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author galaxyp
date Fri, 14 Sep 2018 12:22:31 -0400
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1 <tool id="quantp" name="QuanTP" version="1.0.0">
2 <description>Correlation between protein and transcript abundances</description>
3 <requirements>
4 <requirement type="package" version="1.10.4">r-data.table</requirement>
5 <requirement type="package" version="3.0.1">r-gplots</requirement>
6 <requirement type="package" version="0.7.6">r-dplyr</requirement>
7 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
8 <requirement type="package" version="0.4.5">r-ggfortify</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 Rscript '$__tool_directory__/quantp.r'
12 $experiment_design_option.sample_type
13 $experiment_design_option.method_type
14 $experiment_design_option.exp_design
15 '$pe_exp'
16 '$te_exp'
17 $experiment_design_option.correction_method
18 $cooksd_upper
19 $nclust
20 $hm_nclust
21 $experiment_design_option.volcano_with
22 '$html_file'
23 '$html_file.files_path'
24 ]]></command>
25 <inputs>
26 <param name="pe_exp" type="data" format="tabular" label="Input Protein Abundance File" help="Protein abundance input file"/>
27 <param name="te_exp" type="data" format="tabular" label="Input RNA Abundance File" help="Transcript abundance input file"/>
28 <conditional name="experiment_design_option">
29 <param name="sample_type" type="select" label="Select data input type" help="If the input files already have fold-change values, select Log fold-change. Else, select abundances and the tool will perform the fold-change analysis">
30 <option value="multiple" selected="True">Abundances from different conditions with or without replicates (in multiple columns)</option>
31 <option value="logfold">Log fold-change values (or single condition abundance without replicates in single column) data</option>
32 </param>
33 <when value="logfold">
34 <param name="exp_design" type="hidden" value="none" />
35 <param name="method_type" type="hidden" value="none" />
36 <param name="correction_method" type="hidden" value="none" />
37 <param name="volcano_with" type="hidden" value="pval" />
38 </when>
39 <when value="multiple">
40 <param name="exp_design" type="data" format="tabular" help="Please check the format of the experiment design file">
41 <label>Experiment design File (Please see the format below)</label>
42 </param>
43 <param name="method_type" type="select" label="Data summarization method" help="Perform T-Test on selecting Mean; Wilcoxon Ranksum Test on selecting Median">
44 <option value="mean" selected="True">Mean (Default)</option>
45 <option value="median">Median</option>
46 </param>
47 <param name="correction_method" type="select" label="Multiple testing correction method">
48 <option value="BH" selected="True">Benjamini and Hochberg (BH) (Default)</option>
49 <option value="holm">Holm</option>
50 <option value="hochberg">Hochberg</option>
51 <option value="hommel">Hommel</option>
52 <option value="bonferroni">Bonferroni</option>
53 <option value="BY">Benjamini and Yekutieli (BY)</option>
54 <option value="none">None</option>
55 </param>
56 <param name="volcano_with" type="select" display="radio" label="Volcano plot with p-value or adjusted p-value">
57 <option value="pval" selected="True">P-value (Default)</option>
58 <option value="adj_pval">Adjusted P-value</option>
59 </param>
60 </when>
61 </conditional>
62 <param name="cooksd_upper" type="integer" value="4" optional="false" >
63 <label>Influential Observation cutoff: Observations > value * mean of Cook's distances (Default: "4" * mean(Cook's Distance))</label>
64 </param>
65 <param name="nclust" type="select" label="K-mean clustering: Number of clusters">
66 <option value="1">1</option>
67 <option value="2">2</option>
68 <option value="3">3</option>
69 <option value="4" selected="True">4</option>
70 <option value="5">5</option>
71 <option value="6">6</option>
72 <option value="7">7</option>
73 <option value="8">8</option>
74 <option value="9">9</option>
75 <option value="10">10</option>
76 </param>
77
78 <param name="hm_nclust" type="select" label="Hierarchical clustering: Number of clusters (from Heatmap)">
79 <option value="1">1</option>
80 <option value="2">2</option>
81 <option value="3">3</option>
82 <option value="4">4</option>
83 <option value="5" selected="True">5</option>
84 <option value="6">6</option>
85 <option value="7">7</option>
86 <option value="8">8</option>
87 <option value="9">9</option>
88 <option value="10">10</option>
89 </param>
90 </inputs>
91 <outputs>
92 <data format="html" name="html_file" label="protein transcript correlation on ${pe_exp.name} and ${te_exp.name}"/>
93 </outputs>
94 <tests>
95 <test>
96 <conditional name="experiment_design_option">
97 <param name="sample_type" value="multiple"/>
98 <param name="method_type" value="mean"/>
99 <param name="exp_design" value="exp_design_file.tabular" ftype="tabular" />
100 <param name="correction_method" value="BH"/>
101 <param name="volcano_with" value="pval"/>
102 </conditional>
103 <param name="pe_exp" value="protein_data.tabular" ftype="tabular" />
104 <param name="te_exp" value="transcript_data.tabular" ftype="tabular" />
105 <param name="cooksd_upper" value="4"/>
106 <param name="nclust" value="4"/>
107 <param name="hm_nclust" value="5"/>
108 <output name="html_file">
109 <assert_contents>
110 <has_text text="SAMPLE DISTRIBUTION" />
111 </assert_contents>
112 </output>
113 </test>
114 </tests>
115 <help><![CDATA[
116
117 **What it does**
118
119 QuanTP correlates *transcript abundance* and *protein abundance* to examine the association between them.
120
121 It either takes in the log fold-change of abundances as input or raw abundances from different conditions where it calculates the log ratios of abundances between two conditions.
122
123 Transcript input file can be generated from the quantitative RNA-Seq study whereas Protein input file can be generated from quantitative analysis of mass-spectrometry-based protein data.
124
125 -----
126
127 **Input file formats**
128
129 **Protein data file**
130
131 First column - Gene
132
133 Following columns - Abundance values (or log fold-change values)
134
135 Example of Protein input file
136
137 ====== ========= ========= ========= ========= ========= ========= ========= =========
138 Gene sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8
139 ------ --------- --------- --------- --------- --------- --------- --------- ---------
140 GeneX value value value value value value value value
141 GeneY value value value value value value value value
142 GeneZ value value value value value value value value
143 ====== ========= ========= ========= ========= ========= ========= ========= =========
144
145
146 **Transcript data file**
147
148 First column - Gene
149
150 Following columns - Abundance values (or log fold-change values)
151
152 Example of Transcript input file
153
154 ====== ========= ========= ========= ========= ========= ========= ========= =========
155 Gene sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8
156 ------ --------- --------- --------- --------- --------- --------- --------- ---------
157 GeneX value value value value value value value value
158 GeneY value value value value value value value value
159 GeneZ value value value value value value value value
160 ====== ========= ========= ========= ========= ========= ========= ========= =========
161
162
163 **Data input type**
164
165 If data input type is abundance, experiment design file is required.
166
167 Example of experiment design file
168
169 ======== =========
170 case groupA
171 control groupB
172 sample1 groupA
173 sample2 groupA
174 sample3 groupA
175 sample4 groupA
176 sample5 groupB
177 sample6 groupB
178 sample7 groupB
179 sample8 groupB
180 ======== =========
181
182 Note: No title/header in experiment design file and the first two lines of the experiment design must have keyword "case" and "control"
183
184 ]]>
185 </help>
186 <citations>
187 <citation type="bibtex">
188 @misc{QuanTP: A software resource for quantitative proteo-transcriptomic comparative data analysis and informatics,
189 author={Praveen Kumar, Priyabrata Panigrahi, James Johnson, Wanda Weber, Subina Mehta, Ray Sajulga, Caleb Easterly, Brian Crooker, Mohammad Heydarian, Krishanpal Anamika, Timothy Griffin, and Pratik Jagtap},
190 year={2018},
191 title={QuanTP}
192 }
193 </citation>
194 </citations>
195 </tool>