Mercurial > repos > mingchen0919 > rmarkdown_fastqc_site

comparison fastqc_site.xml @ 0:d732d4526c6d draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit ddb1f6aca7619aea2e660b1729367841b56ba4c9-dirty
author mingchen0919
date Tue, 08 Aug 2017 10:14:46 -0400
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children 1fea15ac7532
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1 <tool id="fastqc_site" name="Fastqc Site" version="1.0.0">
2 <requirements>
3 <requirement type="package" version="1.15.2">pandoc</requirement>
4 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
5 <requirement type="package" version="1.20.0">r-getopt</requirement>
6 <requirement type="package" version="1.2">r-rmarkdown</requirement>
7 <requirement type="package" version="1.8.4">r-plyr</requirement>
8 <requirement type="package" version="1.1.0">r-stringr</requirement>
9 <requirement type="package" version="0.5.0">r-highcharter</requirement>
10 <requirement type="package" version="0.2">r-dt</requirement>
11 <requirement type="package" version="1.4.2">r-reshape2</requirement>
12 <requirement type="package" version="4.5.6">r-plotly</requirement>
13 <requirement type="package" version="0.2.0.1">r-formattable</requirement>
14 <requirement type="package" version="0.3.5">r-htmltools</requirement>
15 <requirement type="package" version="0.11.5">fastqc</requirement>
16 </requirements>
17 <description>
18 Implements FastQC analysis and display results in R Markdown website.
19 </description>
20 <stdio>
21 <regex match="Execution halted"
22 source="both"
23 level="fatal"
24 description="Execution halted." />
25 <regex match="Error in"
26 source="both"
27 level="fatal"
28 description="An undefined error occured, please check your intput carefully and contact your administrator." />
29 <regex match="Fatal error"
30 source="both"
31 level="fatal"
32 description="An undefined error occured, please check your intput carefully and contact your administrator." />
33 </stdio>
34 <command>
35 <![CDATA[
36
37 Rscript '${__tool_directory__}/fastqc_site_render.R'
38
39 ## 1. input data
40 -r $reads
41 -e $echo
42
43 ## 2. output report and report site directory
44 -o $fastqc_site
45 -d $fastqc_site.files_path
46
47 ## 3. Rmd templates sitting in the tool directory
48
49 ## _site.yml and index.Rmd template files
50 -s '${__tool_directory__}/_site.yml'
51 -i '${__tool_directory__}/index.Rmd'
52
53 ## other Rmd body template files
54 -p '${__tool_directory__}/01_evaluation_overview.Rmd'
55 -a '${__tool_directory__}/02_fastqc_original_reports.Rmd'
56 -b '${__tool_directory__}/1_per_base_quality_scores.Rmd'
57 -c '${__tool_directory__}/2_per_base_N_content.Rmd'
58 -f '${__tool_directory__}/3_per_sequence_quality_scores.Rmd'
59 -g '${__tool_directory__}/4_per_sequence_GC_content.Rmd'
60 -h '${__tool_directory__}/5_per_base_sequence_content.Rmd'
61
62 ]]>
63 </command>
64 <inputs>
65 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" multiple="true" name="reads" type="data" label="Short reads data from history" />
66 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
67 </inputs>
68 <outputs>
69 <data format="html" name="fastqc_site" label="fastqc site" />
70 </outputs>
71 <citations>
72 <citation type="bibtex">
73 @misc{bioinformatics2014fastqc,
74 title={FastQC},
75 author={Bioinformatics, Babraham},
76 year={2014}
77 }
78 </citation>
79 <citation type="bibtex">
80 @article{allaire2016rmarkdown,
81 title={rmarkdown: Dynamic Documents for R, 2016},
82 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
83 journal={R package version 0.9},
84 volume={6},
85 year={2016}
86 }
87 </citation>
88 <citation type="bibtex">
89 @book{xie2015dynamic,
90 title={Dynamic Documents with R and knitr},
91 author={Xie, Yihui},
92 volume={29},
93 year={2015},
94 publisher={CRC Press}
95 }
96 </citation>
97 <citation type="bibtex">
98 @Manual{,
99 title = {plotly: Create Interactive Web Graphics via 'plotly.js'},
100 author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy},
101 year = {2017},
102 note = {R package version 4.6.0},
103 url = {https://CRAN.R-project.org/package=plotly},
104 }
105 </citation>
106 <citation type="bibtex">
107 @Manual{,
108 title = {highcharter: A Wrapper for the 'Highcharts' Library},
109 author = {Joshua Kunst},
110 year = {2017},
111 note = {R package version 0.5.0},
112 url = {https://CRAN.R-project.org/package=highcharter},
113 }
114 </citation>
115 <citation type="bibtex">
116 @Manual{,
117 title = {formattable: Create 'Formattable' Data Structures},
118 author = {Kun Ren and Kenton Russell},
119 year = {2016},
120 note = {R package version 0.2.0.1},
121 url = {https://CRAN.R-project.org/package=formattable},
122 }
123 </citation>
124 </citations>
125 </tool>