Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

comparison collection_list.xml @ 0:78018b735124 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
author mingchen0919
date Mon, 25 Sep 2017 14:28:52 -0400
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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>
6 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
7 <requirement type="package" version="1.20.0">r-getopt</requirement>
8 <requirement type="package" version="1.2">r-rmarkdown</requirement>
9 <requirement type="package" version="0.3.5">r-htmltools</requirement>
10 </requirements>
11 <command>
12 <![CDATA[
13 Rscript '${__tool_directory__}/collection_list_render.R'
14 -l $file_list
15 -e $echo
16
17 -r $report
18 -o $list_collection
19 -d $list_collection.files_path
20
21 -t '${__tool_directory__}/collection_list.Rmd'
22 ]]>
23 </command>
24 <inputs>
25 <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 </inputs>
28 <outputs>
29 <data format="html" name="report" label="fastqc report" />
30 <collection type="list" name="list_collection">
31 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="files_directory" />
32 </collection>
33 </outputs>
34 </tool>