comparison rmarkdown_report.xml @ 0:0aeed70b3bc5 draft default tip

planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Fri, 14 Dec 2018 00:38:44 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:0aeed70b3bc5
1 <tool name="aurora_fastqc" id='aurora_fastqc' version="2.1.2">
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 ############ create a hidden file to store r markdown rendering log
39 touch $report.files_path/.r_rendering.log.txt &&
40
41 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
42
43 -o $report
44 -d $report.files_path
45
46 -r $reads_1
47 -n '$reads_1.name'
48 -R $reads_2
49 -N '$reads_2.name'
50 -c $contaminants
51 -l $limits
52
53 ]]></command>
54 <inputs>
55 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_1" type="data" optional="false"
56 label="Short reads before trimming"
57 help="Short reads data from history. This could be reads before trimming."/>
58 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_2" type="data" label="Short reads after trimming"
59 help="Short reads data from history. This could be reads after trimming."/>
60 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
61 help="Specifies a non-default file which contains the list of adapter sequences which will be explicitly
62 searched against the library. The file must contain sets of named adapters in the form name[tab]sequence.
63 Lines prefixed with a hash will be ignored."/>
64 <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
65 help="Specifies a non-default file which contains a set of criteria which will be used to determine the
66 warn/error limits for the various modules. This file can also be used to selectively remove some modules
67 from the output all together. The format needs to mirror the default limits.txt file found in the
68 Configuration folder."/>
69
70 </inputs>
71 <outputs>
72 <data format="html" name="report" label="${tool.name} on ${on_string}"/>
73 </outputs>
74 <citations>
75 <citation type="bibtex"><![CDATA[
76 @misc{bioinformatics2014fastqc,
77 title={FastQC},
78 author={Bioinformatics, Babraham},
79 year={2014}
80 }
81 ]]></citation>
82 <citation type="bibtex"><![CDATA[
83 @article{allaire2016rmarkdown,
84 title={rmarkdown: Dynamic Documents for R, 2016},
85 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
86 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
87 journal={R package version 0.9},
88 volume={6},
89 year={2016}
90 }
91 ]]></citation>
92 <citation type="bibtex"><![CDATA[
93 @book{xie2015dynamic,
94 title={Dynamic Documents with R and knitr},
95 author={Xie, Yihui},
96 volume={29},
97 year={2015},
98 publisher={CRC Press}
99 }
100 ]]></citation>
101 <citation type="bibtex"><![CDATA[
102 @online{jstree,
103 author={Bozhanov, Ivan},
104 year = 2018,
105 url = {https://www.jstree.com/}
106 }
107 ]]></citation>
108 </citations>
109 </tool>