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comparison qiime_alignment_mafft.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_alignment_mafft" name="qiime alignment mafft" version="2018.4">
3 <description> - De novo multiple sequence alignment with MAFFT</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8
9 qiime alignment mafft --i-sequences=$isequences
10 #set $pnthreads = '${GALAXY_SLOTS:-4}'
11
12 #if str($pnthreads):
13 --p-n-threads="$pnthreads"
14 #end if
15
16 #if str($cmdconfig) != 'None':
17 --cmd-config=$cmdconfig
18 #end if
19
20 --o-alignment=oalignment;
21
22 cp oalignment.qza $oalignment
23
24 ]]></command>
25 <inputs>
26 <param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] - The sequences to be aligned. [required]" name="isequences" optional="False" type="data"/>
27 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
28 </inputs>
29 <outputs>
30 <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment"/>
31 </outputs>
32 <help><![CDATA[
33 De novo multiple sequence alignment with MAFFT
34 ----------------------------------------------
35
36 Perform de novo multiple sequence alignment using MAFFT.
37
38 Parameters
39 ----------
40 sequences : FeatureData[Sequence]
41 The sequences to be aligned.
42
43 Returns
44 -------
45 alignment : FeatureData[AlignedSequence]
46 The aligned sequences.
47 ]]>
48 </help>
49 </tool>