comparison amplicon_analysis_pipeline.xml @ 34:3512b135ecb0 draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 601f7d1e21b25c583cc6e1a563029bab3f226921-dirty

33:c4cde1f435f4

<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.3.0">
  <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description>
  <requirements>
    <!-- non-bioconda dependencies -->
    <requirement type="package" version="1.2.3">amplicon_analysis_pipeline</requirement>
    <requirement type="package" version="2010-04-29">microbiomeutil-chimeraslayer</requirement>
    <requirement type="package" version="1.2.22">uclust-qiime</requirement>
    <!-- bioconda dependencies -->
    <requirement type="package" version="2.7">python</requirement>
    <requirement type="package" version="1.11">cutadapt</requirement>
    <requirement type="package" version="1.33">sickle-trim</requirement>
    <requirement type="package" version="1.0">bioawk</requirement>
    <requirement type="package" version="2.8.1">pandaseq</requirement>
    <requirement type="package" version="3.5.0">spades</requirement>
    <requirement type="package" version="0.11.3">fastqc</requirement>
    <requirement type="package" version="1.8.0">qiime</requirement>
    <requirement type="package" version="1.0">libgfortran</requirement>
    <requirement type="package" version="2.2.26">blast-legacy</requirement>
    <requirement type="package" version="0.2.4">fasta-splitter</requirement>
    <requirement type="package" version="2.2">rdp_classifier</requirement>
    <requirement type="package" version="1.1.3">vsearch</requirement>
    <!-- toolshed dependencies -->
    <requirement type="package" version="3.2.1">R</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[

34:3512b135ecb0

<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.3.0">
  <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description>
  <requirements>
    <!-- non-bioconda dependencies -->
    <requirement type="package" version="1.2.3">amplicon_analysis_pipeline-all</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[