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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Fri, 14 Dec 2018 00:40:15 -0500
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1 <tool name="aurora_skewer" id='aurora_skewer_report' version="2.0.1">
2 <description>A fast and accurate adapter trimmer for next-generation sequencing single or paired end reads.
3 </description>
4 <requirements>
5 <requirement type="package" version="2.5">pandoc</requirement>
6 <requirement type="package" version="1.20.2">r-getopt</requirement>
7 <requirement type="package" version="1.10">r-rmarkdown</requirement>
8 <requirement type="package" version="0.2.2">skewer</requirement>
9 <requirement type="package" version="4.5.6">r-plotly</requirement>
10 </requirements>
11 <command><![CDATA[
12
13 ######### each aurora tool generates a html file and have an files path directory associated with it.
14 mkdir -p $report.files_path &&
15
16 ######### three important paths:
17 ######### 1. path to tool installation directory
18 ######### 2. path to report html
19 ######### 3. path to files_path directory associated with the report output.
20 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
21 export REPORT='$report' &&
22 export REPORT_FILES_PATH='$report.files_path' &&
23
24 ############ create a hidden file to store r markdown rendering log
25 touch $report.files_path/.r_rendering.log.txt &&
26
27 ############ finally run the render.R script
28 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
29
30 -o $report
31 -d $report.files_path
32
33 -A '$first_reads'
34 -B '$second_reads'
35 -x '$adapter_first_reads'
36 -y '$adapter_second_reads'
37 -m '$trimming_mode'
38 -r '$maximum_allowed_error_rate'
39 -D '$maximum_allowed_indel_error_rate'
40 -q '$quality_trimming_3_end'
41 -Q '$mean_quality'
42 -l '$minimum_read_length'
43 -j '$advanced_options.junction_adapter'
44 -M '$advanced_options.tab_adapter'
45 -b '$advanced_options.barcode'
46 -c '$advanced_options.cut'
47 -n '$advanced_options.filter_degenerative_reads'
48 -u '$advanced_options.filter_undetermined_mate_pair_reads'
49 -f '$advanced_options.format'
50 -z '$advanced_options.compress'
51 -E '$advanced_options.qiime'
52 -F '$advanced_options.quiet'
53 -i '$advanced_options.intelligent'
54 -1 '$trimmed_r1'
55 -2 '$trimmed_r2'
56 -3 '$trimmed_s'
57
58
59 ]]></command>
60 <inputs>
61 <param type="data" name="first_reads" label="First reads" optional="False" format="fastq,fastqsanger"
62 multiple="False"/>
63 <param type="data" name="second_reads" label="Second reads"
64 help="If it is single end reads, ignore this input field and use the &quot;first reads&quot; field only."
65 optional="True" format="fastq,fastqsanger" multiple="False"/>
66 <param type="data" name="adapter_first_reads" argument="-x" label="Adapter sequence/file for the first reads."
67 optional="True" format="fasta,fa" multiple="False"/>
68 <param type="data" name="adapter_second_reads" argument="-y" label="Adapter sequence/file for the second reads"
69 optional="True" format="fasta,fa" multiple="False"/>
70 <param type="select" name="trimming_mode" argument="-m" label="trimming mode" optional="False" multiple="False">
71 <option value="None" selected="true">--select a model--</option>
72 <option value="head" selected="false">5&#x2019; end trimming (single end reads)</option>
73 <option value="tail" selected="false">3&#x2019; end trimming (single end reads)</option>
74 <option value="any" selected="false">anywhere adapter detection and trimming (single end reads)</option>
75 <option value="pe" selected="false">paired-end trimming</option>
76 <option value="mp" selected="false">mate-pair trimming</option>
77 <option value="ap" selected="false">amplicon trimming</option>
78 </param>
79 <param type="float" name="maximum_allowed_error_rate" argument="-r" label="Maximum allowed error rate"
80 optional="False" value="0.1" min="0" max="0.5"/>
81 <param type="float" name="maximum_allowed_indel_error_rate" argument="-d"
82 label="Maximum allowed indel error rate"
83 help="The valid range of indel error rate is [0, maximum allowed error rate]" optional="False"
84 value="0.03" min="0"/>
85 <param type="integer" name="quality_trimming_3_end" argument="-q" label="3&#x2019; end quality trimming"
86 optional="False" value="0"/>
87 <param type="integer" name="mean_quality" argument="-Q" label="Reads filtering by average quality"
88 optional="False" value="0"/>
89 <param type="integer" name="minimum_read_length" argument="-l"
90 label="Minimum read length allowed after trimming" optional="False" value="18"/>
91 <section name="advanced_options" title="Advanced options" expanded="False">
92 <param type="data" name="junction_adapter" argument="-j"
93 label="Junction adapter sequence/file for Nextera Mate Pair reads" optional="True" format="fasta,fa"
94 multiple="False"/>
95 <param type="text" name="tab_adapter" argument="-M"
96 label="TAB delimited file indicates valid forward/reverse adapter pairing" optional="True"/>
97 <param type="boolean" name="barcode" argument="-b"
98 label="Whether to demultiplex reads according to adapters/primers" optional="False" checked="False"
99 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
100 <param type="text" name="cut" argument="-c"
101 label="To hard clip off the 5&#x2019; leading bases of the forward primer and reverse primer respectively as the barcodes in amplicon mode"
102 optional="False" value="0, 0"/>
103 <param type="boolean" name="filter_degenerative_reads" argument="-n"
104 label="Whether to filter out highly degenerative reads" optional="False" checked="False"
105 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
106 <param type="boolean" name="filter_undetermined_mate_pair_reads" argument="-u"
107 label="Whether to filter out undetermined mate-pair reads" optional="False" checked="False"
108 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
109 <param type="select" name="format" argument="-f" label="Format of FASTQ quality value" optional="False"
110 multiple="False">
111 <option value="sanger" selected="false">sanger</option>
112 <option value="solexa" selected="false">solexa</option>
113 <option value="auto" selected="true">auto</option>
114 </param>
115 <param type="boolean" name="compress" argument="-z" label="Whether to compress output in GZIP format"
116 optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
117 <param type="boolean" name="qiime" argument="-qiime" label="Whether to prepare files required by QIIME"
118 optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
119 <param type="boolean" name="quiet" argument="--quiet" label="Whether in quiet mode" optional="False"
120 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
121 <param type="boolean" name="intelligent" argument="-i" label="Whether to intelligently redistribute reads"
122 optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
123 </section>
124 </inputs>
125 <outputs>
126 <data name="report" format="html" label="${tool.name} report on ${on_string}" hidden="false"/>
127 <data name="trimmed_r1" format="fastq" label="${tool.name} trimmed first reads on ${on_string}" hidden="false"/>
128 <data name="trimmed_r2" format="fastq" label="${tool.name} trimmed second reads on ${on_string}"
129 hidden="false"/>
130 <data name="trimmed_s" format="fastq" label="${tool.name} trimmed single end reads on ${on_string}"
131 hidden="false"/>
132 </outputs>
133 <help>
134 <![CDATA[Read the `tool manual <http://download2.nust.na/pub4/sourceforge/s/project/sk/skewer/skewer_manual.pdf>`_ if you are not sure what parameter values to use.]]></help>
135 <citations>
136 <citation type="bibtex"><![CDATA[
137 @article{allaire2016rmarkdown,
138 title={rmarkdown: Dynamic Documents for R, 2016},
139 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
140 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
141 journal={R package version 0.9},
142 volume={6},
143 year={2016}
144 }
145 ]]></citation>
146 <citation type="bibtex"><![CDATA[
147 @book{xie2015dynamic,
148 title={Dynamic Documents with R and knitr},
149 author={Xie, Yihui},
150 volume={29},
151 year={2015},
152 publisher={CRC Press}
153 }
154 ]]></citation>
155 <citation type="bibtex"><![CDATA[
156 @online{jstree,
157 author={Bozhanov, Ivan},
158 year = 2018,
159 url = {https://www.jstree.com/}
160 }
161 ]]></citation>
162 </citations>
163 </tool>