Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump

annotate fastq_dump_pe.xml @ 14:61ab2acf0205 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
author mingchen0919
date Wed, 27 Sep 2017 17:00:42 -0400
parents 66bc1016ec2a
children 627c487d22e3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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9b778120db0b planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
mingchen0919
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1 <tool id="rmarkdown_fastqc_dump_pe" name="fastqc-dump-pe" version="1.0.0">
0
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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2 <requirements>
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3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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4 <requirement type="package" version="1.20.0">r-getopt</requirement>
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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5 <requirement type="package" version="1.2">r-rmarkdown</requirement>
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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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>
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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8 <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement>
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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9 </requirements>
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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10 <description>
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66bc1016ec2a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
mingchen0919
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11 Download and extract paired end reads in fastq or fasta format from NCBI SRA. The output is a list of paired datasets
0
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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12 collection.
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13 </description>
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14 <stdio>
11
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mingchen0919
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15 <!--All stderr are redirected to a file. "XXX" is used to match with nothing-->
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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16 <regex match="XXX"
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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17 source="stderr"
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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18 level="warning"
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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19 description="Check the warnings_and_errors.txt file for more details."/>
0
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20 </stdio>
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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21 <command>
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22 <![CDATA[
11
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23 Rscript '${__tool_directory__}/fastq_dump_pe_render.R'
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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24 -i '$sra_accession'
0
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25 -e $echo
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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26 -f $format
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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28 -r $report
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29 -s $sink_message
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30
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31 -t '${__tool_directory__}/fastq_dump_pe.Rmd'
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32 ]]>
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33 </command>
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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34 <inputs>
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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35 <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions" optional="false"
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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36 help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/>
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37 <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="false"
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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38 label="output files in fastq (true) or fasta (false)?"/>
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61ab2acf0205 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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39 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="true"
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40 label="Display analysis code in report?"/>
0
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41 </inputs>
7ec600e7dba7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 6e3aaf47c3178dc89ad303c7fd398c08961064c0-dirty
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42 <outputs>
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43 <data format="html" name="report" label="Fastq-dump report" />
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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44 <collection type="list" name="list_collection" label="Fastq-dump (paired end reads)">
d4a9c31d0046 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
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45 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="read_files_directory"/>
0
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46 </collection>
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47 <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" />
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48 </outputs>
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49 </tool>