Mercurial > repos > rnateam > mafft

comparison mafft-add.xml @ 16:8e649f27aa0d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
15:bf28a8cff401 16:8e649f27aa0d
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="rbc_mafft_add" name="MAFFT add" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="rbc_mafft_add" name="MAFFT add" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>Align a sequence,alignment or fragments to an existing alignment.</description> 2 <description>Align a sequence,alignment or fragments to an existing alignment.</description>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
7 <expand macro="biotools"/> 6 <expand macro="biotools"/>
8 <expand macro="requirements"/> 7 <expand macro="requirements"/>
9 <stdio> 8 <version_command>mafft --version</version_command>
10 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> 9 <command detect_errors="exit_code">
11 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
12 </stdio>
13 <version_command> <![CDATA[
14 mafft --version
15 ]]>
16 </version_command>
17 <command>
18 <![CDATA[ 10 <![CDATA[
19 sh mk_symlinks.sh && 11 sh mk_symlinks.sh &&
20 mafft 12 mafft
21 #if $sequences.sequenceType == 'singleseq' 13 #if $sequences.sequenceType == 'singleseq'
22 $sequences.preservegap input_dir/sequence 14 $sequences.preservegap input_dir/sequence
33 #if $mapout 25 #if $mapout
34 && mv input_dir/sequence.map '$outputmap' 26 && mv input_dir/sequence.map '$outputmap'
35 #end if 27 #end if
36 ]]> 28 ]]>
37 </command> 29 </command>
38 <configfiles> 30 <configfiles>
39 <configfile filename="mk_symlinks.sh"><![CDATA[ 31 <configfile filename="mk_symlinks.sh"><![CDATA[
40 mkdir input_dir && 32 mkdir input_dir &&
41 ln -s '$inputSequences' input_dir/sequence && 33 ln -s '$inputSequences' input_dir/sequence &&
42 ln -s '$inputAlignment' input_dir/alignment 34 ln -s '$inputAlignment' input_dir/alignment
43 ]]></configfile> 35 ]]></configfile>
44 </configfiles> 36 </configfiles>
45 <inputs> 37 <inputs>
46 <param name="inputSequences" type="data" format="fasta" label="Sequences to add to the alignment" help="Amino acid or nucleotide sequences in FASTA format."/> 38 <param name="inputSequences" type="data" format="fasta" label="Sequences to add to the alignment" help="Amino acid or nucleotide sequences in FASTA format."/>
47 <param name="inputAlignment" type="data" format="fasta" label="Alignment" help="Amino acid or nucleotide sequences in aligned FASTA format."/> 39 <param name="inputAlignment" type="data" format="fasta" label="Alignment" help="Amino acid or nucleotide sequences in aligned FASTA format."/>
48 <conditional name="sequences"> 40 <conditional name="sequences">
49 <param name="sequenceType" type="select" label="What do you want to add to the alignment?" > 41 <param name="sequenceType" type="select" label="What do you want to add to the alignment?">
50 <option value="singleseq">A single sequence</option> 42 <option value="singleseq">A single sequence</option>
51 <option value="frags" selected="true">Fragments</option> 43 <option value="frags" selected="true">Fragments</option>
52 <option value="group">An alignment</option> 44 <option value="group">An alignment</option>
53 </param> 45 </param>
54 <when value='singleseq'> 46 <when value="singleseq">
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."> 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.">
56 <option value="--add" selected="true" >Yes (--add)</option> 48 <option value="--add" selected="true">Yes (--add)</option>
57 <option value="--seed">No (--seed)</option> 49 <option value="--seed">No (--seed)</option>
58 </param> 50 </param>
59 </when> 51 </when>
60 <when value='frags'/> 52 <when value="frags"/>
61 <when value='group'/> 53 <when value="group"/>
62 </conditional> 54 </conditional>
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" /> 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"/>
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" /> 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"/>
65 <param argument="--reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences." /> 57 <param argument="--reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences."/>
66 </inputs> 58 </inputs>
67 <outputs> 59 <outputs>
68 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/> 60 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/>
69 <data name="outputmap" format="tabular" label="${tool.name} on ${on_string} : Correspondance of positions "> 61 <data name="outputmap" format="tabular" label="${tool.name} on ${on_string} : Correspondance of positions ">
70 <filter>map == True</filter> 62 <filter>map == True</filter>
71 </data> 63 </data>
72 </outputs> 64 </outputs>
73 <tests> 65 <tests>
74 <test expect_num_outputs="1" > 66 <test expect_num_outputs="1">
75 <param name="inputSequences" value="add_seq.fa"/> 67 <param name="inputSequences" value="add_seq.fa"/>
76 <param name="inputAlignment" value="mafft_default.aln"/> 68 <param name="inputAlignment" value="mafft_default.aln"/>
77 <param name="sequenceType" value="singleseq"/> 69 <param name="sequenceType" value="singleseq"/>
78 <param name="preservegap" value="--add"/> 70 <param name="preservegap" value="--add"/>
79 <param name="keeplength" value="--keeplength"/> 71 <param name="keeplength" value="--keeplength"/>
80 <param name="mapout" value=""/> 72 <param name="mapout" value=""/>
81 <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/> 73 <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/>
82 </test> 74 </test>
83 </tests> 75 </tests>
84 <help> 76 <help>
85 <![CDATA[ 77 <![CDATA[
86 Add one of more sequences to an existing alignment. The new sequence(s) can be complete, fragments, or another alignement. 78 Add one of more sequences to an existing alignment. The new sequence(s) can be complete, fragments, or another alignement.
87 79
88 - Sequences in new_sequences are ungapped and then aligned to existing_alignment. 80 - Sequences in new_sequences are ungapped and then aligned to existing_alignment.
89 - new_sequences is a single multi-FASTA format file. 81 - new_sequences is a single multi-FASTA format file.
93 - --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. 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.
94 - Omit --reorder to preserve the original sequence order. 86 - Omit --reorder to preserve the original sequence order.
95 87
96 ]]> 88 ]]>
97 </help> 89 </help>
98 <expand macro="citations" /> 90 <expand macro="citations"/>
99 </tool> 91 </tool>