Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2
comparison mirdeep2_mapper.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_mapper_site" name="mirdeep2_mapper" 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 Mapping reads to genome | |
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_mapper_render.R' | |
33 | |
34 ## 1. input data | |
35 -r $reads | |
36 -g $reference_genome | |
37 -e $echo | |
38 | |
39 ## 2. output report and report site directory | |
40 -o $mirdeep2_mapper_site | |
41 -d $mirdeep2_mapper_site.files_path | |
42 -m $reads_collapsed | |
43 -n $reads_collapsed_vs_genome | |
44 -t $report_log | |
45 | |
46 ## other parameters | |
47 -b $parse_to_fasta | |
48 -c $clean_entries | |
49 -f $clip_3_adapter | |
50 -h $discard_shorter_reads | |
51 -j $collapse_reads_or_not | |
52 -k $map_with_one_mismatch | |
53 -l $map_up_to_position | |
54 | |
55 | |
56 ## 3. Rmd templates sitting in the tool directory | |
57 | |
58 ## other Rmd body template files | |
59 -p '${__tool_directory__}/mirdeep2_mapper.Rmd' | |
60 | |
61 | |
62 | |
63 ]]> | |
64 </command> | |
65 <inputs> | |
66 <param name="reads" type="data" format="fastq,fasta" multiple="False" optional="False" | |
67 label="Read input file" help="Reads in fastq or fasta format"/> | |
68 <param name="reference_genome" type="data" format="fasta" multiple="false" optional="False" argument="-p" | |
69 label="Reference genome from history" /> | |
70 | |
71 <param name="parse_to_fasta" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-h" | |
72 optional="True" label="Parse to fasta format" /> | |
73 <param name="clean_entries" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-j" | |
74 optional="True" label="Remove reads with non-canonical letters" | |
75 help="remove all entries that have a sequence that contains letters other than a,c,g,t,u,n,A,C,G,T,U,N" /> | |
76 <param name="clip_3_adapter" type="text" argument="-k" value="" optional="true" label="Clip 3' adapter sequence (optional)" | |
77 help="Enter an adapter sequence"/> | |
78 <param name="discard_shorter_reads" type="integer" min="0" value="18" argument="-l" | |
79 label="Discard reads shorter than int nts" /> | |
80 <param name="collapse_reads_or_not" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-m" | |
81 label="Collapse reads" /> | |
82 <param name="map_with_one_mismatch" type="boolean" truevalue="TRUE" falsevalue="FALSE" argument="-q" | |
83 label="Map with one mismatch" | |
84 help="map with one mismatch in the seed (mapping takes longer)"/> | |
85 <param name="map_up_to_position" type="integer" min="1" value="5" label="Map up to int nts" argument="-r" | |
86 help="A read is allowed to map up to this number of positions in the genome. Default is 5"/> | |
87 | |
88 <param name="echo" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> | |
89 </inputs> | |
90 <outputs> | |
91 <data name="mirdeep2_mapper_site" format="html" label="mirdeep2_mapper site" /> | |
92 <data name="reads_collapsed" format="fasta" label="reads_collapsed" /> | |
93 <data name="reads_collapsed_vs_genome" format="tabular" label="reads_collapsed_vs_ref_genome" /> | |
94 <data name="report_log" format="txt" label="report log"/> | |
95 </outputs> | |
96 <citations> | |
97 @article{friedlander2011mirdeep2, | |
98 title={miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades}, | |
99 author={Friedl{\"a}nder, Marc R and Mackowiak, Sebastian D and Li, Na and Chen, Wei and Rajewsky, Nikolaus}, | |
100 journal={Nucleic acids research}, | |
101 volume={40}, | |
102 number={1}, | |
103 pages={37--52}, | |
104 year={2011}, | |
105 publisher={Oxford University Press} | |
106 } | |
107 <citation type="bibtex"> | |
108 @article{allaire2016rmarkdown, | |
109 title={rmarkdown: Dynamic Documents for R, 2016}, | |
110 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}, | |
111 journal={R package version 0.9}, | |
112 volume={6}, | |
113 year={2016} | |
114 } | |
115 </citation> | |
116 <citation type="bibtex"> | |
117 @book{xie2015dynamic, | |
118 title={Dynamic Documents with R and knitr}, | |
119 author={Xie, Yihui}, | |
120 volume={29}, | |
121 year={2015}, | |
122 publisher={CRC Press} | |
123 } | |
124 </citation> | |
125 <citation type="bibtex"> | |
126 @book{xie2015dynamic, | |
127 title={Dynamic Documents with R and knitr}, | |
128 author={Xie, Yihui}, | |
129 volume={29}, | |
130 year={2015}, | |
131 publisher={CRC Press} | |
132 } | |
133 </citation> | |
134 </citations> | |
135 </tool> |