Mercurial > repos > mingchen0919 > rmarkdown_i_adhore

annotate i-adhore.xml @ 3:45b64e04ab7d draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
author mingchen0919
date Tue, 08 Aug 2017 14:33:23 -0400
parents dca9b0c49c0e
children 85166d75910b
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mingchen0919
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1 <tool id="i_adhore" name="i-adhore" version="0.1">
1
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2 <requirements>
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3 <requirement type="package" version="1.19.2.1">pandoc</requirement>
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4 <requirement type="package" version="1.20.0">r-getopt</requirement>
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5 <requirement type="package" version="1.2">r-rmarkdown</requirement>
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6 <requirement type="package" version="1.8.4">r-plyr</requirement>
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7 <requirement type="package" version="0.5.0">r-dplyr</requirement>
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8 </requirements>
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9 <description>Generate i-adhore configure file</description>
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10 <stdio>
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11 <exit_code range="1:" />
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12 <exit_code range=":-1" />
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13 <regex match="Error:" />
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14 <regex match="Exception:" />
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15 </stdio>
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16 <command><![CDATA[
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18 Rscript '${__tool_directory__}/i_adhore_configure_render.R'
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20 ## 1. input data
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21 -e $echo
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23 #set $g_analysis_files = ''
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24 #for $g in $genomes
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25 #if str($g.genome_name)
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26 #set $analysis_files = []
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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27 #for $file in $g.analysis_files.to_dataset_instances($g.analysis_files)
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28 #set $analysis_files += [$file.__str__]
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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29 #end for
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30 #set g_analysis_files += str($g.genome_name) + ':' + ','.join($analysis_files) + ';'
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31 #end if
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32 #end for
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33 -G '$g_analysis_files'
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34
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35 -b $blast_table
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36 -g $gap_size
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37 -c $cluster_gap
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38 -q $q_value
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39 -p $prob_cutoff
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40 -a $anchor_points
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41 -m $alignment_method
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42 -l $level2only
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43 -T $table_type
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44 -h $multi_hypothesis_correction
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45
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46 ## 2. output report and file directory
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47 -x $i_adhore_configure_txt
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48 -o $i_adhore_configure
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49 -d $i_adhore_configure.files_path
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50
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51 ## 3. Rmd templates in the tool directory
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52 -t '${__tool_directory__}/i_adhore_configure.Rmd'
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53
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54
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55 ]]></command>
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56 <inputs>
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57 <repeat name="genomes" title="genome" min="1">
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58 <param name="genome_name" type="text" value="" label="Specify genome name" />
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59 <param name="analysis_files" type="data" format="txt" multiple="true" label="analysis files (.lst or .txt files)" />
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60 </repeat>
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61 <param name="blast_table" type="data" format="csv" multiple="false" label="blast table (.csv file)" />
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62 <param name="gap_size" type="text" value="30" label="gap size" />
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63 <param name="cluster_gap" type="text" value="35" label="cluster gap" />
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64 <param name="q_value" type="text" value="0.75" label="q value" />
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65 <param name="prob_cutoff" type="text" value="0.01" label="probability cutoff" />
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66 <param name="anchor_points" type="text" value="3" label="anchor_points" />
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67 <param name="alignment_method" type="text" value="gg4" label="alignment method" />
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68 <param name="level2only" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="level 2 only" />
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69 <param name="table_type" type="text" value="family" label="table type" />
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70 <param name="multi_hypothesis_correction" type="text" value="FDR" label="multiple hypothesis correction" />
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71
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72 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
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73 </inputs>
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74 <outputs>
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75 <data name="i_adhore_configure" format="html" label="i-adhore configure report" />
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76 <data name="i_adhore_configure_txt" format="txt" label="i-adhore configure file" />
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77 </outputs>
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78 <citations>
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79 <citation type="bibtex">
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80 @article{allaire2016rmarkdown,
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81 title={rmarkdown: Dynamic Documents for R, 2016},
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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82 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},
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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83 journal={R package version 0.9},
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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84 volume={6},
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85 year={2016}
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86 }
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87 </citation>
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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88 <citation type="bibtex">
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
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89 @book{xie2015dynamic,
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90 title={Dynamic Documents with R and knitr},
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91 author={Xie, Yihui},
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92 volume={29},
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93 year={2015},
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94 publisher={CRC Press}
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95 }
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96 </citation>
2
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97 <citation type="bibtex">
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98 @book{xie2015dynamic,
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99 title={Dynamic Documents with R and knitr},
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100 author={Xie, Yihui},
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101 volume={29},
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102 year={2015},
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103 publisher={CRC Press}
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104 }
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105 </citation>
0
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106 </citations>
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107 </tool>