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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="edger_design_matrix_creator" name="edgeR Design Matrix Creator">
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3 <description>Create the experimental design for edgeR by a few clicks in Galaxy</description>
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4
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5 <command interpreter="python">
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6 edgeR_Design_Matrix.py
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7 -o $contrast_matrix
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8 -u
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9 #for $unpaired_sample in $unpaired_samples
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10 ${unpaired_sample}
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11 #end for
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12 -p
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13 #for $paired_sample in $paired_samples
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14 #for $sample in $paired_sample.samples
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15 ${sample.sample}
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16 #end for
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17 :
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18 #end for
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19 -t
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20 #for $treatment in $check.treatments
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21 #for $factor in $treatment.factors
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22 "$factor.name"
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23 $factor.samples
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24 #end for
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25 :
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26 #end for
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27 -n
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28 #for $unpaired_sample in $unpaired_samples
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29 "${unpaired_sample}:${unpaired_sample.name}"
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30 #end for
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31 #for $paired_sample in $paired_samples
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32 #for $sample in $paired_sample.samples
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33 "${sample.sample}:${sample.sample.name}"
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34 #end for
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35 #end for
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36 </command>
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37
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38 <code file="edgeR_Design_Matrix.listing.py" />
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39
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40 <inputs>
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41 <param name="unpaired_samples" type="data" format="tabular" label="Unpaired read-count dataset" help="from featureCounts/DEXSeq-count/HTSeq-count, etc. Press [ctrl] and click the sample to unselect it." multiple="true" />
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42
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43 <repeat name="paired_samples" title="Add paired samples; per patient">
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44 <repeat name="samples" title="Add sample for patient" min="2">
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45 <param name="sample" type="data" format="tabular" label="Read-count dataset that belongs to a pair" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." />
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46 </repeat>
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47 </repeat>
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48
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49 <conditional name="check">
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50 <param name="continue" help="When clicking this variable, the treatment menu will appear" type="boolean" truevalue="yes" />
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51
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52 <when value="yes">
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53 <repeat name="treatments" title="Treatments" min="1">
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54 <repeat name="factors" title="Factor" min="2" help="e.g. 'normal' or 'tumor', 'untreated', 'recurrent', 'metastatic', or 'group_1',...,'group_n' etc.">
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55 <param name="name" type="text" />
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56 <param name="samples" type="select" label="Corresponding samples" multiple="true" dynamic_options="listfiles(unpaired_samples,paired_samples)" />
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57 </repeat>
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58 </repeat>
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59 </when>
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60 </conditional>
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61
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62 </inputs>
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63
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64 <outputs>
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65 <data format="tabular" name="contrast_matrix" label="Contrast matrix" />
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66 </outputs>
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67
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68 <help>
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69 Examples::
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70 2 group, unpaired::
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71 Group name 1 = Healthy
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72 Group name 2 = Tumor
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73
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74 </help>
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75 </tool>
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