Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

comparison collection_list_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 66022ba24ac7
children
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5:66022ba24ac7 6:a0c8b2b25774
1 <tool id="rmarkdown_collection_list_paired" name="Collection type: list:paired" version="1.0.0"> 1 <tool id="rmarkdown_collection_list_paired" name="Collection type (list:paired)" version="1.0.0">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> 3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
4 <requirement type="package" version="1.20.0">r-getopt</requirement> 4 <requirement type="package" version="1.20.0">r-getopt</requirement>
5 <requirement type="package" version="1.2">r-rmarkdown</requirement> 5 <requirement type="package" version="1.2">r-rmarkdown</requirement>
6 <requirement type="package" version="0.3.5">r-htmltools</requirement> 6 <requirement type="package" version="0.3.5">r-htmltools</requirement>
7 <requirement type="package" version="0.5.0">r-dplyr</requirement> 7 <requirement type="package" version="0.5.0">r-dplyr</requirement>
8 </requirements> 8 </requirements>
9 <description> 9 <description>
10 Create a 'list:paired' dataset collection from a set of files in Galaxy history. 10 Create a list of paired dataset collection from files in history.
11 </description> 11 </description>
12 <stdio> 12 <stdio>
13 <regex match="Execution halted" 13 <regex match="Execution halted"
14 source="both" 14 source="both"
15 level="fatal" 15 level="fatal"
38 ]]> 38 ]]>
39 </command> 39 </command>
40 <inputs> 40 <inputs>
41 <param type="data" name="forward_file_list" multiple="true" label="forward 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"/> 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)"/> 43 <param type="text" name="format" label="the format (extension) of input files (e.g., fastq, fastqsanger, fasta)"/>
44 44
45 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> 45 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
46 </inputs> 46 </inputs>
47 <outputs> 47 <outputs>
48 <data format="html" name="report" label="Collection builder (list:paired collection)" /> 48 <data format="html" name="report" label="Collection builder (list:paired collection)" />
49 <collection type="list:paired" name="list_collection"> 49 <collection type="list:paired" name="list_collection">
50 <discover_datasets pattern="__name_and_ext__" directory="files_directory" visible="true"/> 50 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="files_directory"/>
51 </collection> 51 </collection>
52 </outputs> 52 </outputs>
53 </tool> 53 </tool>