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annotate mafft-add.xml @ 7:aaefa93c2dd2 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
author rnateam
date Wed, 15 Apr 2020 15:33:37 -0400
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children 6f28e90db932
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7
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="rbc_mafft_add" name="MAFFT add" version="@TOOL_VERSION@+galaxy@VERSION@">
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3 <description>Align a sequence,alignment or fragments to an existing alignment.</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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10 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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11 </stdio>
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12 <version_command> <![CDATA[
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13 mafft --version
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14 ]]>
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15 </version_command>
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16 <command>
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17 <![CDATA[
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18 mafft
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19 #if $sequences.sequenceType == 'singleseq'
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20 $sequences.preservegap '$inputSequences'
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21 #elif $sequences.sequenceType == 'frags'
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22 --addfragments '$inputSequences'
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23 #elif $sequences.sequenceType == 'group'
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24 --addprofile '$inputSequences'
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25 #end if
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26 $keeplength $map $reorder
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27 '$inputAlignment'
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28 > '$outputAlignment'
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29 #if $map == '--mapout'
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30 && mv '${inputSequences}.map' '$outputmap'
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31 #end if
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32 ]]>
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33 </command>
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34 <inputs>
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35 <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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36 <param name="inputAlignment" type="data" format="fasta" label="Alignment" help="Amino acid or nucleotide sequences in aligned FASTA format."/>
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37 <conditional name="sequences">
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38 <param name="sequenceType" type="select" label="What do you want to add to the alignment" >
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39 <option value="singleseq">A single sequence</option>
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40 <option value="frags" selected="true">Fragments</option>
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41 <option value="group">An alignment</option>
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42 </param>
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43 <when value='singleseq'>
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44 <param name="preservegap" type="select" label="Preserve the original alignment" help="Keep the given alignment unchanged (--add .)If not, the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved (--seed)">
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45 <option value="--add" selected="true" >Yes</option>
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46 <option value="--seed">no</option>
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47 </param>
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48 </when>
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49 <when value='frags'/>
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50 <when value='group'/>
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51 </conditional>
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52 <param name="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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53 <param name="map" type="boolean" truevalue="--mapout" falsevalue="" checked="False" label="Output a correspondance table of positions (--mapout)" 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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54 <param name="reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences (--reorder)" />
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55 </inputs>
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56 <outputs>
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57 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/>
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58 <data name="outputmap" format="tabular" label="${tool.name} on ${on_string} : Correspondance of positions ">
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59 <filter>map == True</filter>
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60 </data>
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61 </outputs>
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62 <tests>
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63 <test expect_num_outputs="1" >
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64 <param name="inputSequences" value="add_seq.fa"/>
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65 <param name="inputAlignment" value="mafft_fftns_result.aln"/>
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66 <param name="sequenceType" value="singleseq"/>
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67 <param name="preservegap" value="--add"/>
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68 <param name="keeplength" value="--keeplength"/>
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69 <param name="map" value=""/>
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70 <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/>
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71 </test>
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72 </tests>
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73 <help>
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74 <![CDATA[
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75 Add one of more sequences to an existing alignment. The new sequence(s) can be complete, fragments, or another alignement.
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76
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77 - Sequences in new_sequences are ungapped and then aligned to existing_alignment.
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78 - new_sequences is a single multi-FASTA format file.
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79 - existing_alignment is a single multi-FASTA format file.
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80 - 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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81 - 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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82 - --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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83 - Omit --reorder to preserve the original sequence order.
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84
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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85 ]]>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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86 </help>
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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87 <expand macro="citations" />
aaefa93c2dd2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit eff9db2cd18c82a7de37851571b8989b48014c71"
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88 </tool>