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comparison mafft-add.xml @ 15:bf28a8cff401 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit 2f6456c314c010fd73f5eeaf809a9afce47353af
author bgruening
date Wed, 20 Mar 2024 07:34:52 +0000
parents 6f28e90db932
children
comparison
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14:6f28e90db932 15:bf28a8cff401
14 mafft --version 14 mafft --version
15 ]]> 15 ]]>
16 </version_command> 16 </version_command>
17 <command> 17 <command>
18 <![CDATA[ 18 <![CDATA[
19 sh mk_symlinks.sh &&
19 mafft 20 mafft
20 #if $sequences.sequenceType == 'singleseq' 21 #if $sequences.sequenceType == 'singleseq'
21 $sequences.preservegap '$inputSequences' 22 $sequences.preservegap input_dir/sequence
22 #elif $sequences.sequenceType == 'frags' 23 #elif $sequences.sequenceType == 'frags'
23 --addfragments '$inputSequences' 24 --addfragments input_dir/sequence
24 #elif $sequences.sequenceType == 'group' 25 #elif $sequences.sequenceType == 'group'
25 --addprofile '$inputSequences' 26 --addprofile input_dir/sequence
26 #end if 27 #end if
27 $keeplength $map $reorder 28 $keeplength
28 '$inputAlignment' 29 $mapout
29 > '$outputAlignment' 30 $reorder
30 #if $map == '--mapout' 31 input_dir/alignment > '$outputAlignment'
31 && mv '${inputSequences}.map' '$outputmap' 32
33 #if $mapout
34 && mv input_dir/sequence.map '$outputmap'
32 #end if 35 #end if
33 ]]> 36 ]]>
34 </command> 37 </command>
38 <configfiles>
39 <configfile filename="mk_symlinks.sh"><![CDATA[
40 mkdir input_dir &&
41 ln -s '$inputSequences' input_dir/sequence &&
42 ln -s '$inputAlignment' input_dir/alignment
43 ]]></configfile>
44 </configfiles>
35 <inputs> 45 <inputs>
36 <param name="inputSequences" type="data" format="fasta" label="Sequences to add to the alignment" help="Amino acid or nucleotide sequences in FASTA format."/> 46 <param name="inputSequences" type="data" format="fasta" label="Sequences to add to the alignment" help="Amino acid or nucleotide sequences in FASTA format."/>
37 <param name="inputAlignment" type="data" format="fasta" label="Alignment" help="Amino acid or nucleotide sequences in aligned FASTA format."/> 47 <param name="inputAlignment" type="data" format="fasta" label="Alignment" help="Amino acid or nucleotide sequences in aligned FASTA format."/>
38 <conditional name="sequences"> 48 <conditional name="sequences">
39 <param name="sequenceType" type="select" label="What do you want to add to the alignment" > 49 <param name="sequenceType" type="select" label="What do you want to add to the alignment?" >
40 <option value="singleseq">A single sequence</option> 50 <option value="singleseq">A single sequence</option>
41 <option value="frags" selected="true">Fragments</option> 51 <option value="frags" selected="true">Fragments</option>
42 <option value="group">An alignment</option> 52 <option value="group">An alignment</option>
43 </param> 53 </param>
44 <when value='singleseq'> 54 <when value='singleseq'>
45 <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)"> 55 <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.">
46 <option value="--add" selected="true" >Yes</option> 56 <option value="--add" selected="true" >Yes (--add)</option>
47 <option value="--seed">no</option> 57 <option value="--seed">No (--seed)</option>
48 </param> 58 </param>
49 </when> 59 </when>
50 <when value='frags'/> 60 <when value='frags'/>
51 <when value='group'/> 61 <when value='group'/>
52 </conditional> 62 </conditional>
53 <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" /> 63 <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" />
54 <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" /> 64 <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" />
55 <param name="reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences (--reorder)" /> 65 <param argument="--reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences." />
56 </inputs> 66 </inputs>
57 <outputs> 67 <outputs>
58 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/> 68 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/>
59 <data name="outputmap" format="tabular" label="${tool.name} on ${on_string} : Correspondance of positions "> 69 <data name="outputmap" format="tabular" label="${tool.name} on ${on_string} : Correspondance of positions ">
60 <filter>map == True</filter> 70 <filter>map == True</filter>
61 </data> 71 </data>
62 </outputs> 72 </outputs>
63 <tests> 73 <tests>
64 <test expect_num_outputs="1" > 74 <test expect_num_outputs="1" >
65 <param name="inputSequences" value="add_seq.fa"/> 75 <param name="inputSequences" value="add_seq.fa"/>
66 <param name="inputAlignment" value="mafft_fftns_result.aln"/> 76 <param name="inputAlignment" value="mafft_default.aln"/>
67 <param name="sequenceType" value="singleseq"/> 77 <param name="sequenceType" value="singleseq"/>
68 <param name="preservegap" value="--add"/> 78 <param name="preservegap" value="--add"/>
69 <param name="keeplength" value="--keeplength"/> 79 <param name="keeplength" value="--keeplength"/>
70 <param name="map" value=""/> 80 <param name="mapout" value=""/>
71 <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/> 81 <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/>
72 </test> 82 </test>
73 </tests> 83 </tests>
74 <help> 84 <help>
75 <![CDATA[ 85 <![CDATA[