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comparison qiime2/qiime_alignment_mafft.xml @ 13:887cd4ad8e16 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:46:00 +0000
parents f190567fe3f6
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12:33e7a3470046 13:887cd4ad8e16
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_alignment_mafft" name="qiime alignment mafft" version="2019.7"> 2 <tool id="qiime_alignment_mafft" name="qiime alignment mafft"
3 <description> - De novo multiple sequence alignment with MAFFT</description> 3 version="2020.8">
4 <requirements> 4 <description>De novo multiple sequence alignment with MAFFT</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime alignment mafft 9 qiime alignment mafft
9 10
10 --i-sequences=$isequences 11 --i-sequences=$isequences
11 --o-alignment=oalignment
12 12
13 #set $pnthreads = '${GALAXY_SLOTS:-4}' 13 #if str($pnthreads) != 'None':
14 14 --p-n-threads=$pnthreads
15 #if str($pnthreads):
16 --p-n-threads="$pnthreads"
17 #end if 15 #end if
18
19 16
20 #if $pparttree: 17 #if $pparttree:
21 --p-parttree 18 --p-parttree
22 #end if 19 #end if
20
21 --o-alignment=oalignment
22
23 #if str($examples) != 'None':
24 --examples=$examples
25 #end if
26
23 ; 27 ;
24 cp oalignment.qza $oalignment 28 cp oalignment.qza $oalignment
25 ]]></command> 29
26 <inputs> 30 ]]></command>
27 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be aligned. [required]" name="isequences" optional="False" type="data"/> 31 <inputs>
28 <param label="--p-parttree: --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default [default: False]" name="pparttree" selected="False" type="boolean"/> 32 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be aligned. [required]" name="isequences" optional="False" type="data" />
29 </inputs> 33 <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
30 <outputs> 34 <option selected="True" value="None">Selection is Optional</option>
31 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment"/> 35 <option value="Int % Range(1">Int % Range(1</option>
32 </outputs> 36 <option value="None">None</option>
33 <help><![CDATA[ 37 </param>
38 <param label="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default [default: False]" name="pparttree" selected="False" type="boolean" />
39 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
40
41 </inputs>
42
43 <outputs>
44 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
45
46 </outputs>
47
48 <help><![CDATA[
34 De novo multiple sequence alignment with MAFFT 49 De novo multiple sequence alignment with MAFFT
35 ############################################## 50 ###############################################################
36 51
37 Perform de novo multiple sequence alignment using MAFFT. 52 Perform de novo multiple sequence alignment using MAFFT.
38 53
39 Parameters 54 Parameters
40 ---------- 55 ----------
41 sequences : FeatureData[Sequence] 56 sequences : FeatureData[Sequence]
42 The sequences to be aligned. 57 The sequences to be aligned.
58 n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
59 The number of threads. (Use `auto` to automatically use all available
60 cores)
43 parttree : Bool, optional 61 parttree : Bool, optional
44 This flag is required if the number of sequences being aligned are 62 This flag is required if the number of sequences being aligned are
45 larger than 1000000. Disabled by default 63 larger than 1000000. Disabled by default
46 64
47 Returns 65 Returns
48 ------- 66 -------
49 alignment : FeatureData[AlignedSequence] 67 alignment : FeatureData[AlignedSequence]
50 The aligned sequences. 68 The aligned sequences.
51 ]]></help> 69 ]]></help>
52 <macros> 70 <macros>
53 <import>qiime_citation.xml</import> 71 <import>qiime_citation.xml</import>
54 </macros> 72 </macros>
55 <expand macro="qiime_citation"/> 73 <expand macro="qiime_citation"/>
56 </tool> 74 </tool>