Mercurial > repos > mingchen0919 > aurora_bdss
annotate rmarkdown_report.xml @ 2:845f4b9d7cf3 draft default tip
planemo upload commit 602f5b82864867a81c2e4ea2be9b52f4b635bd7b-dirty
| author | mingchen0919 |
|---|---|
| date | Wed, 30 May 2018 19:52:36 -0400 |
| parents | 8b0ac9578ad4 |
| children |
| rev | line source |
|---|---|
| 1 | 1 <tool name="aurora_bdss" id='aurora_bdss_report' version="1.0.0"> |
| 0 | 2 <description> |
| 3 some description | |
| 4 </description> | |
| 5 <requirements> | |
| 6 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> | |
| 7 <requirement type="package" version="1.20.0">r-getopt</requirement> | |
| 8 <requirement type="package" version="1.6">r-rmarkdown</requirement> | |
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845f4b9d7cf3
planemo upload commit 602f5b82864867a81c2e4ea2be9b52f4b635bd7b-dirty
mingchen0919
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9 <requirement type="package" version="0.6.2">parallel-fastq-dump</requirement> |
| 0 | 10 </requirements> |
| 11 <command><![CDATA[ | |
| 12 | |
| 13 ######### each aurora tool generates a html file and have an files path directory associated with it. | |
| 14 mkdir -p $report.files_path && | |
| 15 | |
| 16 ######### three important paths: | |
| 17 ######### 1. path to tool installation directory | |
| 18 ######### 2. path to report html | |
| 19 ######### 3. path to files_path directory associated with the report output. | |
| 20 export TOOL_INSTALL_DIR='${__tool_directory__}' && | |
| 21 export REPORT='$report' && | |
| 22 export REPORT_FILES_PATH='$report.files_path' && | |
| 23 | |
| 24 ############ create a hidden file to store r markdown rendering log | |
| 25 touch $report.files_path/.r_rendering.log.txt && | |
| 26 | |
| 27 ############ finally run the render.R script | |
| 28 Rscript '${__tool_directory__}/rmarkdown_report_render.R' | |
| 29 | |
| 30 -o $report | |
| 31 -d $report.files_path | |
| 32 | |
| 33 -s '$sra_ids_se' | |
| 34 -p '$sra_ids_pe' | |
| 35 -f $format | |
| 36 | |
| 37 | |
| 38 ]]></command> | |
| 39 <inputs> | |
| 40 <param type="text" name="sra_ids_se" area="true" size="5x25" label="SRR/DRR/ERR accessions of single end SRA" | |
| 41 help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR039885"/> | |
| 42 <param type="text" name="sra_ids_pe" area="true" size="5x25" label="SRR/DRR/ERR accessions of paired end SRA" | |
| 43 help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. ERR1748507"/> | |
| 44 <param type="select" name="format" label="Output format"> | |
| 45 <option value="fastq" selected="true">fastq</option> | |
| 46 <option value="fasta">fasta</option> | |
| 47 </param> | |
| 48 </inputs> | |
| 49 <outputs> | |
| 1 | 50 <data format="html" name="report" label="${tool.name} report on ${on_string}"/> |
| 0 | 51 <!--list dataset collection for single end SRA data--> |
| 52 <collection type="list" name="list_collection" label="BDSS download data (single end reads)"> | |
| 53 <discover_datasets pattern="__name_and_ext__" directory="se_read_files_directory"/> | |
| 54 </collection> | |
| 55 <!--list:paired dataset collection for paired end SRA data--> | |
| 56 <collection type="list:paired" name="list:paired_collection" label="BDSS download data (paired end reads)"> | |
| 57 <discover_datasets | |
| 58 pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.(?P<ext>[^\._]+)?" | |
| 59 directory="pe_read_files_directory"/> | |
| 60 </collection> | |
| 61 </outputs> | |
| 62 <citations> | |
| 63 <citation type="bibtex"><![CDATA[ | |
| 64 @article{allaire2016rmarkdown, | |
| 65 title={rmarkdown: Dynamic Documents for R, 2016}, | |
| 66 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff | |
| 67 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, | |
| 68 journal={R package version 0.9}, | |
| 69 volume={6}, | |
| 70 year={2016} | |
| 71 } | |
| 72 ]]></citation> | |
| 73 <citation type="bibtex"><![CDATA[ | |
| 74 @book{xie2015dynamic, | |
| 75 title={Dynamic Documents with R and knitr}, | |
| 76 author={Xie, Yihui}, | |
| 77 volume={29}, | |
| 78 year={2015}, | |
| 79 publisher={CRC Press} | |
| 80 } | |
| 81 ]]></citation> | |
| 82 <citation type="bibtex"><![CDATA[ | |
| 83 @online{jstree, | |
| 84 author={Bozhanov, Ivan}, | |
| 85 year = 2018, | |
| 86 url = {https://www.jstree.com/} | |
| 87 } | |
| 88 ]]></citation> | |
| 89 </citations> | |
| 90 </tool> |