annotate CustomAnalyse.xml @ 0:27ffdb495852 draft default tip

Imported from capsule None
author sblanck
date Wed, 13 Apr 2016 07:40:02 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
1 <tool id="customAnalyse" name="CustomAnalyse" version="0.1.0">
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
2 <description>Custom Analyse</description>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
3 <requirements>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
4 <container type="docker">sblanck/testtool:latest</container>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
5 </requirements>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
6 <command>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
7
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
8 /galaxy-tools/stderr_wrapper.py Rscript
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
9 /galaxy-tools/transcriptomics/CustomAnalyse/CustomAnalyse.R
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
10 #for $input in $inputs
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
11 "${input}"
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
12 "${input.name}"
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
13 #end for
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
14 "${target}"
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
15 "${selectCondition1}"
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
16 "${selectCondition2}"
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
17 $result_export_eset
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
18 $result_export_conditions
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
19 $result_html
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
20 $result_html.files_path
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
21 /galaxy-tools/transcriptomics/CustomAnalyse/CustomAnalyse_tpl.html
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
22 </command>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
23
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
24 <inputs>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
25
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
26 <param name="inputs" type="data" format="cel" multiple="true" label=".CEL files" help=".CEL files to be used"/>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
27
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
28 <param name="target" type="data" format="txt" label="target file" help="target file associated with the .CEL file dataset"/>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
29
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
30 <!--param name="normalisation" type="select" label="Preprocessing/normalization">
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
31 <options>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
32 <option value="rma">rma</option>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
33 <option value="quantile">quantile normalization</option>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
34 <option value="log2">log2</option>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
35 <option value="none">none</option>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
36 </options>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
37 </param-->
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
38
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
39 <param name="selectCondition1" type="select" display="checkboxes" label="Condition 1" multiple="true">
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
40 <options from_dataset="target">
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
41 <column name="name" index="0"/>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
42 <column name="value" index="0"/>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
43 </options>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
44 </param>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
45
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
46 <param name="selectCondition2" type="select" display="checkboxes" label="Condition 2" multiple="true">
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
47 <options from_dataset="target">
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
48 <column name="name" index="0"/>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
49 <column name="value" index="0"/>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
50 </options>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
51 </param>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
52
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
53 </inputs>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
54 <outputs>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
55 <data format="html" name="result_html" label="Annotations"/>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
56 <data format="rdata" name="result_export_eset" label="export expressionSet"/>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
57 <data format="cond" name="result_export_conditions" label="export conditions"/>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
58 </outputs>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
59
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
60 <help>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
61 NOTE: This wrapper performs p-value combination from multiples studies with the same probes. If you need to normalize your data, use "matrix_normalisation" tool on each file. Then, use "Merge Standard datasets(copied)" tool to make a multiple file dataset.
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
62 </help>
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
63
27ffdb495852 Imported from capsule None
sblanck
parents:
diff changeset
64 </tool>