Mercurial > repos > mingchen0919 > rmarkdown_deseq2
annotate DESeq_results.xml @ 0:7231d7e8d3ed draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 10:43:18 -0400 |
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children | 15a5fb1a2ac8 |
rev | line source |
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7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
parents:
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1 <tool id="DESeq_results" name="DESeq2: Results" version="1.0.0"> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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2 <requirements> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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3 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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4 <requirement type="package" version="1.20.0">r-getopt</requirement> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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5 <requirement type="package" version="1.2">r-rmarkdown</requirement> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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6 <requirement type="package" version="1.8.4">r-plyr</requirement> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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7 <requirement type="package" version="1.1.0">r-stringr</requirement> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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8 <requirement type="package" version="0.4.0">r-highcharter</requirement> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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9 <requirement type="package" version="0.2">r-dt</requirement> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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10 <requirement type="package" version="1.4.2">r-reshape2</requirement> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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11 <requirement type="package" version="4.5.6">r-plotly</requirement> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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12 <requirement type="package" version="0.2.0.1">r-formattable</requirement> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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13 <requirement type="package" version="0.3.5">r-htmltools</requirement> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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14 <requirement type="package" version="1.0.8">r-pheatmap</requirement> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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15 </requirements> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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16 <description> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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17 An R Markdown tool to display DESeq analysis. |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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18 </description> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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19 <stdio> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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20 <regex match="Execution halted" |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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21 source="both" |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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22 level="fatal" |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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23 description="Execution halted." /> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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24 <regex match="Error in" |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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25 source="both" |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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26 level="fatal" |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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27 description="An undefined error occured, please check your intput carefully and contact your administrator." /> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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28 <regex match="Fatal error" |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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29 source="both" |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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30 level="fatal" |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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31 description="An undefined error occured, please check your intput carefully and contact your administrator." /> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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32 </stdio> |
7231d7e8d3ed
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33 <command> |
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34 <![CDATA[ |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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35 |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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36 Rscript '${__tool_directory__}/DESeq_results_render.R' |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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37 |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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38 ## 1. input data |
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39 -e $echo |
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40 -w $deseq_workspace |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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41 -c "$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 = [] |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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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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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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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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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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73 help=""/> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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74 <param type="text" name="treatment" label="Treatment level" /> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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75 <param type="text" name="condition" label="Condition level" /> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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76 |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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77 <repeat name="clustering_groups" title="Gene clustering groups" min="1"> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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78 <param type="data_column" name="group" data_ref="sample_table" use_header_names="true" |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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79 optional="false" |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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80 label="A phenotype column from the sample table" /> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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81 </repeat> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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82 |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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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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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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84 </inputs> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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85 <outputs> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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86 <data name="deseq_results" format="html" label="DESeq Results" /> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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87 </outputs> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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88 </tool> |