Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
view collection_list.xml @ 4:63e9500cdeec draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74
author | mingchen0919 |
---|---|
date | Mon, 25 Sep 2017 16:41:49 -0400 |
parents | 6be61cb4a1d5 |
children | 66022ba24ac7 |
line wrap: on
line source
<tool id="rmarkdown_collection_list" name="Collection type: list" version="1.0.0"> <requirements> <requirement type="package" version="1.15.0.6-0">pandoc</requirement> <requirement type="package" version="1.20.0">r-getopt</requirement> <requirement type="package" version="1.2">r-rmarkdown</requirement> <requirement type="package" version="0.3.5">r-htmltools</requirement> <requirement type="package" version="0.5.0">r-dplyr</requirement> </requirements> <description> Create a 'list' dataset collection from a set of files in Galaxy history. </description> <stdio> <regex match="Execution halted" source="both" level="fatal" description="Execution halted." /> <regex match="Error in" source="both" level="fatal" description="An undefined error occured, please check your intput carefully and contact your administrator." /> <regex match="Fatal error" source="both" level="fatal" description="An undefined error occured, please check your intput carefully and contact your administrator." /> </stdio> <command> <![CDATA[ Rscript '${__tool_directory__}/collection_list_render.R' -l $file_list -e $echo -f $format -r $report -d $report.files_path -t '${__tool_directory__}/collection_list.Rmd' ]]> </command> <inputs> <param type="data" name="file_list" multiple="true" /> <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/> </inputs> <outputs> <data format="html" name="report" label="Collection builder report" /> <collection type="list" name="list_collection"> <discover_datasets pattern="__name_and_ext__" directory="files_directory" /> </collection> </outputs> </tool>