| Next changeset 1:5ec8b052e389 (2016-10-09) |
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Commit message:
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/rarefactionanalyzer commit e5dfdf9aa83af409ee99a0259ceb23b305b8f949-dirty |
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added:
rarefaction_analyzer.xml tool_dependencies.xml |
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| diff -r 000000000000 -r 9543fccd0efe rarefaction_analyzer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rarefaction_analyzer.xml Sun Oct 09 07:05:56 2016 -0400 |
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| @@ -0,0 +1,47 @@ +<tool id="rarefaction_analyzer" name="ResistomeAnalyzer" version="0.1.0"> + <description>A simple tool for creating rarefaction curves for metagenomic sequence data</description> + <requirements> + <requirement type="package" version="0.1">rarefactionanalyzer</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + rarefaction + -ref_fp $reference + -annot_fp $annotation + -sam_fp $sam + -min $min + -max $max + -t $threshold + -samples $samples + -skip $skip + -gene_fp $gene + -mech_fp $mech + -class_fp $class + -group_fp $group + ]]></command> + <inputs> + <param type="data" name="reference" format="fasta" label="Reference sequence" /> + <param type="data" name="sam" format="sam" label="SAM file" /> + <param type="data" name="annotation" format="csv" label="Annotation file" /> + <param name="min" type="integer" label="Starting sample level" + value="1" min="1" max="100" help="(-min)" /> + <param name="max" type="integer" label="Ending sample level" + value="1" min="1" max="100" help="(-max)" /> + <param name="threshold" type="integer" label="Gene fraction threshold" + value="0" min="0" max="100" help="(-t)" /> + <param name="skip" type="integer" label="Amount of sample levels to skip" + value="1" min="1" max="100" help="(-skip)" /> + <param name="samples" type="integer" label="Iterations per sample level" + value="1" min="1" max="100" help="(-samples)" /> + </inputs> + <outputs> + <data name="gene" format="tabular" /> + <data name="mech" format="tabular" /> + <data name="class" format="tabular" /> + <data name="group" format="tabular" /> + </outputs> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r 9543fccd0efe tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Oct 09 07:05:56 2016 -0400 |
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| @@ -0,0 +1,19 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="rarefactionanalyzer" version="0.1"> + <install version="1.0"> + <actions> + <action type="shell_command">git clone --recursive https://github.com/cdeanj/rarefactionanalyzer</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>rarefaction</source> + <destination>$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 rarefaction_analyzer requires a C++ compiler</readme> + </package> +</tool_dependency> |