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1 <tool id="metarnaseq" name="metaRNASeq">
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2 <description>metaRNASeq wrapper</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/MetaRNASeq/MetaRNASeq.R
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10 #for $currentInput in $inputList
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11 "${currentInput}"
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12 "${currentInput.name}"
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13 #end for
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14 $comparison
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15 $method
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16 $mod
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17 $top_table
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18 $diagnostic_html
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19 "$diagnostic_html.files_path"
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20 /galaxy-tools/transcriptomics/MetaRNAseq/MetaRNASeq_tpl.html
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21 </command>
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22
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23 <inputs>
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24 <param format="tabular" name="inputList" multiple="true" type="data" optional="false" label="Counts file" help="Must have the same number of row in each study. The experimental conditions must be specified in the header of each file"/>
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25
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26 <param name="method" type="select" label="Compute dispersion method" help="">
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27 <option value="pooled">Pooled</option>
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28 <option value="pooled-CR">Pooled-CR</option>
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29 <option value="per-condition">Per-condition</option>
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30 <option value="blind">Blind</option>
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31 </param>
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32 <param name="mod" type="select" label="Compute dispersion sharingmod" help="">
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33 <option value="maximum">Maximum</option>
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34 <option value="fit-only">Fit-only</option>
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35 <option value="gene-est-only">Gene-est-only</option>
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36 </param>
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37
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38 <param name="comparison" type="text" size="30" optional="false" label="Comparison type" help="A comma separated tuple (no spaces) of the comparison you want to do. Must use the names from the Column Types list. E.g. comparing kidney to liver: kidney,liver. Comparing liver to kidney: liver,kidney">
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39 <validator type="empty_field"/>
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40 <validator type="regex" message="Must be a comma-separated tuple with no spaces">^\w+,\w+$</validator>
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41 </param>
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42 </inputs>
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43
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44 <outputs>
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45 <data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/>
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46 <data format="html" name="diagnostic_html" label="Charts for ${tool.name} on ${on_string}"/>
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47 </outputs>
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48
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49 <help>
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50 NOTE: This metaRNASeq Galaxy tool can only be run on counts files.
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51 </help>
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52
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53 </tool>
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