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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 2f6456c314c010fd73f5eeaf809a9afce47353af
author | bgruening |
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date | Wed, 20 Mar 2024 07:34:52 +0000 |
parents | 6f28e90db932 |
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<?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> <![CDATA[ sh mk_symlinks.sh && mafft #if $sequences.sequenceType == 'singleseq' $sequences.preservegap input_dir/sequence #elif $sequences.sequenceType == 'frags' --addfragments input_dir/sequence #elif $sequences.sequenceType == 'group' --addprofile input_dir/sequence #end if $keeplength $mapout $reorder input_dir/alignment > '$outputAlignment' #if $mapout && mv input_dir/sequence.map '$outputmap' #end if ]]> </command> <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> <![CDATA[ Add one of more sequences to an existing alignment. The new sequence(s) can be complete, fragments, or another alignement. - Sequences in new_sequences are ungapped and then aligned to existing_alignment. - new_sequences is a single multi-FASTA format file. - existing_alignment is a single multi-FASTA format file. - Gaps in existing_alignment are preserved by default (--add), but it can be deactivated (--seed). In that case the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved. - The alignment length may be conserved if the --keeplength option is given. The alignment length is unchanged. Insertions at the new sequences are deleted. - --mapout options output a correspondence table of positions, new_sequences.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. - Omit --reorder to preserve the original sequence order. ]]> </help> <expand macro="citations" /> </tool>