Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

comparison amplicon_analysis_pipeline.xml @ 5:bbfc9638ba84 draft

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First version with (partial) bioconda deps.
author pjbriggs
date Wed, 13 Jun 2018 08:39:26 -0400
parents 013bf1e2cc8f
children 45db1f97795c
comparison
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4:013bf1e2cc8f 5:bbfc9638ba84
1 <tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.2.0"> 1 <tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.2.1">
2 <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description> 2 <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description>
3 <requirements> 3 <requirements>
4 <!-- amplicon_analysis_pipeline not available in bioconda -->
4 <requirement type="package" version="1.2.2">amplicon_analysis_pipeline</requirement> 5 <requirement type="package" version="1.2.2">amplicon_analysis_pipeline</requirement>
6 <requirement type="package" version="2.7">python</requirement>
5 <requirement type="package" version="1.11">cutadapt</requirement> 7 <requirement type="package" version="1.11">cutadapt</requirement>
6 <requirement type="package" version="1.33">sickle</requirement> 8 <requirement type="package" version="1.33">sickle-trim</requirement>
7 <requirement type="package" version="27-08-2013">bioawk</requirement> 9 <requirement type="package" version="1.0">bioawk</requirement>
8 <requirement type="package" version="2.8.1">pandaseq</requirement> 10 <requirement type="package" version="2.8.1">pandaseq</requirement>
9 <requirement type="package" version="3.5.0">spades</requirement> 11 <requirement type="package" version="3.5.0">spades</requirement>
10 <requirement type="package" version="0.11.3">fastqc</requirement> 12 <requirement type="package" version="0.11.3">fastqc</requirement>
11 <requirement type="package" version="1.8.0">qiime</requirement> 13 <requirement type="package" version="1.8.0">qiime</requirement>
12 <requirement type="package" version="2.2.26">blast</requirement> 14 <requirement type="package" version="2.2.26">blast-legacy</requirement>
13 <requirement type="package" version="0.2.4">fasta-splitter</requirement> 15 <requirement type="package" version="0.2.4">fasta-splitter</requirement>
14 <requirement type="package" version="2.2">rdp-classifier</requirement> 16 <requirement type="package" version="2.2">rdp_classifier</requirement>
15 <requirement type="package" version="3.2.0">R</requirement> 17 <requirement type="package" version="3.2.0">R</requirement>
16 <requirement type="package" version="1.1.3">vsearch</requirement> 18 <requirement type="package" version="1.1.3">vsearch</requirement>
19 <!-- microbiomeutil not available in bioconda -->
17 <requirement type="package" version="2010-04-29">microbiomeutil</requirement> 20 <requirement type="package" version="2010-04-29">microbiomeutil</requirement>
21 <!-- fastq_number not available in bioconda -->
18 <requirement type="package">fasta_number</requirement> 22 <requirement type="package">fasta_number</requirement>
19 </requirements> 23 </requirements>
20 <stdio> 24 <stdio>
21 <exit_code range="1:" /> 25 <exit_code range="1:" />
22 </stdio> 26 </stdio>