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1 <tool id="DESeq_results" name="DESeq2: Results" version="1.0.0">
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2 <requirements>
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3 <requirement type="package" version="1.14.1">bioconductor-deseq2</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="1.1.0">r-stringr</requirement>
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8 <requirement type="package" version="0.4.0">r-highcharter</requirement>
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9 <requirement type="package" version="0.2">r-dt</requirement>
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10 <requirement type="package" version="1.4.2">r-reshape2</requirement>
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11 <requirement type="package" version="4.5.6">r-plotly</requirement>
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12 <requirement type="package" version="0.2.0.1">r-formattable</requirement>
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13 <requirement type="package" version="0.3.5">r-htmltools</requirement>
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12
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14 <requirement type="package" version="1.0.8">r-pheatmap</requirement>
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3
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15 </requirements>
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16 <description>
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17 An R Markdown tool to display DESeq analysis.
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18 </description>
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19 <stdio>
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20 <regex match="Execution halted"
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21 source="both"
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22 level="fatal"
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23 description="Execution halted." />
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24 <regex match="Error in"
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25 source="both"
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26 level="fatal"
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27 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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28 <regex match="Fatal error"
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29 source="both"
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30 level="fatal"
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31 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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32 </stdio>
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33 <command>
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34 <![CDATA[
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35
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36 Rscript '${__tool_directory__}/DESeq_results_render.R'
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37
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38 ## 1. input data
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39 -e $echo
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40 -w $deseq_workspace
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41 -c "$contrast_group"
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42 -t $treatment
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43 -k $condition
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44
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45 #set $groups = []
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46 #for $c_group in $clustering_groups
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47 #if str($c_group.group)
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48 #set $groups = $groups + [str($c_group.group)]
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49 #end if
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50 #end for
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51 #set $groups = ','.join($groups)
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52 -m "$groups"
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53
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54 ## 2. output report and report site directory
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55 -o $deseq_results
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56 -d $deseq_results.files_path
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57
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58 ## 3. Rmd templates sitting in the tool directory
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59
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60 ## _site.yml and index.Rmd template files
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61 -D '${__tool_directory__}/DESeq_results.Rmd'
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62
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63
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64
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65 ]]>
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66 </command>
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67 <inputs>
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68 <param type="data" name="deseq_workspace" format="rdata" multiple="false" label="Workspace from tool DESeq2: DESeq" />
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69 <param type="data" name="sample_table" format="tabular" multiple="false" label="Sample table file" />
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70 <param type="data_column" name="contrast_group" data_ref="sample_table" use_header_names="true"
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71 optional="false"
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72 label="Group for result contrast"
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73 help=""/>
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74 <param type="text" name="treatment" label="Treatment level" />
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75 <param type="text" name="condition" label="Condition level" />
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76
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77 <repeat name="clustering_groups" title="Gene clustering groups" min="1">
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78 <param type="data_column" name="group" data_ref="sample_table" use_header_names="true"
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79 optional="false"
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80 label="A phenotype column from the sample table" />
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81 </repeat>
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82
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83 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
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84 </inputs>
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85 <outputs>
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86 <data name="deseq_results" format="html" label="DESeq Results" />
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87 </outputs>
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88 </tool> |
