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1 <tool id="customAnalyse" name="CustomAnalyse" version="0.1.0">
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2 <description>Custom Analyse</description>
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3 <requirements>
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4 <container type="docker">sblanck/testtool:latest</container>
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5 </requirements>
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6 <command>
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7
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8 /galaxy-tools/stderr_wrapper.py Rscript
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9 /galaxy-tools/transcriptomics/CustomAnalyse/CustomAnalyse.R
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10 #for $input in $inputs
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11 "${input}"
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12 "${input.name}"
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13 #end for
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14 "${target}"
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15 "${selectCondition1}"
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16 "${selectCondition2}"
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17 $result_export_eset
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18 $result_export_conditions
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19 $result_html
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20 $result_html.files_path
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21 /galaxy-tools/transcriptomics/CustomAnalyse/CustomAnalyse_tpl.html
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22 </command>
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23
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24 <inputs>
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25
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26 <param name="inputs" type="data" format="cel" multiple="true" label=".CEL files" help=".CEL files to be used"/>
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27
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28 <param name="target" type="data" format="txt" label="target file" help="target file associated with the .CEL file dataset"/>
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29
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30 <!--param name="normalisation" type="select" label="Preprocessing/normalization">
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31 <options>
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32 <option value="rma">rma</option>
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33 <option value="quantile">quantile normalization</option>
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34 <option value="log2">log2</option>
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35 <option value="none">none</option>
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36 </options>
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37 </param-->
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38
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39 <param name="selectCondition1" type="select" display="checkboxes" label="Condition 1" multiple="true">
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40 <options from_dataset="target">
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41 <column name="name" index="0"/>
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42 <column name="value" index="0"/>
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43 </options>
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44 </param>
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45
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46 <param name="selectCondition2" type="select" display="checkboxes" label="Condition 2" multiple="true">
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47 <options from_dataset="target">
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48 <column name="name" index="0"/>
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49 <column name="value" index="0"/>
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50 </options>
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51 </param>
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52
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53 </inputs>
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54 <outputs>
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55 <data format="html" name="result_html" label="Annotations"/>
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56 <data format="rdata" name="result_export_eset" label="export expressionSet"/>
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57 <data format="cond" name="result_export_conditions" label="export conditions"/>
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58 </outputs>
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59
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60 <help>
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61 NOTE: This wrapper performs p-value combination from multiples studies with the same probes. If you need to normalize your data, use "matrix_normalisation" tool on each file. Then, use "Merge Standard datasets(copied)" tool to make a multiple file dataset.
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62 </help>
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63
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64 </tool>
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