Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

comparison amplicon_analysis_pipeline.xml @ 23:545f23776953 draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 993dae6791b28d776b116153e834192435084ef5
author pjbriggs
date Wed, 29 Aug 2018 10:57:51 -0400
parents 52052235644b
children fe354f5dd0ee
comparison
equal deleted inserted replaced
22:eb7d118dd322 23:545f23776953
1 <tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.2.1"> 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 <!-- non-bioconda dependencies -->
5 <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="2010-04-29">microbiomeutil-chimeraslayer</requirement>
7 <requirement type="package" version="1.2.22">uclust-qiime</requirement>
8 <requirement type="package">fasta_number</requirement>
9 <!-- bioconda dependencies -->
6 <requirement type="package" version="2.7">python</requirement> 10 <requirement type="package" version="2.7">python</requirement>
7 <requirement type="package" version="1.11">cutadapt</requirement> 11 <requirement type="package" version="1.11">cutadapt</requirement>
8 <requirement type="package" version="1.33">sickle-trim</requirement> 12 <requirement type="package" version="1.33">sickle-trim</requirement>
9 <requirement type="package" version="1.0">bioawk</requirement> 13 <requirement type="package" version="1.0">bioawk</requirement>
10 <requirement type="package" version="2.8.1">pandaseq</requirement> 14 <requirement type="package" version="2.8.1">pandaseq</requirement>
12 <requirement type="package" version="0.11.3">fastqc</requirement> 16 <requirement type="package" version="0.11.3">fastqc</requirement>
13 <requirement type="package" version="1.8.0">qiime</requirement> 17 <requirement type="package" version="1.8.0">qiime</requirement>
14 <requirement type="package" version="2.2.26">blast-legacy</requirement> 18 <requirement type="package" version="2.2.26">blast-legacy</requirement>
15 <requirement type="package" version="0.2.4">fasta-splitter</requirement> 19 <requirement type="package" version="0.2.4">fasta-splitter</requirement>
16 <requirement type="package" version="2.2">rdp_classifier</requirement> 20 <requirement type="package" version="2.2">rdp_classifier</requirement>
21 <requirement type="package" version="1.1.3">vsearch</requirement>
17 <requirement type="package" version="3.2.1">R</requirement> 22 <requirement type="package" version="3.2.1">R</requirement>
18 <requirement type="package" version="1.1.3">vsearch</requirement>
19 <requirement type="package" version="1.2.22">uclust-qiime</requirement>
20 <!-- microbiomeutil not available in bioconda -->
21 <requirement type="package" version="2010-04-29">microbiomeutil</requirement>
22 <!-- fastq_number not available in bioconda -->
23 <requirement type="package">fasta_number</requirement>
24 </requirements> 23 </requirements>
25 <stdio> 24 <stdio>
26 <exit_code range="1:" /> 25 <exit_code range="1:" />
27 </stdio> 26 </stdio>
28 <command><![CDATA[ 27 <command><![CDATA[