Mercurial > repos > nikhil-joshi > deseq_and_sam2counts
comparison deseq/deseq.xml @ 3:a49aff09553e draft default tip
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| author | nikhil-joshi |
|---|---|
| date | Wed, 09 Jan 2013 18:39:12 -0500 |
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| 2:669899d20e59 | 3:a49aff09553e |
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| 1 <tool id="deseq" name="DE Seq"> | |
| 2 <description>Run Differential Expression analysis from SAM To Count data</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 stderr_wrapper.py Rscript ${GALAXY_DATA_INDEX_DIR}/deseq.R $counts $column_types $comparison $top_table $diagnostic_html "$diagnostic_html.files_path" "$counts.name" | |
| 6 </command> | |
| 7 | |
| 8 <inputs> | |
| 9 <param format="tabular" name="counts" type="data" optional="false" label="Counts file (from sam2counts)" help="Must have same number of samples as the column types field. E.g. if the column types field is 'kidney,kidney,liver,liver', then there must be 4 sample columns in the counts file."/> | |
| 10 | |
| 11 <param name="column_types" type="text" size="60" optional="false" label="Column Types in counts file" help="A comma separated list (no spaces) of the types of the data columns using the same name for replicates. E.g. kidney,kidney,kidney,liver,liver,liver"> | |
| 12 <validator type="empty_field"/> | |
| 13 <validator type="regex" message="Must be a comma-separated list with no spaces">^(\w+,)+\w+$</validator> | |
| 14 </param> | |
| 15 | |
| 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"> | |
| 17 <validator type="empty_field"/> | |
| 18 <validator type="regex" message="Must be a comma-separated tuple with no spaces">^\w+,\w+$</validator> | |
| 19 </param> | |
| 20 </inputs> | |
| 21 | |
| 22 <outputs> | |
| 23 <data format="tabular" name="top_table" label="Top Table from ${tool.name} on ${on_string}"/> | |
| 24 <data format="html" name="diagnostic_html" label="Diagnostic Plots for ${tool.name} on ${on_string}"/> | |
| 25 </outputs> | |
| 26 | |
| 27 <help> | |
| 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. | |
| 29 </help> | |
| 30 | |
| 31 </tool> |