Mercurial > repos > mingchen0919 > aurora_dustmasker
comparison rmarkdown_report.xml @ 0:b8c76b06d724 draft
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author | mingchen0919 |
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date | Fri, 09 Nov 2018 13:29:21 -0500 |
parents | |
children | e0828838e0f3 |
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-1:000000000000 | 0:b8c76b06d724 |
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1 <tool id="aurora_dustmasker" name="aurora_dustmasker" version="1.0.0"> | |
2 <description>Low complexity region masker based on Symmetric DUST algorithm</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.15.0.6-0">pandoc</requirement><requirement type="package" version="1.20.0">r-getopt</requirement><requirement type="package" version="1.6">r-rmarkdown</requirement><requirement type="package" version="2.7.1">blast</requirement></requirements> | |
5 <command><![CDATA[ ######### each aurora tool generates a html file and have an files path directory associated with it. | |
6 mkdir -p $report.files_path && | |
7 | |
8 ######### three important paths: | |
9 ######### 1. path to tool installation directory | |
10 ######### 2. path to report html | |
11 ######### 3. path to files_path directory associated with the report output. | |
12 export TOOL_INSTALL_DIR='${__tool_directory__}' && | |
13 export REPORT='$report' && | |
14 export REPORT_FILES_PATH='$report.files_path' && | |
15 | |
16 ############ create a hidden file to store r markdown rendering log | |
17 touch $report.files_path/r_rendering.log.txt && | |
18 | |
19 ############ finally run the render.R script | |
20 Rscript '${__tool_directory__}/rmarkdown_report_render.R' | |
21 | |
22 -o $report | |
23 -d $report.files_path | |
24 | |
25 -A $input_fasta | |
26 -B $level | |
27 -C $linker | |
28 -D $input_format | |
29 -E $output_format | |
30 -F $parse_seqids | |
31 | |
32 -G $out | |
33 | |
34 | |
35 ]]></command> | |
36 <inputs> | |
37 <param type="data" name="input_fasta" argument="-in" label="Input file name" optional="False" format="fasta,fa"/><param type="integer" name="level" argument="-level" label="DUST level (score threshold for subwindows)" optional="False" value="20"/><param type="integer" name="linker" argument="-linker" label="DUST linker (how close masked intervals should be to get merged together)." optional="False" value="1"/><param type="integer" name="window_length" argument="window" label="DUST window length" optional="False" value="64"/><param type="select" name="input_format" label="Input format (possible values: fasta, blastdb)" optional="False" multiple="False"><option value="input_format_fasta" selected="true">fasta</option><option value="input_format_blastdb" selected="false">blastdb</option></param><param type="select" name="output_format" argument="-outfmt" label="Output format" optional="False" multiple="False"><option value="output_acclist" selected="false">acclist</option><option value="output_fasta" selected="false">fasta</option><option value="output_interval" selected="false">interval</option><option value="output_maskinfo_asn1_bin" selected="false">maskinfo_asn1_bin</option><option value="output_maskinfo_asn1_text" selected="false">maskinfo_asn1_text</option><option value="output_maskinfo_xml" selected="false">maskinfo_xml</option><option value="output_seqloc_asn1_bin" selected="false">output_seqloc_asn1_bin</option><option value="output_seqloc_asn1_text" selected="false">seqloc_asn1_text</option><option value="output_seqloc_xml" selected="false">seqloc_xml</option></param><param type="boolean" name="parse_seqids" argument="-parse_seqids" label="Parse Seq-ids in FASTA input" optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/></inputs> | |
38 <outputs> | |
39 <data format="html" name="report" label="${tool.name} report on ${on_string}"/><data name="out" label="${tool.name} on ${on_string}" hidden="false"/></outputs> | |
40 <citations> | |
41 <citation type="bibtex"><![CDATA[ | |
42 @article{allaire2016rmarkdown, | |
43 title={rmarkdown: Dynamic Documents for R, 2016}, | |
44 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff | |
45 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, | |
46 journal={R package version 0.9}, | |
47 volume={6}, | |
48 year={2016} | |
49 } | |
50 ]]></citation><citation type="bibtex"><![CDATA[ | |
51 @book{xie2015dynamic, | |
52 title={Dynamic Documents with R and knitr}, | |
53 author={Xie, Yihui}, | |
54 volume={29}, | |
55 year={2015}, | |
56 publisher={CRC Press} | |
57 } | |
58 ]]></citation><citation type="bibtex"><![CDATA[ | |
59 @online{jstree, | |
60 author={Bozhanov, Ivan}, | |
61 year = 2018, | |
62 url = {https://www.jstree.com/} | |
63 } | |
64 ]]></citation></citations> | |
65 </tool> |