Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

comparison collection_list.xml @ 1:6be61cb4a1d5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
author mingchen0919
date Mon, 25 Sep 2017 16:19:52 -0400
parents 78018b735124
children 63e9500cdeec
comparison
equal deleted inserted replaced
0:78018b735124 1:6be61cb4a1d5
5 <requirements> 5 <requirements>
6 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> 6 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
7 <requirement type="package" version="1.20.0">r-getopt</requirement> 7 <requirement type="package" version="1.20.0">r-getopt</requirement>
8 <requirement type="package" version="1.2">r-rmarkdown</requirement> 8 <requirement type="package" version="1.2">r-rmarkdown</requirement>
9 <requirement type="package" version="0.3.5">r-htmltools</requirement> 9 <requirement type="package" version="0.3.5">r-htmltools</requirement>
10 <requirement type="package" version="0.5.0">r-dplyr</requirement>
10 </requirements> 11 </requirements>
11 <command> 12 <command>
12 <![CDATA[ 13 <![CDATA[
13 Rscript '${__tool_directory__}/collection_list_render.R' 14 Rscript '${__tool_directory__}/collection_list_render.R'
14 -l $file_list 15 -l $file_list
15 -e $echo 16 -e $echo
17 -f $format
16 18
17 -r $report 19 -r $report
18 -o $list_collection 20 -d $report.files_path
19 -d $list_collection.files_path
20 21
21 -t '${__tool_directory__}/collection_list.Rmd' 22 -t '${__tool_directory__}/collection_list.Rmd'
22 ]]> 23 ]]>
23 </command> 24 </command>
24 <inputs> 25 <inputs>
25 <param type="data" name="file_list" multiple="true" /> 26 <param type="data" name="file_list" multiple="true" />
26 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> 27 <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)"/>
27 </inputs> 29 </inputs>
28 <outputs> 30 <outputs>
29 <data format="html" name="report" label="fastqc report" /> 31 <data format="html" name="report" label="fastqc report" />
30 <collection type="list" name="list_collection"> 32 <collection type="list" name="list_collection">
31 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="files_directory" /> 33 <discover_datasets pattern="__name_and_ext__" directory="files_directory" />
32 </collection> 34 </collection>
33 </outputs> 35 </outputs>
34 </tool> 36 </tool>