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view kraken-mpa-report.xml @ 1:688428f6800f draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit ce0de4de3fa3fc25c375e378ac84f78452dd61c3
author | devteam |
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date | Wed, 05 Aug 2015 12:09:35 -0400 |
parents | f2757ab26483 |
children | c4fb5dc47fce |
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<?xml version="1.0"?> <tool id="kraken-mpa-report" name="Kraken-mpa-report" version="1.1.1"> <description>view report of classification for multiple samples</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command> <![CDATA[ #for $input_count, $input_classification in enumerate( $classification ): ln -s "${input_classification}" "sample_${input_count}" && #end for @SET_DATABASE_PATH@ && kraken-mpa-report @INPUT_DATABASE@ #for $input_count, $input_classification in enumerate( $classification ): "sample_${input_count}" #end for ${show_zeros} ${header_line} > "$output_report" ]]> </command> <inputs> <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" /> <param checked="False" falsevalue="" help="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros" truevalue="--show-zeros" type="boolean" /> <param checked="False" falsevalue="" help="--header-line" label="Display a header line indicating sample IDs" name="header_line" truevalue="--header-line" type="boolean" /> <expand macro="input_database" /> </inputs> <outputs> <data format="tabular" name="output_report" /> </outputs> <help> <![CDATA[ .. class:: warningmark **Note**: the database used must be the same as the one used in the original Kraken run ----- **What is Does** Kraken-mpa-report summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple expreriments, conditions, locations, etc. It support sthe following parameters:: --show-zeros Display taxa even if they lack a read in any sample --header-line Display a header line indicating sample IDs (sample IDs are the filenames) ----- **Output** The output of kraken-mpa-report is tab-delimited, with one line per taxon. ]]> </help> <expand macro="citations" /> </tool>