Mercurial > repos > mingchen0919 > aurora_skewer_site

annotate rmarkdown_report.xml @ 0:a42e58c71e5b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 12:55:49 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
1 <tool name="aurora_skewer_site" id='aurora_skewer_site_report' version="2.0.1">
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
2 <description>A fast and accurate adapter trimmer for next-generation sequencing single or paired end reads.
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
3 </description>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
4 <requirements>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
5 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
6 <requirement type="package" version="1.20.0">r-getopt</requirement>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
7 <requirement type="package" version="1.6">r-rmarkdown</requirement>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
8 <requirement type="package" version="0.2.2">skewer</requirement>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
9 <requirement type="package" version="4.5.6">r-plotly</requirement>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
10 </requirements>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
11 <command><![CDATA[
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
12
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
13 ######### each aurora tool generates a html file and have an files path directory associated with it.
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
14 mkdir -p $report.files_path &&
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
15
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
16 ######### three important paths:
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
17 ######### 1. path to tool installation directory
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
18 ######### 2. path to report html
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
19 ######### 3. path to files_path directory associated with the report output.
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
20 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
21 export REPORT='$report' &&
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
22 export REPORT_FILES_PATH='$report.files_path' &&
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
23
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
24 ############ create a hidden file to store r markdown rendering log
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
25 touch $report.files_path/.r_rendering.log.txt &&
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
26
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
27 ############ finally run the render.R script
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
28 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
29
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
30 -o $report
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
31 -d $report.files_path
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
32
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
33 -A '$first_reads'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
34 -B '$second_reads'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
35 -x '$adapter_first_reads'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
36 -y '$adapter_second_reads'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
37 -m '$trimming_mode'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
38 -r '$maximum_allowed_error_rate'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
39 -D '$maximum_allowed_indel_error_rate'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
40 -q '$quality_trimming_3_end'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
41 -Q '$mean_quality'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
42 -l '$minimum_read_length'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
43 -j '$advanced_options.junction_adapter'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
44 -M '$advanced_options.tab_adapter'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
45 -b '$advanced_options.barcode'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
46 -c '$advanced_options.cut'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
47 -n '$advanced_options.filter_degenerative_reads'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
48 -u '$advanced_options.filter_undetermined_mate_pair_reads'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
49 -f '$advanced_options.format'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
50 -z '$advanced_options.compress'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
51 -E '$advanced_options.qiime'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
52 -F '$advanced_options.quiet'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
53 -i '$advanced_options.intelligent'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
54 -1 '$trimmed_r1'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
55 -2 '$trimmed_r2'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
56 -3 '$trimmed_s'
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
57
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
58
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
59 ]]></command>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
60 <inputs>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
61 <param type="data" name="first_reads" label="First reads" optional="False" format="fastq,fastqsanger"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
62 multiple="False"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
63 <param type="data" name="second_reads" label="Second reads"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
64 help="If it is single end reads, ignore this input field and use the &quot;first reads&quot; field only."
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
65 optional="True" format="fastq,fastqsanger" multiple="False"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
66 <param type="data" name="adapter_first_reads" argument="-x" label="Adapter sequence/file for the first reads."
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
67 optional="True" format="fasta,fa" multiple="False"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
68 <param type="data" name="adapter_second_reads" argument="-y" label="Adapter sequence/file for the second reads"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
69 optional="True" format="fasta,fa" multiple="False"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
70 <param type="select" name="trimming_mode" argument="-m" label="trimming mode" optional="False" multiple="False">
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
71 <option value="None" selected="true">--select a model--</option>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
72 <option value="head" selected="false">5&#x2019; end trimming (single end reads)</option>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
73 <option value="tail" selected="false">3&#x2019; end trimming (single end reads)</option>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
74 <option value="any" selected="false">anywhere adapter detection and trimming (single end reads)</option>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
75 <option value="pe" selected="false">paired-end trimming</option>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
76 <option value="mp" selected="false">mate-pair trimming</option>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
77 <option value="ap" selected="false">amplicon trimming</option>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
78 </param>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
79 <param type="float" name="maximum_allowed_error_rate" argument="-r" label="Maximum allowed error rate"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
80 optional="False" value="0.1" min="0" max="0.5"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
81 <param type="float" name="maximum_allowed_indel_error_rate" argument="-d"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
82 label="Maximum allowed indel error rate"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
83 help="The valid range of indel error rate is [0, maximum allowed error rate]" optional="False"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
84 value="0.03" min="0"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
85 <param type="integer" name="quality_trimming_3_end" argument="-q" label="3&#x2019; end quality trimming"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
86 optional="False" value="0"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
87 <param type="integer" name="mean_quality" argument="-Q" label="Reads filtering by average quality"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
88 optional="False" value="0"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
89 <param type="integer" name="minimum_read_length" argument="-l"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
90 label="Minimum read length allowed after trimming" optional="False" value="18"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
91 <section name="advanced_options" title="Advanced options" expanded="False">
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
92 <param type="data" name="junction_adapter" argument="-j"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
93 label="Junction adapter sequence/file for Nextera Mate Pair reads" optional="True" format="fasta,fa"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
94 multiple="False"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
95 <param type="text" name="tab_adapter" argument="-M"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
96 label="TAB delimited file indicates valid forward/reverse adapter pairing" optional="True"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
97 <param type="boolean" name="barcode" argument="-b"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
98 label="Whether to demultiplex reads according to adapters/primers" optional="False" checked="False"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
99 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
100 <param type="text" name="cut" argument="-c"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
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"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
102 optional="False" value="0, 0"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
103 <param type="boolean" name="filter_degenerative_reads" argument="-n"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
104 label="Whether to filter out highly degenerative reads" optional="False" checked="False"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
105 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
106 <param type="boolean" name="filter_undetermined_mate_pair_reads" argument="-u"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
107 label="Whether to filter out undetermined mate-pair reads" optional="False" checked="False"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
108 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
109 <param type="select" name="format" argument="-f" label="Format of FASTQ quality value" optional="False"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
110 multiple="False">
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
111 <option value="sanger" selected="false">sanger</option>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
112 <option value="solexa" selected="false">solexa</option>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
113 <option value="auto" selected="true">auto</option>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
114 </param>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
115 <param type="boolean" name="compress" argument="-z" label="Whether to compress output in GZIP format"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
116 optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
117 <param type="boolean" name="qiime" argument="-qiime" label="Whether to prepare files required by QIIME"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
118 optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
119 <param type="boolean" name="quiet" argument="--quiet" label="Whether in quiet mode" optional="False"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
120 truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
121 <param type="boolean" name="intelligent" argument="-i" label="Whether to intelligently redistribute reads"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
122 optional="False" checked="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
123 </section>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
124 </inputs>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
125 <outputs>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
126 <data name="report" format="html" label="${tool.name} report on ${on_string}" hidden="false"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
127 <data name="trimmed_r1" format="fastq" label="${tool.name} trimmed first reads on ${on_string}" hidden="false"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
128 <data name="trimmed_r2" format="fastq" label="${tool.name} trimmed second reads on ${on_string}"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
129 hidden="false"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
130 <data name="trimmed_s" format="fastq" label="${tool.name} trimmed single end reads on ${on_string}"
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
131 hidden="false"/>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
132 </outputs>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
133 <help>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
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>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
135 <citations>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
136 <citation type="bibtex"><![CDATA[
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
137 @article{allaire2016rmarkdown,
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
138 title={rmarkdown: Dynamic Documents for R, 2016},
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
139 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
140 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
141 journal={R package version 0.9},
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
142 volume={6},
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
143 year={2016}
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
144 }
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
145 ]]></citation>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
146 <citation type="bibtex"><![CDATA[
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
147 @book{xie2015dynamic,
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
148 title={Dynamic Documents with R and knitr},
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
149 author={Xie, Yihui},
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
150 volume={29},
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
151 year={2015},
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
152 publisher={CRC Press}
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
153 }
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
154 ]]></citation>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
155 <citation type="bibtex"><![CDATA[
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
156 @online{jstree,
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
157 author={Bozhanov, Ivan},
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
158 year = 2018,
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
159 url = {https://www.jstree.com/}
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
160 }
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
161 ]]></citation>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
162 </citations>
a42e58c71e5b planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
163 </tool>