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1 <tool id="deseq" name="DE Seq">
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2 <description>Run Differential Expression analysis from SAM To Count data</description>
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3
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4 <command interpreter="python">
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5 stderr_wrapper.py Rscript ${GALAXY_DATA_INDEX_DIR}/deseq.R $counts $column_types $comparison $top_table $diagnostic_html "$diagnostic_html.files_path" "$counts.name"
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6 </command>
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7
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8 <inputs>
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9 <param format="tabular" name="counts" type="data" optional="false" label="Counts file (from sam2counts)" help="Must have same number of samples as the column types field. E.g. if the column types field is 'kidney,kidney,liver,liver', then there must be 4 sample columns in the counts file."/>
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10
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11 <param name="column_types" type="text" size="40" optional="false" label="Column Types in counts file" help="A comma separated list (no spaces) of the types of the data columns using the same name for replicates. E.g. kidney,kidney,kidney,liver,liver,liver">
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12 <validator type="empty_field"/>
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13 <validator type="regex" message="Must be a comma-separated list with no spaces">^(\w+,)+\w+$</validator>
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14 </param>
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15
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16 <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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17 <validator type="empty_field"/>
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18 <validator type="regex" message="Must be a comma-separated tuple with no spaces">^\w+,\w+$</validator>
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19 </param>
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20 </inputs>
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21
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22 <outputs>
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23 <data format="tabular" name="top_table" label="Top Table from ${tool.name} on ${on_string}"/>
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24 <data format="html" name="diagnostic_html" label="Diagnostic Plots for ${tool.name} on ${on_string}"/>
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25 </outputs>
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26
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27 <help>
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28 NOTE: This DEseq Galaxy tool can only be run on counts files that are created from SAM files that have been aligned to a transcriptome.
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29 </help>
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30
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31 </tool>
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