help="Older option for preventing over-alignment by not trying to force gap-rich regions into an alignment. Can be used alone or in combination with the over-alignment correction factor, but has a much higher impact on run time and becomes less effective with more sequences. Not recommended for > ~1000 sequences."/> </section> </xml> <xml name="citations"> |
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| diff -r bf28a8cff401 -r 8e649f27aa0d mafft-add.xml --- a/mafft-add.xml Wed Mar 20 07:34:52 2024 +0000 +++ b/mafft-add.xml Thu Aug 22 19:20:24 2024 +0000 |
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| @@ -1,20 +1,12 @@ -<?xml version="1.0" encoding="UTF-8"?> <tool id="rbc_mafft_add" name="MAFFT add" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> - <description>Align a sequence,alignment or fragments to an existing alignment.</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="biotools"/> - <expand macro="requirements"/> - <stdio> - <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> - <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> - </stdio> - <version_command> <![CDATA[ - mafft --version - ]]> - </version_command> - <command> + <description>Align a sequence,alignment or fragments to an existing alignment.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="biotools"/> + <expand macro="requirements"/> + <version_command>mafft --version</version_command> + <command detect_errors="exit_code"> <![CDATA[ sh mk_symlinks.sh && mafft @@ -35,53 +27,53 @@ #end if ]]> </command> - <configfiles> - <configfile filename="mk_symlinks.sh"><![CDATA[ + <configfiles> + <configfile filename="mk_symlinks.sh"><![CDATA[ mkdir input_dir && ln -s '$inputSequences' input_dir/sequence && ln -s '$inputAlignment' input_dir/alignment ]]></configfile> - </configfiles> - <inputs> - <param name="inputSequences" type="data" format="fasta" label="Sequences to add to the alignment" help="Amino acid or nucleotide sequences in FASTA format."/> - <param name="inputAlignment" type="data" format="fasta" label="Alignment" help="Amino acid or nucleotide sequences in aligned FASTA format."/> - <conditional name="sequences"> - <param name="sequenceType" type="select" label="What do you want to add to the alignment?" > - <option value="singleseq">A single sequence</option> - <option value="frags" selected="true">Fragments</option> - <option value="group">An alignment</option> - </param> - <when value='singleseq'> - <param name="preservegap" type="select" label="Preserve the original alignment." help="Keep the given alignment unchanged .If not, the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved."> - <option value="--add" selected="true" >Yes (--add)</option> - <option value="--seed">No (--seed)</option> - </param> - </when> - <when value='frags'/> - <when value='group'/> - </conditional> - <param argument="--keeplength" type="boolean" truevalue="--keeplength" falsevalue="" checked="True" label="Keep alignment length" help="The alignment length is unchanged. Insertions at the additional sequences are deleted" /> - <param argument="--mapout" type="boolean" truevalue="--mapout" falsevalue="" checked="False" label="Output a correspondance table of position." help="Output a correspondence table of positions, sequence.map, between before and after the calculation. The mapout option automatically turns on the keeplength option, to keep the numbering of sites in the reference alignment" /> - <param argument="--reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences." /> - </inputs> - <outputs> - <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/> - <data name="outputmap" format="tabular" label="${tool.name} on ${on_string} : Correspondance of positions "> - <filter>map == True</filter> - </data> - </outputs> - <tests> - <test expect_num_outputs="1" > - <param name="inputSequences" value="add_seq.fa"/> - <param name="inputAlignment" value="mafft_default.aln"/> - <param name="sequenceType" value="singleseq"/> - <param name="preservegap" value="--add"/> - <param name="keeplength" value="--keeplength"/> - <param name="mapout" value=""/> - <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/> - </test> - </tests> - <help> + </configfiles> + <inputs> + <param name="inputSequences" type="data" format="fasta" label="Sequences to add to the alignment" help="Amino acid or nucleotide sequences in FASTA format."/> + <param name="inputAlignment" type="data" format="fasta" label="Alignment" help="Amino acid or nucleotide sequences in aligned FASTA format."/> + <conditional name="sequences"> + <param name="sequenceType" type="select" label="What do you want to add to the alignment?"> + <option value="singleseq">A single sequence</option> + <option value="frags" selected="true">Fragments</option> + <option value="group">An alignment</option> + </param> + <when value="singleseq"> + <param name="preservegap" type="select" label="Preserve the original alignment." help="Keep the given alignment unchanged .If not, the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved."> + <option value="--add" selected="true">Yes (--add)</option> + <option value="--seed">No (--seed)</option> + </param> + </when> + <when value="frags"/> + <when value="group"/> + </conditional> + <param argument="--keeplength" type="boolean" truevalue="--keeplength" falsevalue="" checked="True" label="Keep alignment length" help="The alignment length is unchanged. Insertions at the additional sequences are deleted"/> + <param argument="--mapout" type="boolean" truevalue="--mapout" falsevalue="" checked="False" label="Output a correspondance table of position." help="Output a correspondence table of positions, sequence.map, between before and after the calculation. The mapout option automatically turns on the keeplength option, to keep the numbering of sites in the reference alignment"/> + <param argument="--reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences."/> + </inputs> + <outputs> + <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/> + <data name="outputmap" format="tabular" label="${tool.name} on ${on_string} : Correspondance of positions "> + <filter>map == True</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="inputSequences" value="add_seq.fa"/> + <param name="inputAlignment" value="mafft_default.aln"/> + <param name="sequenceType" value="singleseq"/> + <param name="preservegap" value="--add"/> + <param name="keeplength" value="--keeplength"/> + <param name="mapout" value=""/> + <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/> + </test> + </tests> + <help> <![CDATA[ Add one of more sequences to an existing alignment. The new sequence(s) can be complete, fragments, or another alignement. @@ -95,5 +87,5 @@ ]]> </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool> |
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| diff -r bf28a8cff401 -r 8e649f27aa0d mafft.xml --- a/mafft.xml Wed Mar 20 07:34:52 2024 +0000 +++ b/mafft.xml Thu Aug 22 19:20:24 2024 +0000 |
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| @@ -6,12 +6,8 @@ </macros> <expand macro="biotools"/> <expand macro="requirements" /> - <stdio> - <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> - <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> - </stdio> - <version_command><![CDATA[mafft --version]]></version_command> - <command><![CDATA[ + <version_command>mafft --version</version_command> + <command detect_errors="exit_code"><![CDATA[ ## Concatenate all input datasets no matter how they were provided bash inputs.sh && @@ -170,7 +166,7 @@ </when> <when value="merge"> <repeat name="batches" title="Input batch" default="1" min="1"> - <param name="inputs" multiple="true" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/> + <param name="inputs" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format." multiple="true"/> </repeat> </when> </conditional> @@ -187,7 +183,7 @@ <option value="--kimura">Kimura</option> </param> <when value="--kimura"> - <param argument="--kimura" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix" /> + <param name="coefficient" argument="--kimura" type="integer" min="1" value="200" label="PAM value of the matrix" /> </when> </conditional> <expand macro="misc_scoring_scheme" /> @@ -201,7 +197,7 @@ <option value="custom">custom matrix</option> </param> <when value="--bl"> - <param argument="--bl" name="coefficient" type="select" display="radio" label="Coefficient of the BLOSUM matrix"> + <param name="coefficient" argument="--bl" type="select" label="Coefficient of the BLOSUM matrix" display="radio"> <option value="30">30</option> <option value="45">45</option> <option value="62" selected="true">62</option> @@ -209,10 +205,10 @@ </param> </when> <when value="--jtt"> - <param argument="--jtt" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix" /> + <param name="coefficient" argument="--jtt" type="integer" min="1" value="200" label="PAM value of the matrix" /> </when> <when value="--tm"> - <param argument="--tm" name="coefficient" type="integer" value="200" min="1" label="PAM value of the matrix"/> + <param name="coefficient" argument="--tm" type="integer" min="1" value="200" label="PAM value of the matrix"/> </when> <when value="custom"> <param argument="--aamatrix" type="data" format="txt" label="User-defined AA scoring matrix" help="The expected format of the matrix is the same as that used by BLAST."/> @@ -267,7 +263,7 @@ <option value="--fastapair">All pairwise alignments are computed with FASTA (--fastapair)</option> </param> <when value="--6merpair"> - <param argument="--retree" type="integer" value="2" min="1" max="3" label="Guide tree is build this number of times in the progressive stage."/> + <param argument="--retree" type="integer" min="1" max="3" value="2" label="Guide tree is build this number of times in the progressive stage."/> </when> <when value="--globalpair"> <expand macro="global_align_options"/> @@ -312,7 +308,7 @@ </when> </conditional> <section name="progressive_alignment_calculation" title="Progressive alignment calculation" expanded="true"> - <param argument="--maxiterate" type="integer" value="0" min="0" max="1000" label="Maximum number of iterations" help="1000 for maximum quality" /> + <param argument="--maxiterate" type="integer" min="0" max="1000" value="0" label="Maximum number of iterations" help="1000 for maximum quality" /> <param argument="--fft" type="boolean" truevalue="--fft" falsevalue="--nofft" checked="True" label="Use FFT approximation in group-to-group alignment?" /> <param argument="--noscore" type="boolean" truevalue="" falsevalue="--noscore" checked="True" label="Check alignment score in the iterative refinement stage?" /> </section> @@ -391,7 +387,7 @@ <param name="type" value="mafft-fftns"/> </conditional> <param name="outputFormat" value="--clustalout"/> - <output name="outputAlignment" ftype="clustal" file="mafft_explicit_amino_blosum80.clustal.aln" /> + <output name="outputAlignment" ftype="clustal" file="mafft_explicit_amino_blosum80.clustal.aln" lines_diff="2" /> </test> <test expect_num_outputs="1" > <conditional name="input"> @@ -437,7 +433,7 @@ </section> </conditional> <param name="outputFormat" value="--clustalout"/> - <output name="outputAlignment" ftype="clustal" file="mafft_custom_original.clustal.aln"> + <output name="outputAlignment" ftype="clustal" file="mafft_custom_original.clustal.aln" lines_diff="2"> </output> </test> <test expect_num_outputs="1"> |