Mercurial > repos > mingchen0919 > rmarkdown_fastqc_site

annotate fastqc_site.xml @ 10:600c39b11913 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit 60ea96204588be4348bd5d7879d1eb0d73f487c7-dirty
author mingchen0919
date Tue, 15 Aug 2017 15:50:21 -0400
parents 848cf699c443
children 507eec497730
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d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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1 <tool id="fastqc_site" name="Fastqc Site" version="1.0.0">
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2 <requirements>
9
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3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
7
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4 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
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6 <requirement type="package" version="1.2">r-rmarkdown</requirement>
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7 <requirement type="package" version="1.8.4">r-plyr</requirement>
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8 <requirement type="package" version="1.1.0">r-stringr</requirement>
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9 <requirement type="package" version="0.5.0">r-highcharter</requirement>
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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10 <requirement type="package" version="0.2">r-dt</requirement>
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11 <requirement type="package" version="1.4.2">r-reshape2</requirement>
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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12 <requirement type="package" version="4.5.6">r-plotly</requirement>
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13 <requirement type="package" version="0.2.0.1">r-formattable</requirement>
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14 <requirement type="package" version="0.3.5">r-htmltools</requirement>
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15 <requirement type="package" version="0.11.5">fastqc</requirement>
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16 </requirements>
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17 <description>
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18 Implements FastQC analysis and display results in R Markdown website.
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19 </description>
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20 <stdio>
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21 <regex match="Execution halted"
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22 source="both"
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23 level="fatal"
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24 description="Execution halted." />
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25 <regex match="Error in"
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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26 source="both"
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27 level="fatal"
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28 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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29 <regex match="Fatal error"
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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30 source="both"
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31 level="fatal"
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32 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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33 </stdio>
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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34 <command>
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35 <![CDATA[
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36
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37 Rscript '${__tool_directory__}/fastqc_site_render.R'
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38
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39 ## 1. input data
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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40 -r $reads
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41 -e $echo
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42
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43 ## 2. output report and report site directory
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44 -o $fastqc_site
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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45 -d $fastqc_site.files_path
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46
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47 ## 3. Rmd templates sitting in the tool directory
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48
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49 ## _site.yml and index.Rmd template files
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50 -s '${__tool_directory__}/_site.yml'
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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51 -i '${__tool_directory__}/index.Rmd'
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52
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53 ## other Rmd body template files
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54 -p '${__tool_directory__}/01_evaluation_overview.Rmd'
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55 -a '${__tool_directory__}/02_fastqc_original_reports.Rmd'
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56 -b '${__tool_directory__}/1_per_base_quality_scores.Rmd'
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57 -c '${__tool_directory__}/2_per_base_N_content.Rmd'
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58 -f '${__tool_directory__}/3_per_sequence_quality_scores.Rmd'
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59 -g '${__tool_directory__}/4_per_sequence_GC_content.Rmd'
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60 -h '${__tool_directory__}/5_per_base_sequence_content.Rmd'
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61
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62 ]]>
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63 </command>
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64 <inputs>
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65 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" multiple="true" name="reads" type="data" label="Short reads data from history" />
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66 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
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67 </inputs>
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68 <outputs>
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69 <data format="html" name="fastqc_site" label="fastqc site" />
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70 </outputs>
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71 <citations>
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72 <citation type="bibtex">
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73 @misc{bioinformatics2014fastqc,
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74 title={FastQC},
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75 author={Bioinformatics, Babraham},
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76 year={2014}
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77 }
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78 </citation>
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79 <citation type="bibtex">
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80 @article{allaire2016rmarkdown,
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81 title={rmarkdown: Dynamic Documents for R, 2016},
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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},
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83 journal={R package version 0.9},
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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84 volume={6},
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85 year={2016}
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86 }
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87 </citation>
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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88 <citation type="bibtex">
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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89 @book{xie2015dynamic,
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90 title={Dynamic Documents with R and knitr},
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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91 author={Xie, Yihui},
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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92 volume={29},
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93 year={2015},
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94 publisher={CRC Press}
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95 }
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96 </citation>
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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97 <citation type="bibtex">
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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98 @misc{plotly2017,
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99 title = {plotly: Create Interactive Web Graphics via 'plotly.js'},
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100 author = {Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy},
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101 year = {2017},
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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102 note = {R package version 4.6.0},
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103 url = {https://CRAN.R-project.org/package=plotly},
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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104 }
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105 </citation>
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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106 <citation type="bibtex">
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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107 @misc{highcharter2017,
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108 title = {highcharter: A Wrapper for the 'Highcharts' Library},
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109 author = {Joshua Kunst},
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110 year = {2017},
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111 note = {R package version 0.5.0},
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112 url = {https://CRAN.R-project.org/package=highcharter},
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113 }
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114 </citation>
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115 <citation type="bibtex">
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116 @misc{formattable2016,
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117 title = {formattable: Create 'Formattable' Data Structures},
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118 author = {Kun Ren and Kenton Russell},
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119 year = {2016},
d820be692d74 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastqc_site commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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120 note = {R package version 0.2.0.1},
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121 url = {https://CRAN.R-project.org/package=formattable},
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122 }
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123 </citation>
10
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124 <citation>
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125 @article{ewels2016multiqc,
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126 title={MultiQC: summarize analysis results for multiple tools and samples in a single report},
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127 author={Ewels, Philip and Magnusson, M{\aa}ns and Lundin, Sverker and K{\"a}ller, Max},
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128 journal={Bioinformatics},
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129 volume={32},
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130 number={19},
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131 pages={3047--3048},
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132 year={2016},
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133 publisher={Oxford University Press}
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134 }
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135 </citation>
7
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136 </citations>
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137 </tool>