Mercurial > repos > rnateam > mafft
comparison mafft-add.xml @ 15:bf28a8cff401 draft default tip
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 |
children |
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14:6f28e90db932 | 15:bf28a8cff401 |
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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[ |