Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

annotate collection_list_paired.xml @ 54:79b375ee134c draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 88ca36a41aa577ba888cee39cf81b176bf7e68db-dirty
author mingchen0919
date Tue, 26 Sep 2017 16:13:18 -0400
parents fb05ca474127
children
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d3675bae374e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 8399aeb3d68e39b9d6b331fe8fcbcc9d920c55ae-dirty
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1 <tool id="rmarkdown_collection_list_paired" name="Collection type (list:paired)" version="1.0.0">
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2 <requirements>
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3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
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4 <requirement type="package" version="1.20.0">r-getopt</requirement>
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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5 <requirement type="package" version="1.2">r-rmarkdown</requirement>
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6 <requirement type="package" version="0.3.5">r-htmltools</requirement>
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7 <requirement type="package" version="0.5.0">r-dplyr</requirement>
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8 </requirements>
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9 <description>
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10 Create a list of paired dataset collection from files in history.
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11 </description>
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12 <stdio>
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13 <regex match="Execution halted"
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14 source="both"
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15 level="fatal"
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16 description="Execution halted." />
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17 <regex match="Error in"
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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18 source="both"
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19 level="fatal"
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20 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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21 <regex match="Fatal error"
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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22 source="both"
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23 level="fatal"
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24 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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25 </stdio>
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26 <command>
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27 <![CDATA[
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28 Rscript '${__tool_directory__}/collection_list_paired_render.R'
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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29 -L $forward_file_list
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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30 -R $reverse_file_list
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31 -e $echo
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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32 -f $format
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34 -r $report
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35 -d $report.files_path
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37 -t '${__tool_directory__}/collection_list_paired.Rmd'
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38 ]]>
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39 </command>
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40 <inputs>
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41 <param type="data" name="forward_file_list" multiple="true" label="forward inputs"/>
2f6a7c67440f planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74-dirty
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42 <param type="data" name="reverse_file_list" multiple="true" label="reverse inputs"/>
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43 <param type="text" name="format" label="the format (extension) of input files (e.g., fastq, fastqsanger, fasta)"/>
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44
17
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45 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
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46 </inputs>
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47 <outputs>
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48 <data format="html" name="report" label="Collection builder (list:paired collection)" />
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49 <collection type="list:paired" name="list_collection">
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50 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="files_directory"/>
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51 </collection>
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52 </outputs>
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53 </tool>