comparison metaphlan.xml @ 4:80b22b31633f

Updated for MetaPhlAn v1.7 and tool_dependencies added for auto install

3:e88fa24fa837

<tool id="metaphlan" name="MetaPhlAn" version="1.6.0">
<requirements>
<requirement type="package">metaphlan</requirement>
<requirement type="package">bowtie2</requirement>
</requirements>
  <description>Metagenomic Phylogenetic Analysis</description>
  <command>
	  metaphlan.py 
	  $input  
	  --bowtie2db ${GALAXY_DATA_INDEX_DIR}/shared/metaphlan/bowtie2db/mpa  
	  --no_map  
	  -o $output  
	  --bt2_ps $PresetsForBowtie2 
  </command>

  <inputs>
	<param format="fasta" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param>
	<param name="PresetsForBowtie2" type="select" format="text">
		<label>Sensitivity options for read-marker similarity (as described by BowTie2)</label>
			<option value="very-sensitive-local">Very Sensitive  Local</option>
			<option value="sensitive-local">Sensitive  Local</option>
			<option value="very-sensitive">Very Sensitive</option>
			<option value="sensitive">Sensitive</option>
	</param>			
</inputs>
<outputs>
	<data format="tabular" name="output" />
</outputs>
 
<tests>

4:80b22b31633f

<tool id="metaphlan" name="MetaPhlAn" version="1.7.0">
  <requirements>
    <requirement type="package" version="1.7.0">metaphlan</requirement>
    <requirement type="package">bowtie2</requirement>
  </requirements>
  <description>Metagenomic Phylogenetic Analysis</description>
  <command>
	  python \${METAPHLAN_PATH}/metaphlan.py 
	  $input  
	  --bowtie2db \${METAPHLAN_PATH}/bowtie2db/mpa  
	  --no_map  
	  -o $output  
	  --bt2_ps $PresetsForBowtie2 
  </command>

  <inputs>
	<param format="fasta,fastq" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param>
	<param name="PresetsForBowtie2" type="select" format="text">
		<label>Sensitivity options for read-marker similarity (as described by BowTie2)</label>
                <help>sensitive-local is recommended for avoiding overly-sensitive hits when using non-preprocessed fastq files</help>
			<option value="very-sensitive-local">Very Sensitive  Local</option>
			<option value="sensitive-local">Sensitive  Local</option>
			<option value="very-sensitive">Very Sensitive</option>
			<option value="sensitive">Sensitive</option>
	</param>			
</inputs>
<stdio>
    <exit_code range="1:"  level="fatal"   description="MetaPhlAn error" />
</stdio>
<outputs>
	<data format="tabular" name="output" />
</outputs>
 
<tests>