Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
author mingchen0919
date Tue, 17 Oct 2017 14:09:01 -0400
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512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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1 <tool id="rmarkdown_bdss_client" name="BDSS client" version="1.0.3">
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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="3.3.2">r-base</requirement>
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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6 <requirement type="package" version="1.2">r-rmarkdown</requirement>
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7 <requirement type="package" version="0.3.5">r-htmltools</requirement>
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8 <requirement type="package" version="0.5.0">r-dplyr</requirement>
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9 <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement>
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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10 <requirement type="package" version="1.95_4.8">r-rcurl</requirement>
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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11 </requirements>
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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12 <description>
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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13 Download data with BDSS client.
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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14 </description>
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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15 <stdio>
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16 <!--All stderr are redirected to a file. "XXX" is used to match with nothing-->
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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17 <regex match="XXX"
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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18 source="stderr"
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19 level="warning"
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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20 description="Check the warnings_and_errors.txt file for more details."/>
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
mingchen0919
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21 </stdio>
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mingchen0919
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22 <command>
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23 <![CDATA[
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24 Rscript '${__tool_directory__}/bdss_client_render.R'
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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25 -i '$urls'
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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26 -e $echo
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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27
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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28 -r $report
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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29 -d $report.files_path
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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30 -s $sink_message
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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31
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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32 -t '${__tool_directory__}/bdss_client.Rmd'
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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33 ]]>
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34 </command>
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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35 <inputs>
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36 <param type="text" name="urls" area="true" size="5x25" label="URLs to data files" />
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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37 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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38 label="Display analysis code in report?"/>
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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39 </inputs>
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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40 <outputs>
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41 <data format="html" name="report" label="BDSS client report"/>
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42 <data name="output" label="BDSS downloaded data">
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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43 <discover_datasets pattern="__name_and_ext__" directory="read_files_directory" visible="true"/>
512d008295db planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
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44 </data>
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45 <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
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46 </outputs>
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47 </tool>