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comparison galaxy/wrappers/FactorFileGenerator.xml @ 0:4764dc6a1019 draft

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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
author vandelj
date Fri, 26 Jun 2020 09:51:15 -0400
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1 <tool name="GIANT-Factor file generator" id="giant_factor_generator" version="0.1.2">
2 <description>Generate factor file used by other GIANT tools</description>
3 <requirements>
4 </requirements>
5 <code file="../../src/General_functions.py"/>
6 <stdio>
7 <regex match="Execution halted"
8 source="both"
9 level="fatal"
10 description="Execution halted, please contact tool developer or administrators." />
11 <regex match="Error in"
12 source="both"
13 level="fatal"
14 description="An error occured during R execution, please contact tool developer." />
15 <exit_code range="1:9" level="fatal" description="Error during factor file generation, see log file for more information." />
16 </stdio>
17 <command> <![CDATA[
18
19 #import imp
20 #set $general_functions=$imp.load_source('General_functions', $__tool_directory__+'/../../src/General_functions.py')
21
22 #set $ret_code=$general_functions.generateFactorFile($inputCondition['inputData'],$factorsSection['factorList'],$outputData.file_name,$log.file_name)
23
24 if [ $ret_code != 0 ]; then
25 printf "[ERROR]Error during factor file generation\n" >> $log;
26 exit $ret_code;
27 fi;
28
29 printf "[INFO]End of tool script" >> $log;
30 ]]>
31 </command>
32 <inputs>
33 <param type="text" name="title" value="ConditionsGenerator_toPersonalize" label="Title for output"/>
34
35 <conditional name="inputCondition">
36 <param name="selection" type="select" label="Input data type for sample names" force_select="true">
37 <option value="normalizedData">Expression tabular file</option>
38 <option value="CELcollection">.CEL files</option>
39 </param>
40 <when value="normalizedData">
41 <param type="data" name="inputData" format="tabular" label="Select file" optional="false" multiple="false"/>
42 </when>
43 <when value="CELcollection">
44 <param type="data" name="inputData" format="cel" label="Select files" optional="false" multiple="true">
45 <validator type="empty_dataset" message="At least one data file should be selected"></validator>
46 </param>
47 </when>
48 </conditional>
49
50 <section name="factorsSection" title="Factor definition" expanded="True">
51 <repeat name="factorList" title="Factor">
52 <param type="text" name="factorName" value="" label="Factor name"/>
53 <repeat name="valueList" title="Value">
54 <param type="text" name="valueName" value="" label="Value name"/>
55 <param name="valueConditions" type="select" optional="false" multiple="true" label="Select sample sharing this value"
56 refresh_on_change="true" dynamic_options="get_condition_file_names(inputCondition['inputData'])">
57 </param>
58 </repeat>
59 </repeat>
60 </section>
61
62 </inputs>
63
64 <outputs>
65 <data format="tabular" name="outputData" label="${title}_conditionsFile"/>
66
67 <data format="txt" name="log" label="${title}_Log" />
68 </outputs>
69
70 <tests>
71 <test maxseconds="3600">
72 <param name="wfile" value="wiggle.wig" />
73 <param name="bfile" value="bedfile.bed" />
74 <param name="span" value="3000" />
75 <param name="pfres" value="50" />
76 <param name="lowersize" value="1000" />
77 <param name="middlesize" value="2000" />
78 <param name="uppersize" value="3000" />
79 <param name="lowerbisize" value="2500" />
80 <param name="upperbisize" value="5000" />
81 <param name="reldist" value="3000" />
82 <param name="genome" value="hg18" />
83 <param name="imagetype" value="PDF" />
84 <param name="enable" value="no" />
85 <output name="outputData" file="ceas_1/ceas_1.pdf" />
86 </test>
87 </tests>
88 <help>
89 <![CDATA[
90 **What it does ?**
91
92 This tool generates factor information file used by other tools of GIANT tool suite.
93
94 -----
95
96 **Parameters**
97
98 \- **Title** to personalize output file names (please avoid special characters and spaces).
99
100 \- **Input Data** used only to extract sample names
101
102 - **Expression tabular file** with samples as columns and genes as rows (only the header row will be used to extract sample names).
103
104 ::
105
106 Conditions 157_(HuGene-2_0-st).CEL 156_(HuGene-2_0-st).CEL 155_(HuGene-2_0-st).CEL 154_(HuGene-2_0-st).CEL
107 DDX11L2 4.500872 4.429759 4.780281 4.996189
108 MIR1302-2 3.415065 3.520472 3.471503 3.567988
109 OR4F5 3.737956 3.011586 3.424494 3.497545
110 VWA1 5.189621 5.129595 4.806793 5.227014
111
112 OR
113
114 - **.CEL files** of your study (you should select multiple .CEL files or unique collection file).
115
116 \- **Factor definition**
117
118 - **Factor name** to discriminate between samples as 'Treatments', 'Year', 'Strain' (please avoid special characters)
119
120 - **Value name** of different states for the current factor as 'KO' or 'WT' for 'Strain' factor (please avoid special characters)
121
122 - **Select sample** to assign to current value
123
124 -----
125
126 **Outputs**
127
128 - **Factor information tabular file** with factors as columns and samples as rows (header row contains factor names and first column sample names).
129
130 ::
131
132 Conditions Sex Treatment Reaction
133 138_(HuGene-2_0-st).CEL 1 TreatA Pos
134 148_(HuGene-2_0-st).CEL 0 NoTreat Pos
135 139_(HuGene-2_0-st).CEL 0 TreatB Neg
136 149_(HuGene-2_0-st).CEL 0 NoTreat Neg
137
138 - **LOG file** for job log. If you see errors, please attached this in the bug report
139
140 ]]> </help>
141
142 <citations>
143 </citations>
144
145 </tool>