Mercurial > repos > testtool > find_dmr
comparison findDMR/findDMR.xml @ 4:0d1957068766 draft
Uploaded
| author | testtool |
|---|---|
| date | Mon, 20 Feb 2017 08:32:26 -0500 |
| parents | 42cfcac7779d |
| children | 715d03e1fd83 |
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| 3:42cfcac7779d | 4:0d1957068766 |
|---|---|
| 1 <tool id="DMR" name="findDMR" version="1.16.2"> | 1 <tool id="DMR" name="findDMR" version="1.16.2"> |
| 2 <description> | 2 <description> |
| 3 from series of samples | 3 from series of samples |
| 4 </description> | 4 </description> |
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="package" version="3.2.1">R</requirement> | 6 <requirement type="package" version="3.2.1">R</requirement> |
| 7 </requirements> | 7 </requirements> |
| 8 <stdio> | 8 <stdio> |
| 9 <exit_code range="1:" /> | 9 <exit_code range="1:" /> |
| 10 </stdio> | 10 </stdio> |
| 11 <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$IlmnTable" "$gmTable" "$cutoff" "$clusterSize" "$DMR"</command> | 11 <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$platform" "$Data_Table" "$cutoff" "$clusterSize" "$DMR"</command> |
| 12 <inputs> | 12 <inputs> |
| 13 <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable"> | 13 <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable"> |
| 14 <validator type="empty_field" message="This field is required."/> | 14 <validator type="empty_field" message="This field is required."/> |
| 15 </param> | 15 </param> |
| 16 <param optional="false" format="csv" name="IlmnTable" type="data" value="" help="CG, CHR, BP table." label="[required] IlmnTable"> | 16 <param optional="false" format="csv" name="platform" type="data" value="" help="CG, CHR, BP table." label="[required] platform"> |
| 17 <validator type="empty_field" message="This field is required."/> | 17 <validator type="empty_field" message="This field is required."/> |
| 18 </param> | 18 </param> |
| 19 <param optional="false" format="csv" name="gmTable" type="data" value="" help="gmSet of data." label="[required] gmTable"> | 19 <param optional="false" format="csv" name="Data_Table" type="data" value="" help="Matrix of data." label="[required] Data_Table"> |
| 20 <validator type="empty_field" message="This field is required."/> | 20 <validator type="empty_field" message="This field is required."/> |
| 21 </param> | 21 </param> |
| 22 <param name="cutoff" type="float" value="" | 22 <param name="cutoff" type="float" value="" |
| 23 label="Enter cutoff size (number)" | 23 label="Enter cutoff size (number)" |
| 24 help="e.g. '0.2'" > | 24 help="e.g. '0.2'" > |
| 35 <test> | 35 <test> |
| 36 <param name="test"> | 36 <param name="test"> |
| 37 <element name="test-data"> | 37 <element name="test-data"> |
| 38 <collection type="data"> | 38 <collection type="data"> |
| 39 <element name="GSMTable" value="test-data/input.csv"/> | 39 <element name="GSMTable" value="test-data/input.csv"/> |
| 40 <element name="IlmnTable" value="test-data/IlmnTable.csv"/> | 40 <element name="platform" value="test-data/platform.csv"/> |
| 41 <element name="gmTable" value="test-data/gmTable.csv"/> | 41 <element name="Data_Table" value="test-data/Data_Table.csv"/> |
| 42 <element name="cutoff" value="0.2"/> | 42 <element name="cutoff" value="0.2"/> |
| 43 <element name="clusterSize" value="2"/> | 43 <element name="clusterSize" value="2"/> |
| 44 </collection> | 44 </collection> |
| 45 </element> | 45 </element> |
| 46 </param> | 46 </param> |