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comparison mafft-add.xml @ 6:e4a0bd9ea48c draft default tip

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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 19:28:51 +0000
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5:dd4a533a0e3c 6:e4a0bd9ea48c
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="rbc_mafft_add" name="MAFFT add" version="@TOOL_VERSION@+galaxy@VERSION@">
3 <description>Align a sequence,alignment or fragments to an existing alignment.</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <stdio>
9 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
10 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
11 </stdio>
12 <version_command> <![CDATA[
13 mafft --version
14 ]]>
15 </version_command>
16 <command>
17 <![CDATA[
18 mafft
19 #if $sequences.sequenceType == 'singleseq'
20 $sequences.preservegap '$inputSequences'
21 #elif $sequences.sequenceType == 'frags'
22 --addfragments '$inputSequences'
23 #elif $sequences.sequenceType == 'group'
24 --addprofile '$inputSequences'
25 #end if
26 $keeplength $map $reorder
27 '$inputAlignment'
28 > '$outputAlignment'
29 #if $map == '--mapout'
30 && mv '${inputSequences}.map' '$outputmap'
31 #end if
32 ]]>
33 </command>
34 <inputs>
35 <param name="inputSequences" type="data" format="fasta" label="Sequences to add to the alignment" help="Amino acid or nucleotide sequences in FASTA format."/>
36 <param name="inputAlignment" type="data" format="fasta" label="Alignment" help="Amino acid or nucleotide sequences in aligned FASTA format."/>
37 <conditional name="sequences">
38 <param name="sequenceType" type="select" label="What do you want to add to the alignment" >
39 <option value="singleseq">A single sequence</option>
40 <option value="frags" selected="true">Fragments</option>
41 <option value="group">An alignment</option>
42 </param>
43 <when value='singleseq'>
44 <param name="preservegap" type="select" label="Preserve the original alignment" help="Keep the given alignment unchanged (--add .)If not, the aligned letters in the seed alignment are preserved but gaps are not necessarily preserved (--seed)">
45 <option value="--add" selected="true" >Yes</option>
46 <option value="--seed">no</option>
47 </param>
48 </when>
49 <when value='frags'/>
50 <when value='group'/>
51 </conditional>
52 <param name="keeplength" type="boolean" truevalue="--keeplength" falsevalue="" checked="True" label="Keep alignment length" help="The alignment length is unchanged. Insertions at the additional sequences are deleted" />
53 <param name="map" type="boolean" truevalue="--mapout" falsevalue="" checked="False" label="Output a correspondance table of positions (--mapout)" help="Output a correspondence table of positions, sequence.map, between before and after the calculation. The --mapout option automatically turns on the --keeplength option, to keep the numbering of sites in the reference alignment" />
54 <param name="reorder" type="boolean" truevalue="" falsevalue="--reorder" checked="True" label="Preserve the original order of sequences (--reorder)" />
55 </inputs>
56 <outputs>
57 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string} : New alignment"/>
58 <data name="outputmap" format="tabular" label="${tool.name} on ${on_string} : Correspondance of positions ">
59 <filter>map == True</filter>
60 </data>
61 </outputs>
62 <tests>
63 <test expect_num_outputs="1" >
64 <param name="inputSequences" value="add_seq.fa"/>
65 <param name="inputAlignment" value="mafft_fftns_result.aln"/>
66 <param name="sequenceType" value="singleseq"/>
67 <param name="preservegap" value="--add"/>
68 <param name="keeplength" value="--keeplength"/>
69 <param name="map" value=""/>
70 <output name="outputAlignment" ftype="fasta" file="mafft_add_result.aln"/>
71 </test>
72 </tests>
73 <help>
74 <![CDATA[
75 Add one of more sequences to an existing alignment. The new sequence(s) can be complete, fragments, or another alignement.
76
77 - Sequences in new_sequences are ungapped and then aligned to existing_alignment.
78 - new_sequences is a single multi-FASTA format file.
79 - existing_alignment is a single multi-FASTA format file.
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.
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.
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.
83 - Omit --reorder to preserve the original sequence order.
84
85 ]]>
86 </help>
87 <expand macro="citations" />
88 </tool>