Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump

annotate fastq_dump_se.xml @ 21:3c859d094074 draft default tip

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/aurora-tools/rmarkdown_fastq_dump commit ffa886b188215708786e3c49877fc08fea60659e
author mingchen0919
date Wed, 04 Apr 2018 10:10:26 -0400
parents d4a9c31d0046
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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3c859d094074 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/aurora-tools/rmarkdown_fastq_dump commit ffa886b188215708786e3c49877fc08fea60659e
mingchen0919
parents: 11
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1 <tool id="rmarkdown_fastq_dump_se" name="fastq-dump-se" version="1.0.2">
0
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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>
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3c859d094074 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/aurora-tools/rmarkdown_fastq_dump commit ffa886b188215708786e3c49877fc08fea60659e
mingchen0919
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5 <requirement type="package" version="1.6">r-rmarkdown</requirement>
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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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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 <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>
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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11 Download and extract single end reads in fastq or fasta format from NCBI SRA. The output is a list of datasets
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.
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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13 </description>
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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14 <stdio>
11
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15 <!--All stderr are redirected to a file. "XXX" is used to match with nothing-->
10
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16 <regex match="XXX"
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17 source="stderr"
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18 level="warning"
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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[
5
a2ba5619f51b planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit c9517f0b061cdca3b79678d9a2620e1e43115d42-dirty
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23 Rscript '${__tool_directory__}/fastq_dump_se_render.R'
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24 -i '$sra_accession'
0
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25 -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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27 -r $report
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 -d $report.files_path
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29 -s $sink_message
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31 -t '${__tool_directory__}/fastq_dump_se.Rmd'
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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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>
4
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35 <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions"
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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="select" name="format" label="Output format">
3c859d094074 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/aurora-tools/rmarkdown_fastq_dump commit ffa886b188215708786e3c49877fc08fea60659e
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38 <option value="fastq" selected="true">fastq</option>
3c859d094074 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/aurora-tools/rmarkdown_fastq_dump commit ffa886b188215708786e3c49877fc08fea60659e
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39 <option value="fasta">fasta</option>
3c859d094074 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/aurora-tools/rmarkdown_fastq_dump commit ffa886b188215708786e3c49877fc08fea60659e
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40 </param>
0
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41 </inputs>
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42 <outputs>
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43 <data format="html" name="report" label="Fastq-dump report"/>
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44 <collection type="list" name="list_collection" label="Fastq-dump (single end reads)">
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45 <discover_datasets pattern="__name_and_ext__" 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"/>
0
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48 </outputs>
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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49 </tool>