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comparison align_families.xml @ 8:658eefb99fd7 draft

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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
author nick
date Fri, 12 Jan 2018 19:18:41 -0500
parents e7b88ffb8294
children fa563fa9b330
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7:e7b88ffb8294 8:658eefb99fd7
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="align_families" name="Du Novo: Align families" version="2.0.9"> 2 <tool id="align_families" name="Du Novo: Align families" version="2.0.12">
3 <description>of duplex sequencing reads</description> 3 <description>of duplex sequencing reads</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="7.221">mafft</requirement> 5 <requirement type="package" version="7.221">mafft</requirement>
6 <requirement type="package" version="2.0.9">dunovo</requirement> 6 <requirement type="package" version="2.0.12">dunovo</requirement>
7 <!-- TODO: require Python 2.7 --> 7 <!-- TODO: require Python 2.7 -->
8 </requirements> 8 </requirements>
9 <version_command>align-families.py --version</version_command> 9 <version_command>align-families.py --version</version_command>
10 <command detect_errors="exit_code">align-families.py --aligner $aligner --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' &gt; '$output' 10 <command detect_errors="exit_code">align-families.py --aligner $aligner --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' &gt; '$output'
11 </command> 11 </command>
59 59
60 ----- 60 -----
61 61
62 **Alignments** 62 **Alignments**
63 63
64 The alignments are done using MAFFT, specifically the command 64 When "MAFFT" is selected as the multiple sequence aligner, the alignments are done with the command
65 :: 65 ::
66 66
67 $ mafft --nuc --quiet family.fa &gt; family.aligned.fa 67 $ mafft --nuc --quiet family.fa &gt; family.aligned.fa
68 68
69 </help> 69 </help>