Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

annotate bdss_client_sra_pe.xml @ 14:c0b8476fbc85 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
author mingchen0919
date Wed, 11 Oct 2017 14:36:19 -0400
parents 04100e773314
children afecbcdaba60
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mingchen0919
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1 <tool id="rmarkdown_bdss_client_sra_pe" name="BDSS client SRA PE" 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>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-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>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
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8 <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement>
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9 <requirement type="package" version="1.95_4.8">r-rcurl</requirement>
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10 </requirements>
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11 <description>
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mingchen0919
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12 Download and extract paired end reads in fastq or fasta format from NCBI SRA. The output is a list of paired
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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13 datasets
0
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14 collection.
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15 </description>
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16 <stdio>
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17 <!--All stderr are redirected to a file. "XXX" is used to match with nothing-->
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
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18 <regex match="XXX"
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
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19 source="stderr"
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20 level="warning"
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21 description="Check the warnings_and_errors.txt file for more details."/>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
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22 </stdio>
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23 <command>
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24 <![CDATA[
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
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25 Rscript '${__tool_directory__}/bdss_client_sra_pe_render.R'
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
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26 -i '$sra_accession'
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
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27 -e $echo
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
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28 -f $format
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29 -S $sra
0
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30
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31 -r $report
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32 -d $report.files_path
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33 -s $sink_message
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34
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35 -t '${__tool_directory__}/bdss_client_sra_pe.Rmd'
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
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36 ]]>
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37 </command>
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38 <inputs>
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39 <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions" optional="false"
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40 help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/>
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41 <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true"
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42 label="output files in fastq (Yes) or fasta (No)?"/>
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43 <param type="boolean" name="sra" truevalue="TRUE" falsevalue="FALSE" checked="true"
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44 label="Download SRA or Fastq"/>
0
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45 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
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46 label="Display analysis code in report?"/>
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47 </inputs>
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48 <outputs>
3
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49 <data format="html" name="report" label="BDSS report"/>
1
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50 <collection type="list:paired" name="list_collection" label="BDSS fastq/fasta (paired end reads)">
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51 <discover_datasets
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52 pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?"
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53 directory="read_files_directory"/>
0
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54 </collection>
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55 <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
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56 </outputs>
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57 </tool>