| Previous changeset 3:e88fa24fa837 (2012-06-06) Next changeset 5:73f082e9fa2d (2012-12-23) |
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Commit message:
Updated for MetaPhlAn v1.7 and tool_dependencies added for auto install |
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modified:
metaphlan.xml |
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added:
tool_dependencies.xml |
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| diff -r e88fa24fa837 -r 80b22b31633f metaphlan.xml --- a/metaphlan.xml Wed Jun 06 10:41:23 2012 -0400 +++ b/metaphlan.xml Thu Oct 11 12:01:20 2012 -0500 |
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| @@ -1,28 +1,32 @@ -<tool id="metaphlan" name="MetaPhlAn" version="1.6.0"> -<requirements> -<requirement type="package">metaphlan</requirement> -<requirement type="package">bowtie2</requirement> -</requirements> +<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> - metaphlan.py + python \${METAPHLAN_PATH}/metaphlan.py $input - --bowtie2db ${GALAXY_DATA_INDEX_DIR}/shared/metaphlan/bowtie2db/mpa + --bowtie2db \${METAPHLAN_PATH}/bowtie2db/mpa --no_map -o $output --bt2_ps $PresetsForBowtie2 </command> <inputs> - <param format="fasta" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param> + <param format="fasta,fastq" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param> <param name="PresetsForBowtie2" type="select" format="text"> <label>Sensitivity options for read-marker similarity (as described by BowTie2)</label> + <help>sensitive-local is recommended for avoiding overly-sensitive hits when using non-preprocessed fastq files</help> <option value="very-sensitive-local">Very Sensitive Local</option> <option value="sensitive-local">Sensitive Local</option> <option value="very-sensitive">Very Sensitive</option> <option value="sensitive">Sensitive</option> </param> </inputs> +<stdio> + <exit_code range="1:" level="fatal" description="MetaPhlAn error" /> +</stdio> <outputs> <data format="tabular" name="output" /> </outputs> |
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| diff -r e88fa24fa837 -r 80b22b31633f tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Oct 11 12:01:20 2012 -0500 |
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| @@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="metaphlan" version="1.7.0"> + <install version="1.0"> + <actions> + <action type="shell_command">hg clone http://bitbucket.org/nsegata/metaphlan</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + <action type="set_environment"> + <environment_variable name="METAPHLAN_PATH" action="set_to">$INSTALL_DIR</environment_variable> + </action> + + </actions> + </install> + <readme> +These links provide information for the metaphlan package: +http://huttenhower.sph.harvard.edu/metaphlan +https://groups.google.com/forum/#!forum/metaphlan-users + </readme> + </package> +</tool_dependency> + |