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
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>