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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
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">
2 <description>
3 Evaluate short reads with FastQC software on a single or a paired of untrimmed and trimmed reads
4 files.
5 </description>
6 <requirements>
7 <requirement type="package" version="2.5">pandoc</requirement>
8 <requirement type="package" version="1.20.2">r-getopt</requirement>
9 <requirement type="package" version="1.10">r-rmarkdown</requirement>
10 <requirement type="package" version="1.8.4">r-plyr</requirement>
11 <requirement type="package" version="1.3.1">r-stringr</requirement>
12 <requirement type="package" version="0.4">r-dt</requirement>
13 <requirement type="package" version="1.4.3">r-reshape2</requirement>
14 <requirement type="package" version="4.8.0">r-plotly</requirement>
15 <requirement type="package" version="0.3.6">r-htmltools</requirement>
16 <requirement type="package" version="0.11.5">fastqc</requirement>
17 <requirement type="package" version="0.9.10">xorg-libxrender</requirement>
18 <requirement type="package" version="1.2.3">xorg-libsm</requirement>
19 <requirement type="package" version="6.0">unzip</requirement>
20 </requirements>
21 <stdio>
22 <regex match="XXX" source="stderr" level="warning"
23 description="Check the warnings_and_errors.txt file for more details."/>
24 </stdio>
25 <command><![CDATA[
26
27 ######### each aurora tool generates a html file and have an files path directory associated with it.
28 mkdir -p $report.files_path &&
29
30 ######### three important paths:
31 ######### 1. path to tool installation directory
32 ######### 2. path to report html
33 ######### 3. path to files_path directory associated with the report output.
34 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
35 export REPORT='$report' &&
36 export REPORT_FILES_PATH='$report.files_path' &&
37
38 ############ copy jstree directory cp -r ${__tool_directory__}/vakata-jstree-3.3.5 ./ &&
39
40 ############ create a hidden file to store r markdown rendering log
41 touch $report.files_path/.r_rendering.log.txt &&
42
43 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
44
45 -o $report
46 -d $report.files_path
47
48 -r $reads_1
49 -n '$reads_1.name'
50 -R $reads_2
51 -N '$reads_2.name'
52 -c $contaminants
53 -l $limits
54
55 ]]></command>
56 <inputs>
57 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_1" type="data" optional="false"
58 label="Short reads before trimming"
59 help="Short reads data from history. This could be reads before trimming."/>
60 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_2" type="data" label="Short reads after trimming"
61 help="Short reads data from history. This could be reads after trimming."/>
62 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
63 help="Specifies a non-default file which contains the list of adapter sequences which will be explicitly
64 searched against the library. The file must contain sets of named adapters in the form name[tab]sequence.
65 Lines prefixed with a hash will be ignored."/>
66 <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
67 help="Specifies a non-default file which contains a set of criteria which will be used to determine the
68 warn/error limits for the various modules. This file can also be used to selectively remove some modules
69 from the output all together. The format needs to mirror the default limits.txt file found in the
70 Configuration folder."/>
71
72 </inputs>
73 <outputs>
74 <data format="html" name="report" label="${tool.name} on ${on_string}"/>
75 </outputs>
76 <citations>
77 <citation type="bibtex"><![CDATA[
78 @online{jstree,
79 author={Bozhanov, Ivan},
80 year = 2018,
81 url = {https://www.jstree.com/}
82 }
83 ]]></citation>
84 <citation type="bibtex"><![CDATA[
85 @misc{bioinformatics2014fastqc,
86 title={FastQC},
87 author={Bioinformatics, Babraham},
88 year={2014}
89 }
90 ]]></citation>
91 <citation type="bibtex"><![CDATA[
92 @article{allaire2016rmarkdown,
93 title={rmarkdown: Dynamic Documents for R, 2016},
94 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
95 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
96 journal={R package version 0.9},
97 volume={6},
98 year={2016}
99 }
100 ]]></citation>
101 <citation type="bibtex"><![CDATA[
102 @book{xie2015dynamic,
103 title={Dynamic Documents with R and knitr},
104 author={Xie, Yihui},
105 volume={29},
106 year={2015},
107 publisher={CRC Press}
108 }
109 ]]></citation>
110 </citations>
111 </tool>