Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2

annotate mirdeep2_mapper.xml @ 0:963905bcb754 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
author mingchen0919
date Tue, 08 Aug 2017 13:14:41 -0400
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963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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1 <tool id="mirdeep2_mapper_site" name="mirdeep2_mapper" version="1.0.0">
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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2 <requirements>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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3 <requirement type="package" version="2.0.0.8">mirdeep2</requirement>
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4 <requirement type="package" version="1.20.0">r-getopt</requirement>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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5 <requirement type="package" version="1.2">r-rmarkdown</requirement>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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6 <requirement type="package" version="1.8.4">r-plyr</requirement>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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7 <requirement type="package" version="0.5.0">r-dplyr</requirement>
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8 <requirement type="package" version="0.3.5">r-htmltools</requirement>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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9 </requirements>
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10 <description>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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11 Mapping reads to genome
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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12 </description>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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13 <stdio>
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14 <regex match="Execution halted"
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15 source="both"
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16 level="fatal"
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17 description="Execution halted." />
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18 <regex match="Error in"
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19 source="both"
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20 level="fatal"
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21 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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22 <regex match="Fatal error"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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23 source="both"
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24 level="fatal"
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25 description="An undefined error occured, please check your intput carefully and contact your administrator." />
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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26 </stdio>
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27 <command>
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28 <![CDATA[
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29 ## Add tools to PATH
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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30 export PATH=/opt/R-3.2.5/bin:\$PATH &&
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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31
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32 Rscript '${__tool_directory__}/mirdeep2_mapper_render.R'
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33
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34 ## 1. input data
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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35 -r $reads
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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36 -g $reference_genome
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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37 -e $echo
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38
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39 ## 2. output report and report site directory
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40 -o $mirdeep2_mapper_site
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41 -d $mirdeep2_mapper_site.files_path
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42 -m $reads_collapsed
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43 -n $reads_collapsed_vs_genome
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44 -t $report_log
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45
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46 ## other parameters
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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47 -b $parse_to_fasta
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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48 -c $clean_entries
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49 -f $clip_3_adapter
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50 -h $discard_shorter_reads
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51 -j $collapse_reads_or_not
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52 -k $map_with_one_mismatch
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53 -l $map_up_to_position
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54
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55
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56 ## 3. Rmd templates sitting in the tool directory
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57
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58 ## other Rmd body template files
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59 -p '${__tool_directory__}/mirdeep2_mapper.Rmd'
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60
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61
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62
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63 ]]>
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64 </command>
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65 <inputs>
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66 <param name="reads" type="data" format="fastq,fasta" multiple="False" optional="False"
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67 label="Read input file" help="Reads in fastq or fasta format"/>
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68 <param name="reference_genome" type="data" format="fasta" multiple="false" optional="False" argument="-p"
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69 label="Reference genome from history" />
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70
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71 <param name="parse_to_fasta" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-h"
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72 optional="True" label="Parse to fasta format" />
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73 <param name="clean_entries" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-j"
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74 optional="True" label="Remove reads with non-canonical letters"
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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" />
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76 <param name="clip_3_adapter" type="text" argument="-k" value="" optional="true" label="Clip 3' adapter sequence (optional)"
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77 help="Enter an adapter sequence"/>
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78 <param name="discard_shorter_reads" type="integer" min="0" value="18" argument="-l"
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79 label="Discard reads shorter than int nts" />
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80 <param name="collapse_reads_or_not" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-m"
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81 label="Collapse reads" />
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82 <param name="map_with_one_mismatch" type="boolean" truevalue="TRUE" falsevalue="FALSE" argument="-q"
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83 label="Map with one mismatch"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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84 help="map with one mismatch in the seed (mapping takes longer)"/>
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85 <param name="map_up_to_position" type="integer" min="1" value="5" label="Map up to int nts" argument="-r"
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86 help="A read is allowed to map up to this number of positions in the genome. Default is 5"/>
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87
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88 <param name="echo" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
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89 </inputs>
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90 <outputs>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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91 <data name="mirdeep2_mapper_site" format="html" label="mirdeep2_mapper site" />
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92 <data name="reads_collapsed" format="fasta" label="reads_collapsed" />
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93 <data name="reads_collapsed_vs_genome" format="tabular" label="reads_collapsed_vs_ref_genome" />
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94 <data name="report_log" format="txt" label="report log"/>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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95 </outputs>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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96 <citations>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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97 @article{friedlander2011mirdeep2,
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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98 title={miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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99 author={Friedl{\"a}nder, Marc R and Mackowiak, Sebastian D and Li, Na and Chen, Wei and Rajewsky, Nikolaus},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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100 journal={Nucleic acids research},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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101 volume={40},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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102 number={1},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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103 pages={37--52},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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104 year={2011},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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105 publisher={Oxford University Press}
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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106 }
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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107 <citation type="bibtex">
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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108 @article{allaire2016rmarkdown,
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109 title={rmarkdown: Dynamic Documents for R, 2016},
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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},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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111 journal={R package version 0.9},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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112 volume={6},
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113 year={2016}
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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114 }
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115 </citation>
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116 <citation type="bibtex">
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117 @book{xie2015dynamic,
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118 title={Dynamic Documents with R and knitr},
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119 author={Xie, Yihui},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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120 volume={29},
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121 year={2015},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
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122 publisher={CRC Press}
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123 }
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124 </citation>
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125 <citation type="bibtex">
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126 @book{xie2015dynamic,
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127 title={Dynamic Documents with R and knitr},
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128 author={Xie, Yihui},
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129 volume={29},
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130 year={2015},
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131 publisher={CRC Press}
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132 }
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133 </citation>
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134 </citations>
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135 </tool>