Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

comparison collection_list.xml @ 4:63e9500cdeec draft

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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
comparison
equal deleted inserted replaced
3:cb6efa0f0cb6 4:63e9500cdeec
1 <tool id="rmarkdown_collection_list" name="Collection type: list" version="1.0.0"> 1 <tool id="rmarkdown_collection_list" name="Collection type: list" version="1.0.0">
2 <description>
3 Create a 'list' dataset collection from a set of files in Galaxy history.
4 </description>
5 <requirements> 2 <requirements>
6 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> 3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
7 <requirement type="package" version="1.20.0">r-getopt</requirement> 4 <requirement type="package" version="1.20.0">r-getopt</requirement>
8 <requirement type="package" version="1.2">r-rmarkdown</requirement> 5 <requirement type="package" version="1.2">r-rmarkdown</requirement>
9 <requirement type="package" version="0.3.5">r-htmltools</requirement> 6 <requirement type="package" version="0.3.5">r-htmltools</requirement>
10 <requirement type="package" version="0.5.0">r-dplyr</requirement> 7 <requirement type="package" version="0.5.0">r-dplyr</requirement>
11 </requirements> 8 </requirements>
9 <description>
10 Create a 'list' 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>
12 <command> 26 <command>
13 <![CDATA[ 27 <![CDATA[
14 Rscript '${__tool_directory__}/collection_list_render.R' 28 Rscript '${__tool_directory__}/collection_list_render.R'
15 -l $file_list 29 -l $file_list
16 -e $echo 30 -e $echo
26 <param type="data" name="file_list" multiple="true" /> 40 <param type="data" name="file_list" multiple="true" />
27 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> 41 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
28 <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/> 42 <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/>
29 </inputs> 43 </inputs>
30 <outputs> 44 <outputs>
31 <data format="html" name="report" label="fastqc report" /> 45 <data format="html" name="report" label="Collection builder report" />
32 <collection type="list" name="list_collection"> 46 <collection type="list" name="list_collection">
33 <discover_datasets pattern="__name_and_ext__" directory="files_directory" /> 47 <discover_datasets pattern="__name_and_ext__" directory="files_directory" />
34 </collection> 48 </collection>
35 </outputs> 49 </outputs>
36 </tool> 50 </tool>