comparison GRsetFromGEO/GRsetFromGEO.xml @ 29:118e636a5f95 draft

Uploaded
author testtool
date Thu, 13 Apr 2017 11:49:05 -0400
parents 3d281ad15b83
children ceced09589d9
comparison
equal deleted inserted replaced
28:3d281ad15b83 29:118e636a5f95
1 <tool id="GRset" name="GRsetFromGEO" version="1.16.2"> 1 <tool id="GRset" name="GRsetFromGEO" version="1.16.2">
2 <description>
3 Reading Illumina methylation array data from GEO.
4 </description>
5 <requirements> 2 <requirements>
6 <requirement type="package" version="3.2.1">R</requirement> 3 <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
7 </requirements> 4 </requirements>
8 <stdio> 5 <stdio>
9 <exit_code range="1:" /> 6 <exit_code range="1:" />
10 </stdio> 7 </stdio>
11 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command> 8 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
12 <inputs> 9 <inputs>
13 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> 10 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
14 </inputs> 11 </inputs>
15 <outputs> 12 <outputs>
16 <data format="txt" name="output" label="GenomicRatioSet.txt"/> 13 <data type="galaxy.datatypes.binary:RData" name="output" label="GenomicRatioSet.RData"/>
17 </outputs> 14 </outputs>
18 <tests> 15 <tests>
19 <test> 16 <test>
20 <param name="test"> 17 <param name="test">
21 <element name="test-data"> 18 <element name="test-data">
22 <collection type="data"> 19 <collection type="data">
23 <element name="GSE" value="GSE51547"/> 20 <element name="GSE" value="GSE51547"/>
24 </collection> 21 </collection>
25 </element> 22 </element>
26 </param> 23 </param>
27 <output format="txt" name="output" label="test-data/GenomicRatioSet.txt"/> 24 <output type="galaxy.datatypes.binary:RData" name="output" label="test-data/GenomicRatioSet.RData"/>
28 </test> 25 </test>
29 </tests> 26 </tests>
30 <help> 27 <help>
31 Reading Illumina methylation array data from GEO. 28 Reading Illumina methylation array data from GEO
32 </help> 29 </help>
33 <citations> 30 <citations>
34 Aryee, Martin J, et al "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays" Bioinformatics 3010 (2014): 1363-1369 31 xxx
35 </citations> 32 </citations>
36 </tool> 33 </tool>