Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
comparison 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 |
parents | |
children | cd86400bbaed |
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-1:000000000000 | 0:1a11c4fd13d0 |
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1 <tool id="rmarkdown_fastqc_dump_pe" name="fastqc-dump-pe" version="1.0.0"> | |
2 <requirements> | |
3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> | |
4 <requirement type="package" version="1.20.0">r-getopt</requirement> | |
5 <requirement type="package" version="1.2">r-rmarkdown</requirement> | |
6 <requirement type="package" version="0.3.5">r-htmltools</requirement> | |
7 <requirement type="package" version="0.5.0">r-dplyr</requirement> | |
8 <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement> | |
9 </requirements> | |
10 <description> | |
11 Download and extract paired end reads in fastq or fasta format from NCBI SRA. The output is a list of paired datasets | |
12 collection. | |
13 </description> | |
14 <stdio> | |
15 <!--All stderr are redirected to a file. "XXX" is used to match with nothing--> | |
16 <regex match="XXX" | |
17 source="stderr" | |
18 level="warning" | |
19 description="Check the warnings_and_errors.txt file for more details."/> | |
20 </stdio> | |
21 <command> | |
22 <![CDATA[ | |
23 Rscript '${__tool_directory__}/fastq_dump_pe_render.R' | |
24 -i '$sra_accession' | |
25 -e $echo | |
26 -f $format | |
27 | |
28 -r $report | |
29 -d $report.files_path | |
30 -s $sink_message | |
31 | |
32 -t '${__tool_directory__}/fastq_dump_pe.Rmd' | |
33 ]]> | |
34 </command> | |
35 <inputs> | |
36 <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions" optional="false" | |
37 help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/> | |
38 <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true" | |
39 label="output files in fastq (Yes) or fasta (No)?"/> | |
40 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" | |
41 label="Display analysis code in report?"/> | |
42 </inputs> | |
43 <outputs> | |
44 <data format="html" name="report" label="Fastq-dump report" /> | |
45 <collection type="list:paired" name="list_collection" label="Fastq-dump (paired end reads)"> | |
46 <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.(?P<ext>[^\._]+)?" directory="read_files_directory"/> | |
47 </collection> | |
48 <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" /> | |
49 </outputs> | |
50 </tool> |