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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 3d98df472498e1273369d23822d10db14f337443
author bgruening
date Thu, 22 Aug 2024 19:20:24 +0000
parents bf28a8cff401
children
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1 <tool id="rbc_mafft_add" name="MAFFT add" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Align a sequence,alignment or fragments to an existing alignment.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <version_command>mafft --version</version_command>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 sh mk_symlinks.sh &&
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12 mafft
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13 #if $sequences.sequenceType == 'singleseq'
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14 $sequences.preservegap input_dir/sequence
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15 #elif $sequences.sequenceType == 'frags'
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16 --addfragments input_dir/sequence
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17 #elif $sequences.sequenceType == 'group'
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18 --addprofile input_dir/sequence
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19 #end if
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20 $keeplength
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21 $mapout
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22 $reorder
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23 input_dir/alignment > '$outputAlignment'
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25 #if $mapout
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26 && mv input_dir/sequence.map '$outputmap'
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27 #end if
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28 ]]>
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29 </command>
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30 <configfiles>
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31 <configfile filename="mk_symlinks.sh"><![CDATA[
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32 mkdir input_dir &&
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33 ln -s '$inputSequences' input_dir/sequence &&
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34 ln -s '$inputAlignment' input_dir/alignment
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35 ]]></configfile>
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36 </configfiles>
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37 <inputs>
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38 <param name="inputSequences" type="data" format="fasta" label="Sequences to add to the alignment" help="Amino acid or nucleotide sequences in FASTA format."/>
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39 <param name="inputAlignment" type="data" format="fasta" label="Alignment" help="Amino acid or nucleotide sequences in aligned FASTA format."/>
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40 <conditional name="sequences">
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41 <param name="sequenceType" type="select" label="What do you want to add to the alignment?">
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42 <option value="singleseq">A single sequence</option>
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43 <option value="frags" selected="true">Fragments</option>
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44 <option value="group">An alignment</option>
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45 </param>
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46 <when value="singleseq">
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47 <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.">
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48 <option value="--add" selected="true">Yes (--add)</option>
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49 <option value="--seed">No (--seed)</option>
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50 </param>
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51 </when>
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52 <when value="frags"/>
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53 <when value="group"/>
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54 </conditional>
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55 <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"/>
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56 <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"/>
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57 <param argument="--reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences."/>
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58 </inputs>
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59 <outputs>
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60 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/>
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61 <data name="outputmap" format="tabular" label="${tool.name} on ${on_string} : Correspondance of positions ">
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62 <filter>map == True</filter>
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63 </data>
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64 </outputs>
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65 <tests>
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66 <test expect_num_outputs="1">
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67 <param name="inputSequences" value="add_seq.fa"/>
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68 <param name="inputAlignment" value="mafft_default.aln"/>
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69 <param name="sequenceType" value="singleseq"/>
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70 <param name="preservegap" value="--add"/>
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71 <param name="keeplength" value="--keeplength"/>
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72 <param name="mapout" value=""/>
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73 <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/>
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74 </test>
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75 </tests>
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76 <help>
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77 <![CDATA[
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78 Add one of more sequences to an existing alignment. The new sequence(s) can be complete, fragments, or another alignement.
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79
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80 - Sequences in new_sequences are ungapped and then aligned to existing_alignment.
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81 - new_sequences is a single multi-FASTA format file.
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82 - existing_alignment is a single multi-FASTA format file.
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83 - 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.
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84 - The alignment length may be conserved if the --keeplength option is given. The alignment length is unchanged. Insertions at the new sequences are deleted.
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85 - --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.
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86 - Omit --reorder to preserve the original sequence order.
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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87
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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88 ]]>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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89 </help>
16
8e649f27aa0d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 3d98df472498e1273369d23822d10db14f337443
bgruening
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90 <expand macro="citations"/>
7
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
rnateam
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91 </tool>