Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
annotate fastq_dump_pe.xml @ 0:1a11c4fd13d0 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
author | mingchen0919 |
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date | Wed, 27 Sep 2017 21:41:29 -0400 |
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children | cd86400bbaed |
rev | line source |
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1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
parents:
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1 <tool id="rmarkdown_fastqc_dump_pe" name="fastqc-dump-pe" version="1.0.0"> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
parents:
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2 <requirements> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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4 <requirement type="package" version="1.20.0">r-getopt</requirement> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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5 <requirement type="package" version="1.2">r-rmarkdown</requirement> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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6 <requirement type="package" version="0.3.5">r-htmltools</requirement> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
parents:
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7 <requirement type="package" version="0.5.0">r-dplyr</requirement> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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8 <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
parents:
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9 </requirements> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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10 <description> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
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 |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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12 collection. |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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13 </description> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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14 <stdio> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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15 <!--All stderr are redirected to a file. "XXX" is used to match with nothing--> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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16 <regex match="XXX" |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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17 source="stderr" |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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18 level="warning" |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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19 description="Check the warnings_and_errors.txt file for more details."/> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
parents:
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20 </stdio> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
parents:
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21 <command> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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22 <![CDATA[ |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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23 Rscript '${__tool_directory__}/fastq_dump_pe_render.R' |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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24 -i '$sra_accession' |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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25 -e $echo |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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26 -f $format |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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27 |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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28 -r $report |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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29 -d $report.files_path |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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30 -s $sink_message |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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31 |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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32 -t '${__tool_directory__}/fastq_dump_pe.Rmd' |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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33 ]]> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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34 </command> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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35 <inputs> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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36 <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions" optional="false" |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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37 help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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38 <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true" |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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39 label="output files in fastq (Yes) or fasta (No)?"/> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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40 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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41 label="Display analysis code in report?"/> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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42 </inputs> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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43 <outputs> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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44 <data format="html" name="report" label="Fastq-dump report" /> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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45 <collection type="list:paired" name="list_collection" label="Fastq-dump (paired end reads)"> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
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46 <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.(?P<ext>[^\._]+)?" directory="read_files_directory"/> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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47 </collection> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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48 <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" /> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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49 </outputs> |
1a11c4fd13d0
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 65063d5b207a70df38a0bcb6fb57a8f9170d9e9b
mingchen0919
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50 </tool> |