Mercurial > repos > mingchen0919 > aurora_fastqc_site

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author mingchen0919
date Sun, 30 Dec 2018 12:48:14 -0500
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1 <tool name="aurora_fastqc_site" id='aurora_fastqc_site' version="2.2.1">
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2 <description>
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3 Evaluate short reads with FastQC software on a single or a paired of untrimmed and trimmed reads
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4 files.
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5 </description>
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6 <requirements>
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7 <requirement type="package" version="2.5">pandoc</requirement>
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8 <requirement type="package" version="1.20.2">r-getopt</requirement>
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9 <requirement type="package" version="1.10">r-rmarkdown</requirement>
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10 <requirement type="package" version="1.8.4">r-plyr</requirement>
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11 <requirement type="package" version="1.3.1">r-stringr</requirement>
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12 <requirement type="package" version="0.4">r-dt</requirement>
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13 <requirement type="package" version="1.4.3">r-reshape2</requirement>
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14 <requirement type="package" version="4.8.0">r-plotly</requirement>
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15 <requirement type="package" version="0.3.6">r-htmltools</requirement>
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16 <requirement type="package" version="0.11.5">fastqc</requirement>
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17 <requirement type="package" version="0.9.10">xorg-libxrender</requirement>
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18 <requirement type="package" version="1.2.3">xorg-libsm</requirement>
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19 <requirement type="package" version="6.0">unzip</requirement>
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20 </requirements>
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21 <stdio>
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22 <regex match="XXX" source="stderr" level="warning"
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23 description="Check the warnings_and_errors.txt file for more details."/>
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24 </stdio>
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25 <command><![CDATA[
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26
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27 ######### each aurora tool generates a html file and have an files path directory associated with it.
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28 mkdir -p $report.files_path &&
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29
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30 ######### three important paths:
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31 ######### 1. path to tool installation directory
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32 ######### 2. path to report html
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33 ######### 3. path to files_path directory associated with the report output.
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34 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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35 export REPORT='$report' &&
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36 export REPORT_FILES_PATH='$report.files_path' &&
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37
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38 ############ copy jstree directory cp -r ${__tool_directory__}/vakata-jstree-3.3.5 ./ &&
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39
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40 ############ create a hidden file to store r markdown rendering log
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41 touch $report.files_path/.r_rendering.log.txt &&
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42
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43 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
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44
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45 -o $report
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46 -d $report.files_path
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47
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48 -r $reads_1
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49 -n '$reads_1.name'
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50 -R $reads_2
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51 -N '$reads_2.name'
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52 -c $contaminants
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53 -l $limits
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54
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55 ]]></command>
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56 <inputs>
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57 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_1" type="data" optional="false"
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58 label="Short reads before trimming"
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59 help="Short reads data from history. This could be reads before trimming."/>
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60 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_2" type="data" label="Short reads after trimming"
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61 help="Short reads data from history. This could be reads after trimming."/>
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62 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
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63 help="Specifies a non-default file which contains the list of adapter sequences which will be explicitly
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64 searched against the library. The file must contain sets of named adapters in the form name[tab]sequence.
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65 Lines prefixed with a hash will be ignored."/>
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66 <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
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67 help="Specifies a non-default file which contains a set of criteria which will be used to determine the
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68 warn/error limits for the various modules. This file can also be used to selectively remove some modules
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69 from the output all together. The format needs to mirror the default limits.txt file found in the
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70 Configuration folder."/>
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71
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72 </inputs>
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73 <outputs>
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74 <data format="html" name="report" label="${tool.name} on ${on_string}"/>
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75 </outputs>
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76 <citations>
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77 <citation type="bibtex"><![CDATA[
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78 @online{jstree,
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79 author={Bozhanov, Ivan},
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80 year = 2018,
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81 url = {https://www.jstree.com/}
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82 }
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83 ]]></citation>
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84 <citation type="bibtex"><![CDATA[
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85 @misc{bioinformatics2014fastqc,
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86 title={FastQC},
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87 author={Bioinformatics, Babraham},
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88 year={2014}
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89 }
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90 ]]></citation>
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91 <citation type="bibtex"><![CDATA[
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92 @article{allaire2016rmarkdown,
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93 title={rmarkdown: Dynamic Documents for R, 2016},
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94 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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95 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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96 journal={R package version 0.9},
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97 volume={6},
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98 year={2016}
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99 }
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100 ]]></citation>
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101 <citation type="bibtex"><![CDATA[
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102 @book{xie2015dynamic,
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103 title={Dynamic Documents with R and knitr},
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104 author={Xie, Yihui},
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105 volume={29},
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106 year={2015},
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107 publisher={CRC Press}
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108 }
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109 ]]></citation>
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110 </citations>
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111 </tool>