Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2
comparison mirdeep2.xml @ 0:963905bcb754 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 13:14:41 -0400 |
parents | |
children | 75e53be98c51 |
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1 <tool id="mirdeep2" name="mirdeep2" version="1.0.0"> | |
2 <requirements> | |
3 <requirement type="package" version="2.0.0.8">mirdeep2</requirement> | |
4 <requirement type="package" version="1.20.0">r-getopt</requirement> | |
5 <requirement type="package" version="1.2">r-rmarkdown</requirement> | |
6 <requirement type="package" version="1.8.4">r-plyr</requirement> | |
7 <requirement type="package" version="0.5.0">r-dplyr</requirement> | |
8 <requirement type="package" version="0.3.5">r-htmltools</requirement> | |
9 </requirements> | |
10 <description> | |
11 miRNA identification | |
12 </description> | |
13 <stdio> | |
14 <regex match="Execution halted" | |
15 source="both" | |
16 level="fatal" | |
17 description="Execution halted." /> | |
18 <regex match="Error in" | |
19 source="both" | |
20 level="fatal" | |
21 description="An undefined error occured, please check your intput carefully and contact your administrator." /> | |
22 <regex match="Fatal error" | |
23 source="both" | |
24 level="fatal" | |
25 description="An undefined error occured, please check your intput carefully and contact your administrator." /> | |
26 </stdio> | |
27 <command> | |
28 <![CDATA[ | |
29 ## Add tools to PATH | |
30 export PATH=/opt/R-3.2.5/bin:\$PATH && | |
31 | |
32 Rscript '${__tool_directory__}/mirdeep2_render.R' | |
33 | |
34 ## 1. input data | |
35 -e $echo | |
36 -a $collapsed_reads | |
37 -b $reference_genome | |
38 -c $reads_mapping | |
39 | |
40 ## 2. output report and report site directory | |
41 -o $mirdeep2_site | |
42 -d $mirdeep2_site.files_path | |
43 -r $csv_result | |
44 -t $html_result | |
45 -u $report_log | |
46 | |
47 ## other paramters | |
48 | |
49 -f $species_mature_mirna | |
50 -g $related_species_mature_mirna | |
51 -h $precursor_sequences | |
52 -j $min_read_stack_height | |
53 -k $min_score_cutoff | |
54 -l $randfold_analysis | |
55 -m $max_precursor_number | |
56 -n $species | |
57 -q $switch | |
58 | |
59 ## 3. Rmd templates sitting in the tool directory | |
60 | |
61 ## other Rmd body template files | |
62 -p '${__tool_directory__}/mirdeep2.Rmd' | |
63 | |
64 | |
65 ]]> | |
66 </command> | |
67 <inputs> | |
68 <param name="collapsed_reads" type="data" format="fasta" multiple="False" optional="False" | |
69 label="Read input file" help="Reads in fastq or fasta format"/> | |
70 <param name="reference_genome" type="data" format="fasta" multiple="False" optional="False" | |
71 label="Reference genome from history" | |
72 help="Reference genome in fasta format"/> | |
73 <param name="reads_mapping" type="data" format="tabular" multiple="False" optional="False" | |
74 label="reads mappings" help="reads mappings in arf format"/> | |
75 <param name="species_mature_mirna" type="data" format="fasta" multiple="False" optional="True" | |
76 label="miRBase mature miRNA for this species" | |
77 help="mature miRNA in fasta format"/> | |
78 <param name="related_species_mature_mirna" type="data" format="fasta" multiple="False" optional="TRUE" | |
79 label="miRBase mature miRNA from related species" | |
80 help="mature miRNA in fasta format"/> | |
81 <param name="precursor_sequences" type="data" format="fasta" multiple="False" optional="TRUE" | |
82 label="precursor sequences" help="miRBase miRNA precursor sequences in fasta format"/> | |
83 <param name="min_read_stack_height" type="integer" argument="-a" optional="True" | |
84 label="minimum read stack height" | |
85 help="minimum read stack height that triggers analysis. Using this option disables | |
86 automatic estimation of the optimal value."/> | |
87 <param name="min_score_cutoff" type="integer" value="0" argument="-b" label="minimum score cut-off" | |
88 help="minimum score cut-off for predicted novel miRNAs to be displayed in the overview | |
89 table. This score cut-off is by default 0."/> | |
90 <param name="randfold_analysis" type="boolean" truevalue="TRUE" falsevalue="FALSE" argument="-c" checked="False" | |
91 label="randfold analysis" help="disable randfold analysis"/> | |
92 <param name="max_precursor_number" type="integer" value="50000" argument="-g" label="maximum number of precursors" | |
93 help="maximum number of precursors to analyze when automatic excision gearing is used. | |
94 default=50000, if set to -1 all precursors will be analyzed"/> | |
95 <param name="species" type="select" label="Search in species"> | |
96 <option value="all">All species</option> | |
97 <option value="tni">tetraodon</option> | |
98 <option value="dps">d.pseudoobscura</option> | |
99 <option value="dya">d.yakuba</option> | |
100 <option value="ame">a.mellifera</option> | |
101 <option value="dmo">d.mojavensis</option> | |
102 <option value="cel">worm</option> | |
103 <option value="aga">a.gambiae</option> | |
104 <option value="cbr">c.briggsae</option> | |
105 <option value="cin">c.intestinalis</option> | |
106 <option value="mmu">mouse</option> | |
107 <option value="xtr">x.tropicalis</option> | |
108 <option value="eca">horse</option> | |
109 <option value="cfa">dog</option> | |
110 <option value="fru">fugu</option> | |
111 <option value="bta">cow</option> | |
112 <option value="der">d.erecta</option> | |
113 <option value="dgr">d.grimshawi</option> | |
114 <option value="gga">chicken</option> | |
115 <option value="spu">s.purpuratus</option> | |
116 <option value="bfl">lancelet</option> | |
117 <option value="ptr">chimp</option> | |
118 <option value="dse">d.sechellia</option> | |
119 <option value="dpe">d.persimilis</option> | |
120 <option value="dvi">d.virilis</option> | |
121 <option value="rno">rat</option> | |
122 <option value="dme">d.melanogaster</option> | |
123 <option value="lca">cat</option> | |
124 <option value="sja">c.japonica</option> | |
125 <option value="dan">d.ananassae</option> | |
126 <option value="hsa">human</option> | |
127 <option value="dsi">d.simulans</option> | |
128 </param> | |
129 <param name="switch" type="boolean" truevalue="TRUE" falsevalue="FALSE" | |
130 label="mature_ref_miRNAs contain miRBase v18 identifiers?" | |
131 help="use this switch if mature_ref_miRNAs contain miRBase v18 identifiers (5p and 3p) instead of previous ids from v17"/> | |
132 | |
133 | |
134 <param name="echo" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> | |
135 </inputs> | |
136 <outputs> | |
137 <data format="html" name="mirdeep2_site" label="mirdeep2 miRNA identification" /> | |
138 <data name="csv_result" format="csv" label="miRNA in csv format" /> | |
139 <data name="html_result" format="html" label="miRNA in html format" from_work_dir="result.html"/> | |
140 <data name="report_log" format="txt" label="report log" from_work_dir="result.csv"/> | |
141 </outputs> | |
142 <citations> | |
143 @article{friedlander2011mirdeep2, | |
144 title={miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades}, | |
145 author={Friedl{\"a}nder, Marc R and Mackowiak, Sebastian D and Li, Na and Chen, Wei and Rajewsky, Nikolaus}, | |
146 journal={Nucleic acids research}, | |
147 volume={40}, | |
148 number={1}, | |
149 pages={37--52}, | |
150 year={2011}, | |
151 publisher={Oxford University Press} | |
152 } | |
153 <citation type="bibtex"> | |
154 @article{allaire2016rmarkdown, | |
155 title={rmarkdown: Dynamic Documents for R, 2016}, | |
156 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, | |
157 journal={R package version 0.9}, | |
158 volume={6}, | |
159 year={2016} | |
160 } | |
161 </citation> | |
162 <citation type="bibtex"> | |
163 @book{xie2015dynamic, | |
164 title={Dynamic Documents with R and knitr}, | |
165 author={Xie, Yihui}, | |
166 volume={29}, | |
167 year={2015}, | |
168 publisher={CRC Press} | |
169 } | |
170 </citation> | |
171 <citation type="bibtex"> | |
172 @book{xie2015dynamic, | |
173 title={Dynamic Documents with R and knitr}, | |
174 author={Xie, Yihui}, | |
175 volume={29}, | |
176 year={2015}, | |
177 publisher={CRC Press} | |
178 } | |
179 </citation> | |
180 </citations> | |
181 </tool> |