Mercurial > repos > chrisd > resistome_analyzer
changeset 0:c590e36e113c draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/resistomeanalyzer commit d70c0260c1b03b3f27c18b4b6f31b5122a2c01c3
| author | chrisd |
|---|---|
| date | Sun, 09 Oct 2016 03:54:57 -0400 |
| parents | |
| children | fce9a55cb059 |
| files | resistome_analyzer.xml tool_dependencies.xml |
| diffstat | 2 files changed, 48 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/resistome_analyzer.xml Sun Oct 09 03:54:57 2016 -0400 @@ -0,0 +1,29 @@ +<tool id="resistome_analyzer" name="ResistomeAnalyzer" version="0.1.0"> + <description>A simple tool for analyzing the resistome of metagenomic sequence data</description> + <requirements> + <requirement type="package" version="0.1">resistome_analyzer</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + resistome + -ref_fp $reference + -annot_fp $annotation + -sam_fp $sam + -prefix $prefix + ]]></command> + <inputs> + <param type="data" name="reference" format="fasta" label="Reference sequence" /> + <param type="data" name="sam" format="sam" label="SAM file" /> + <param type="data" name="annotation" format="csv" label="Annotation file" /> + </inputs> + <outputs> + <data name="prefix_gene_level_resistome" format="tabular" /> + <data name="prefix_class_level_resistome" format="tabular" /> + <data name="prefix_mechanism_level_resistome" format="tabular" /> + <data name="prefix_group_level_resistome" format="tabular" /> + </outputs> + <citations> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Oct 09 03:54:57 2016 -0400 @@ -0,0 +1,19 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="resistome_analyzer" version="0.1"> + <install version="1.0"> + <actions> + <action type="shell_command">git clone --recursive https://github.com/cdeanj/resistomeanalyzer.git</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>resistome</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>Compiling resistome_analyzer requires a C++ compiler</readme> + </package> +</tool_dependency>