Mercurial > repos > erasmus-medical-center > voom_transform

annotate voom_transform.xml @ 0:c6a3a93a237e draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
author erasmus-medical-center
date Wed, 25 Jan 2017 10:13:10 -0500
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0
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="voom_transform" name="Voom transform" version="3.29.0-0">
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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3 <description>transform count data to fit linear modelling</description>
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4 <requirements>
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5 <requirement type="package" version="3.29.0">bioconductor-limma</requirement>
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6 <requirement type="package" version="1.20.0">r-getopt</requirement>
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7 </requirements>
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8
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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9 <version_command>echo $(R --version | grep -i version | head -n 1)", Limma: "$(R --vanilla --slave -e "library(limma) ; cat(sessionInfo()\$otherPkgs\$limma\$Version)")</version_command>
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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10
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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11 <command detect_errors="exit_code"><![CDATA[
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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12 Rscript
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13 #if str($include_rdata) == 'true'
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14 --save
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15 #end if
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16 '${__tool_directory__}/voom_transform.R'
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17 -e '${input_select.expression_matrix}'
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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18 -t '${output_matrix}'
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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19
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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20 #if str($include_rdata) == 'true'
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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21 && cp '.RData' '$output_rdata'
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22 #end if
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23
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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24 ]]></command>
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25
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26 <inputs>
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27 <conditional name="input_select">
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28 <param name="input_format" type="select" label="Output format">
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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29 <option value="1">Single expression matrix (header + multi column)</option>
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30 <!-- <option value="2">Count files (no header + 1 sample per file)</option>-->
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31 </param>
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32
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33 <when value="1">
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34 <param name="expression_matrix" type="data" format="txt,tabular" />
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35 </when>
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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36 <!--
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37 <when value="2">
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38 repeat / input type = multiple
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39 </when>
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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40 -->
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41 </conditional>
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42
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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43 <param name="include_rdata" type="boolean" truevalue="true" falsevalue="" label="Save RData object" />
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44
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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45 <!-- normalization param
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46 -->
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47
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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48 </inputs>
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49
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50 <outputs>
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51 <data name="output_matrix" format="tabular"
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52 label="${tool.name} on $on_string" />
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53
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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54 <data name="output_rdata" format="RData" label="${tool.name} on $on_string (RData)">
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55 <filter>str(include_rdata) in ['true', true]</filter>
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56 </data>
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57 </outputs>
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58
c6a3a93a237e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
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59 <tests>
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60 <test>
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61 <param name="input_format" value="1" />
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62 <param name="expression_matrix" value="em.txt" />
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63
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64 <output name="output_matrix" value="em_transformed.txt" />
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65 </test>
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66 </tests>
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67
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68 <help><![CDATA[
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69
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70 ]]></help>
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71
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72 <citations>
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73 <citation type="doi">10.1093/nar/gkv007</citation>
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74 </citations>
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75 </tool>