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1 <tool id="DESeq" name="DESeq2: DESeq" 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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14 </requirements>
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15 <description>
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16 An R Markdown tool to perform DESeq analysis.
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17 </description>
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18 <stdio>
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19 <regex match="Execution halted"
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20 source="both"
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21 level="fatal"
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22 description="Execution halted." />
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23 <regex match="Error in"
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24 source="both"
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25 level="fatal"
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26 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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27 <regex match="Fatal error"
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28 source="both"
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29 level="fatal"
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30 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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31 </stdio>
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32 <command>
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33 <![CDATA[
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34 ## Add tools to PATH
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35 export PATH=/opt/R-3.2.5/bin:\$PATH &&
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36
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37 Rscript '${__tool_directory__}/DESeq_render.R'
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38
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39 ## 1. input data
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40 -e $echo
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41 -c $count_files
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42 -s $sample_table
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43 -p "$design_formula"
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44
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45 ## 2. output report and report site directory
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46 -o $DESeq
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47 -d $DESeq.files_path
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48 -w $deseq_workspace
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49
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50 ## 3. Rmd templates sitting in the tool directory
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51
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52 ## _site.yml and index.Rmd template files
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53 -D '${__tool_directory__}/DESeq.Rmd'
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54
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55
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56
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57 ]]>
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58 </command>
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59 <inputs>
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60 <param type="data" name="count_files" format="tabular" multiple="true" label="Count files from htseq-count" />
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61 <param type="data" name="sample_table" format="tabular" multiple="false" label="sample table file"
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62 help="The sample table file contains a table. The first column is the sample name, the second column is
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63 the count file name and the rest of columns are treatment columns. The file names in this table have
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64 to be in the same order as the count files uploaded in the previous step. "/>
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65 <param type="text" name="design_formula" value="~ condition_1 + condition_2" label="Design formula"
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66 help="The simplest design formula for differential expression would be ~ condition, where condition
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67 is a column in colData(dds) that specifies which of two (or more groups) the samples belong to">
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68 <sanitizer>
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69 <valid initial="default">
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70 <add preset="string.printable"/>
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71 <add value="~"/>
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72 </valid>
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73 </sanitizer>
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74 </param>
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75 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
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76 </inputs>
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77 <outputs>
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78 <data name="DESeq" format="html" label="DESeq Analysis" />
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79 <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis" />
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80 </outputs>
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81 </tool> |
