Mercurial > repos > iuc > qiime_align_seqs

comparison align_seqs.xml @ 5:c97f432af74f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
author iuc
date Fri, 04 Aug 2017 18:17:39 -0400
parents 31be13116b46
children b7b9c1d8b4d9
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4:1deb24bab589 5:c97f432af74f
1 <tool id="qiime_align_seqs" name="Align sequences" version="@WRAPPER_VERSION@.0"> 1 <tool id="qiime_align_seqs" name="Align sequences" version="@WRAPPER_VERSION@.0">
2 <description>using a variety of alignment methods</description> 2 <description> using a variety of alignment methods (align_seqs)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="1.0.2">infernal</requirement> 7 <requirement type="package" version="1.0.2">infernal</requirement>
10 <requirement type="package" version="7.305">mafft</requirement> 10 <requirement type="package" version="7.305">mafft</requirement>
11 <requirement type="package" version="2.2.22">blast-legacy</requirement> 11 <requirement type="package" version="2.2.22">blast-legacy</requirement>
12 </expand> 12 </expand>
13 <version_command>align_seqs.py --version</version_command> 13 <version_command>align_seqs.py --version</version_command>
14 <command detect_errors="aggressive"><![CDATA[ 14 <command detect_errors="aggressive"><![CDATA[
15 align_seqs.py 15 align_seqs.py
16 --input_fasta_fp '$input_fasta_fp' 16 --input_fasta_fp '$input_fasta_fp'
17 -o output 17 -o output
18 --alignment_method '$alignment.alignment_method' 18 --alignment_method '$alignment.alignment_method'
19 #if $alignment.alignment_method == 'pynast' 19 #if $alignment.alignment_method == 'pynast'
20 --pairwise_alignment_method '$alignment.pairwise_alignment_method' 20 --pairwise_alignment_method '$alignment.pairwise_alignment_method'
21 #if str($alignment.template_fp) != 'None': 21 #if str($alignment.template_fp) != 'None':
22 --template_fp '$alignment.template_fp' 22 --template_fp '$alignment.template_fp'
23 #end if 23 #end if
24 #elif $alignment.alignment_method == 'infernal' 24 #elif $alignment.alignment_method == 'infernal'
25 --template_fp '$alignment.template_fp' 25 --template_fp '$alignment.template_fp'
26 #end if 26 #end if
27 27
28 #if $min_length: 28 #if $min_length:
29 --min_length '$min_length' 29 --min_length '$min_length'
30 #end if 30 #end if
31 --min_percent_id '$min_percent_id' 31 --min_percent_id '$min_percent_id'
32 ]]></command> 32 ]]></command>
33 <inputs> 33 <inputs>
34 <param argument="--input_fasta_fp" type="data" format="fasta" label="Input fasta file"/> 34 <param argument="--input_fasta_fp" type="data" format="fasta" label="Input fasta file"/>
35 <conditional name="alignment"> 35 <conditional name="alignment">
36 <param argument="--alignment_method" type="select" label="Method for aligning sequences"> 36 <param argument="--alignment_method" type="select" label="Method for aligning sequences">