Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

comparison collection_paired.xml @ 6:a0c8b2b25774 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 88ca36a41aa577ba888cee39cf81b176bf7e68db
author mingchen0919
date Tue, 26 Sep 2017 13:33:22 -0400
parents 78018b735124
children f555686ca340
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5:66022ba24ac7 6:a0c8b2b25774
1 <tool id="rmarkdown_collection_paired" name="Collection type (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 paired dataset collection from files in 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_paired_render.R'
29 -L $forward_input
30 -R $reverse_input
31 -e $echo
32 -f $format
33
34 -r $report
35 -d $report.files_path
36
37 -t '${__tool_directory__}/collection_paired.Rmd'
38 ]]>
39 </command>
40 <inputs>
41 <param type="data" name="forward_input" multiple="false" label="forward input"/>
42 <param type="data" name="reverse_input" multiple="false" label="reverse input"/>
43 <param type="text" name="format" label="the format (extension) 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 (paired collection)" />
49 <collection type="paired" name="list_collection">
50 </collection>
51 </outputs>
52 </tool>