Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
comparison collection_list_paired.xml @ 5:66022ba24ac7 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
| author | mingchen0919 |
|---|---|
| date | Tue, 26 Sep 2017 00:16:09 -0400 |
| parents | |
| children | a0c8b2b25774 |
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| 4:63e9500cdeec | 5:66022ba24ac7 |
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| 1 <tool id="rmarkdown_collection_list_paired" name="Collection type: list:paired" version="1.0.0"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> | |
| 4 <requirement type="package" version="1.20.0">r-getopt</requirement> | |
| 5 <requirement type="package" version="1.2">r-rmarkdown</requirement> | |
| 6 <requirement type="package" version="0.3.5">r-htmltools</requirement> | |
| 7 <requirement type="package" version="0.5.0">r-dplyr</requirement> | |
| 8 </requirements> | |
| 9 <description> | |
| 10 Create a 'list:paired' dataset collection from a set of files in Galaxy history. | |
| 11 </description> | |
| 12 <stdio> | |
| 13 <regex match="Execution halted" | |
| 14 source="both" | |
| 15 level="fatal" | |
| 16 description="Execution halted." /> | |
| 17 <regex match="Error in" | |
| 18 source="both" | |
| 19 level="fatal" | |
| 20 description="An undefined error occured, please check your intput carefully and contact your administrator." /> | |
| 21 <regex match="Fatal error" | |
| 22 source="both" | |
| 23 level="fatal" | |
| 24 description="An undefined error occured, please check your intput carefully and contact your administrator." /> | |
| 25 </stdio> | |
| 26 <command> | |
| 27 <![CDATA[ | |
| 28 Rscript '${__tool_directory__}/collection_list_paired_render.R' | |
| 29 -L $forward_file_list | |
| 30 -R $reverse_file_list | |
| 31 -e $echo | |
| 32 -f $format | |
| 33 | |
| 34 -r $report | |
| 35 -d $report.files_path | |
| 36 | |
| 37 -t '${__tool_directory__}/collection_list_paired.Rmd' | |
| 38 ]]> | |
| 39 </command> | |
| 40 <inputs> | |
| 41 <param type="data" name="forward_file_list" multiple="true" label="forward inputs"/> | |
| 42 <param type="data" name="reverse_file_list" multiple="true" label="reverse inputs"/> | |
| 43 <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/> | |
| 44 | |
| 45 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> | |
| 46 </inputs> | |
| 47 <outputs> | |
| 48 <data format="html" name="report" label="Collection builder (list:paired collection)" /> | |
| 49 <collection type="list:paired" name="list_collection"> | |
| 50 <discover_datasets pattern="__name_and_ext__" directory="files_directory" visible="true"/> | |
| 51 </collection> | |
| 52 </outputs> | |
| 53 </tool> |