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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 12:52:51 -0500
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1 <tool name="aurora_htseq_site" id='aurora_htseq_site_report' version="2.0.1">
2 <description>
3 counting reads in features
4 </description>
5 <requirements>
6 <requirement type="package" version="1.15.0.6">pandoc</requirement>
7 <requirement type="package" version="1.20.2">r-getopt</requirement>
8 <requirement type="package" version="1.10">r-rmarkdown</requirement>
9 <requirement type="package" version="0.11.0">htseq</requirement>
10 <requirement type="package" version="0.4">r-dt</requirement>
11 </requirements>
12 <command><![CDATA[
13
14 ######### each aurora tool generates a html file and have an files path directory associated with it.
15 mkdir -p $report.files_path &&
16
17 ######### three important paths:
18 ######### 1. path to tool installation directory
19 ######### 2. path to report html
20 ######### 3. path to files_path directory associated with the report output.
21 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
22 export REPORT='$report' &&
23 export REPORT_FILES_PATH='$report.files_path' &&
24
25 ############ create a hidden file to store r markdown rendering log
26 touch $report.files_path/.r_rendering.log.txt &&
27
28 ############ finally run the render.R script
29 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
30
31 -o $report
32 -d $report.files_path
33
34 -A '$alignment_files'
35 -B '$sample_names'
36 -G $gff
37 -f $format
38 -r $order
39 -S $stranded
40 -a $minaqual
41 -T $feature_type
42 -i $idattr
43 -m $mode
44 -c $count
45
46
47 ]]></command>
48 <inputs>
49 <param type="data" name="alignment_files" label="Alignment file (SAM/BAM)" optional="False" format="sam,bam"
50 multiple="True"/>
51 <param type="text" name="sample_names" label="Sample names"
52 help="sample names for each input SAM/BAM file. Use comma to separate multiple names, for example, sample_1, sample_2, sample_3. The number of sample names should be the same as the number of input SAM/BAM files."
53 optional="False" size="5x25"/>
54 <param type="select" name="format" argument="-f" label="Input data format" optional="False" multiple="False">
55 <option value="sam" selected="false">SAM</option>
56 <option value="bam" selected="true">BAM</option>
57 </param>
58 <param type="data" name="gff" label="GFF file" optional="False" format="gff,gff3"/>
59 <param type="select" name="order" argument="-r" label="Order"
60 help="Use this option to indicate how the input data has been sorted. The default is name.&#13;&#10;&#13;&#10;"
61 optional="False" multiple="False">
62 <option value="name" selected="false">Name</option>
63 <option value="pos" selected="false">Position</option>
64 </param>
65 <param type="select" name="stranded" argument="-s" label="Stranded" optional="False" multiple="False">
66 <option value="yes" selected="true">Yes</option>
67 <option value="no" selected="false">No</option>
68 <option value="reverse" selected="false">Reverse</option>
69 </param>
70 <param type="integer" name="minaqual" argument="-a" label="Alignment quality "
71 help="Skip all reads with alignment quality lower than the given minimum value (default: 10)"
72 optional="False" value="10" min="0"/>
73 <param type="text" name="feature_type" argument="-t" label="Feature type"
74 help="Feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for RNA-Seq analysis using an Ensembl GTF file: exon)"
75 optional="False" value="exon"/>
76 <param type="text" name="idattr" argument="-i" label="ID attribute"
77 help="GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table. The default, suitable for RNA-Seq analysis using an Ensembl GTF file, is gene_id."
78 optional="False" value="gene_id"/>
79 <param type="select" name="mode" argument="-m" label="Mode"
80 help="Mode to handle reads overlapping more than one feature. Possible values for &lt;mode&gt; are union, intersection-strict and intersection-nonempty (default: union)"
81 optional="False" multiple="False">
82 <option value="union" selected="true">Union</option>
83 <option value="intersection-strict" selected="false">Intersection (strict)</option>
84 <option value="intersection-nonempty" selected="false">Intersection (nonempty)</option>
85 </param>
86 </inputs>
87 <outputs>
88 <data name="report" format="html" label="${tool.name} report on ${on_string}" hidden="false"/>
89 <data name="count" format="csv" label="${tool.name} txt count on ${on_string}" hidden="false"/>
90 </outputs>
91 <citations>
92 <citation type="bibtex"><![CDATA[
93 @article{allaire2016rmarkdown,
94 title={rmarkdown: Dynamic Documents for R, 2016},
95 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
96 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
97 journal={R package version 0.9},
98 volume={6},
99 year={2016}
100 }
101 ]]></citation>
102 <citation type="bibtex"><![CDATA[
103 @book{xie2015dynamic,
104 title={Dynamic Documents with R and knitr},
105 author={Xie, Yihui},
106 volume={29},
107 year={2015},
108 publisher={CRC Press}
109 }
110 ]]></citation>
111 <citation type="bibtex"><![CDATA[
112 @online{jstree,
113 author={Bozhanov, Ivan},
114 year = 2018,
115 url = {https://www.jstree.com/}
116 }
117 ]]></citation>
118 <citation type="bibtex"><![CDATA[
119 @article{anders2015htseq,
120 title={HTSeq—a Python framework to work with high-throughput sequencing data},
121 author={Anders, Simon and Pyl, Paul Theodor and Huber, Wolfgang},
122 journal={Bioinformatics},
123 volume={31},
124 number={2},
125 pages={166--169},
126 year={2015},
127 publisher={Oxford University Press}
128 }
129 ]]></citation>
130 </citations>
131 </tool>