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comparison fastqc_report.xml @ 14:2efa46ce2c4c draft

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upgrade fastqc_report
author mingchen0919
date Wed, 18 Oct 2017 22:06:39 -0400
parents 9d3586701985
children d1d20f341632
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13:9d3586701985 14:2efa46ce2c4c
1 <tool id="fastqc_report" name="Fastqc report" version="1.0.1"> 1 <tool id="fastqc_report" name="Fastqc report" version="2.0.0">
2 <description> 2 <description>
3 Implements FastQC analysis and display results in R Markdown html. 3 Implements FastQC analysis and display results in R Markdown html.
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> 6 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
7 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement> 7 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
8 <requirement type="package" version="1.20.0">r-getopt</requirement> 8 <requirement type="package" version="1.20.0">r-getopt</requirement>
9 <requirement type="package" version="1.2">r-rmarkdown</requirement> 9 <requirement type="package" version="1.3">r-rmarkdown</requirement>
10 <requirement type="package" version="1.8.4">r-plyr</requirement> 10 <requirement type="package" version="1.8.4">r-plyr</requirement>
11 <requirement type="package" version="1.1.0">r-stringr</requirement> 11 <requirement type="package" version="1.1.0">r-stringr</requirement>
12 <requirement type="package" version="0.5.0">r-highcharter</requirement> 12 <requirement type="package" version="0.5.0">r-highcharter</requirement>
13 <requirement type="package" version="0.2">r-dt</requirement> 13 <requirement type="package" version="0.2">r-dt</requirement>
14 <requirement type="package" version="1.4.2">r-reshape2</requirement> 14 <requirement type="package" version="1.4.2">r-reshape2</requirement>
16 <requirement type="package" version="0.2.0.1">r-formattable</requirement> 16 <requirement type="package" version="0.2.0.1">r-formattable</requirement>
17 <requirement type="package" version="0.3.5">r-htmltools</requirement> 17 <requirement type="package" version="0.3.5">r-htmltools</requirement>
18 <requirement type="package" version="0.11.5">fastqc</requirement> 18 <requirement type="package" version="0.11.5">fastqc</requirement>
19 </requirements> 19 </requirements>
20 <stdio> 20 <stdio>
21 <regex match="Execution halted" 21 <!--redirecting stderr to a file. "XXX" is used to match with nothing so that tool running won't be interrupted during testing-->
22 source="both" 22 <regex match="XXX"
23 level="fatal" 23 source="stderr"
24 description="Execution halted." /> 24 level="warning"
25 <regex match="Error in" 25 description="Check the warnings_and_errors.txt file for more details."/>
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> 26 </stdio>
34 <command> 27 <command>
35 <![CDATA[ 28 <![CDATA[
36 29
37 Rscript '${__tool_directory__}/fastqc_report_render.R' 30 Rscript '${__tool_directory__}/fastqc_report_render.R'
31 -e $echo
38 -r $reads 32 -r $reads
39 -p '${__tool_directory__}/fastqc_report.Rmd' 33
40 -o $report 34 -o $report
41 -d $report.files_path 35 -d $report.files_path
36 -s $sink_message
42 37
43 -e $echo 38 -p '${__tool_directory__}/fastqc_report.Rmd'
44
45 ]]> 39 ]]>
46 </command> 40 </command>
47 <inputs> 41 <inputs>
48 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads" type="data" label="Short reads data from history" /> 42 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads" type="data"
49 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> 43 label="Short reads data from history"/>
44 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
45 label="Display analysis code in report?"/>
50 </inputs> 46 </inputs>
51 <outputs> 47 <outputs>
52 <data format="html" name="report" label="fastqc report" /> 48 <data format="html" name="report" label="fastqc report"/>
49 <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
53 </outputs> 50 </outputs>
54 <citations> 51 <citations>
55 <citation type="bibtex"> 52 <citation type="bibtex">
56 @misc{bioinformatics2014fastqc, 53 @misc{bioinformatics2014fastqc,
57 title={FastQC}, 54 title={FastQC},
60 } 57 }
61 </citation> 58 </citation>
62 <citation type="bibtex"> 59 <citation type="bibtex">
63 @article{allaire2016rmarkdown, 60 @article{allaire2016rmarkdown,
64 title={rmarkdown: Dynamic Documents for R, 2016}, 61 title={rmarkdown: Dynamic Documents for R, 2016},
65 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}, 62 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
63 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
66 journal={R package version 0.9}, 64 journal={R package version 0.9},
67 volume={6}, 65 volume={6},
68 year={2016} 66 year={2016}
69 } 67 }
70 </citation> 68 </citation>
78 } 76 }
79 </citation> 77 </citation>
80 <citation type="bibtex"> 78 <citation type="bibtex">
81 @misc{plotly2017, 79 @misc{plotly2017,
82 title = {plotly: Create Interactive Web Graphics via 'plotly.js'}, 80 title = {plotly: Create Interactive Web Graphics via 'plotly.js'},
83 author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy}, 81 author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and
82 Marianne Corvellec and Pedro Despouy},
84 year = {2017}, 83 year = {2017},
85 note = {R package version 4.6.0}, 84 note = {R package version 4.6.0},
86 url = {https://CRAN.R-project.org/package=plotly}, 85 url = {https://CRAN.R-project.org/package=plotly},
87 } 86 }
88 </citation> 87 </citation>