Mercurial > repos > mingchen0919 > rmarkdown_deseq2
annotate DESeq.xml @ 1:312e9bcc02f1 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 10:47:41 -0400 |
parents | 7231d7e8d3ed |
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" name="DESeq2: DESeq" 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
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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
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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
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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> |
7231d7e8d3ed
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
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17 An R Markdown tool to perform 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" |
7231d7e8d3ed
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" |
7231d7e8d3ed
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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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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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 |
7231d7e8d3ed
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_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 |
7231d7e8d3ed
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39 -e $echo |
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40 -c $count_files |
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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 -s $sample_table |
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42 -p "$design_formula" |
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43 |
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44 ## 2. output report and report site directory |
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45 -o $DESeq |
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 -d $DESeq.files_path |
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47 -w $deseq_workspace |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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48 |
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49 ## 3. Rmd templates sitting in the tool directory |
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50 |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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51 ## _site.yml and index.Rmd template files |
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52 -D '${__tool_directory__}/DESeq.Rmd' |
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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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53 |
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54 |
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55 |
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56 ]]> |
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57 </command> |
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58 <inputs> |
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59 <param type="data" name="count_files" format="tabular" multiple="true" label="Count files from htseq-count" /> |
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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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60 <param type="data" name="sample_table" format="tabular" multiple="false" label="sample table file" |
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61 help="The sample table file contains a table. The first column is the sample name, the second column is |
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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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62 the count file name and the rest of columns are treatment columns. The file names in this table have |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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63 to be in the same order as the count files uploaded in the previous step. "/> |
7231d7e8d3ed
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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64 <param type="text" name="design_formula" value="~ condition_1 + condition_2" label="Design formula" |
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65 help="The simplest design formula for differential expression would be ~ condition, where condition |
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66 is a column in colData(dds) that specifies which of two (or more groups) the samples belong to"> |
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67 <sanitizer> |
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68 <valid initial="default"> |
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69 <add preset="string.printable"/> |
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70 <add value="~"/> |
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71 </valid> |
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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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72 </sanitizer> |
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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 </param> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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74 <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
mingchen0919
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75 </inputs> |
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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76 <outputs> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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77 <data name="DESeq" format="html" label="DESeq Analysis" /> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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78 <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis" /> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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79 </outputs> |
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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80 </tool> |