Mercurial > repos > galaxyp > quantp

annotate quantp.xml @ 2:ed0bb50d7ffe draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
author galaxyp
date Wed, 09 Jan 2019 16:59:24 -0500
parents bcc7a4c4cc29
children a8bedebab467
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
1 <tool id="quantp" name="QuanTP" version="1.1.1">
0
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
2 <description>Correlation between protein and transcript abundances</description>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
3 <requirements>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
4 <requirement type="package" version="1.10.4">r-data.table</requirement>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
5 <requirement type="package" version="3.0.1">r-gplots</requirement>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
6 <requirement type="package" version="0.7.6">r-dplyr</requirement>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
7 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
8 <requirement type="package" version="0.4.5">r-ggfortify</requirement>
1
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f
galaxyp
parents: 0
diff changeset
9 <requirement type="package" version="4.8.0">r-plotly</requirement>
2
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
10 <requirement type="package" version="0.6.1.1">r-d3heatmap</requirement>
0
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
11 </requirements>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
13 Rscript '$__tool_directory__/quantp.r'
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
14 $experiment_design_option.sample_type
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
15 $experiment_design_option.method_type
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
16 $experiment_design_option.exp_design
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
17 '$pe_exp'
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
18 '$te_exp'
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
19 $experiment_design_option.correction_method
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
20 $cooksd_upper
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
21 $nclust
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
22 $hm_nclust
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
23 $experiment_design_option.volcano_with
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
24 '$html_file'
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
25 '$html_file.files_path'
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
26 ]]></command>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
27 <inputs>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
28 <param name="pe_exp" type="data" format="tabular" label="Input Protein Abundance File" help="Protein abundance input file"/>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
29 <param name="te_exp" type="data" format="tabular" label="Input RNA Abundance File" help="Transcript abundance input file"/>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
30 <conditional name="experiment_design_option">
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
31 <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">
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
32 <option value="multiple" selected="True">Abundances from different conditions with or without replicates (in multiple columns)</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
33 <option value="logfold">Log fold-change values (or single condition abundance without replicates in single column) data</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
34 </param>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
35 <when value="logfold">
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
36 <param name="exp_design" type="hidden" value="none" />
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
37 <param name="method_type" type="hidden" value="none" />
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
38 <param name="correction_method" type="hidden" value="none" />
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
39 <param name="volcano_with" type="hidden" value="pval" />
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
40 </when>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
41 <when value="multiple">
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
42 <param name="exp_design" type="data" format="tabular" help="Please check the format of the experiment design file">
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
43 <label>Experiment design File (Please see the format below)</label>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
44 </param>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
45 <param name="method_type" type="select" label="Data summarization method" help="Perform T-Test on selecting Mean; Wilcoxon Ranksum Test on selecting Median">
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
46 <option value="mean" selected="True">Mean (Default)</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
47 <option value="median">Median</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
48 </param>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
49 <param name="correction_method" type="select" label="Multiple testing correction method">
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
50 <option value="BH" selected="True">Benjamini and Hochberg (BH) (Default)</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
51 <option value="holm">Holm</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
52 <option value="hochberg">Hochberg</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
53 <option value="hommel">Hommel</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
54 <option value="bonferroni">Bonferroni</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
55 <option value="BY">Benjamini and Yekutieli (BY)</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
56 <option value="none">None</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
57 </param>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
58 <param name="volcano_with" type="select" display="radio" label="Volcano plot with p-value or adjusted p-value">
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
59 <option value="pval" selected="True">P-value (Default)</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
60 <option value="adj_pval">Adjusted P-value</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
61 </param>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
62 </when>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
63 </conditional>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
64 <param name="cooksd_upper" type="integer" value="4" optional="false" >
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
65 <label>Influential Observation cutoff: Observations > value * mean of Cook's distances (Default: "4" * mean(Cook's Distance))</label>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
66 </param>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
67 <param name="nclust" type="select" label="K-mean clustering: Number of clusters">
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
68 <option value="1">1</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
69 <option value="2">2</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
70 <option value="3">3</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
71 <option value="4" selected="True">4</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
72 <option value="5">5</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
73 <option value="6">6</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
74 <option value="7">7</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
75 <option value="8">8</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
76 <option value="9">9</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
77 <option value="10">10</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
78 </param>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
79
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
80 <param name="hm_nclust" type="select" label="Hierarchical clustering: Number of clusters (from Heatmap)">
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
81 <option value="1">1</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
82 <option value="2">2</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
83 <option value="3">3</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
84 <option value="4">4</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
85 <option value="5" selected="True">5</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
86 <option value="6">6</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
87 <option value="7">7</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
88 <option value="8">8</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
89 <option value="9">9</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
90 <option value="10">10</option>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
91 </param>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
92 </inputs>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
93 <outputs>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
94 <data format="html" name="html_file" label="protein transcript correlation on ${pe_exp.name} and ${te_exp.name}"/>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
95 </outputs>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
96 <tests>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
97 <test>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
98 <conditional name="experiment_design_option">
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
99 <param name="sample_type" value="multiple"/>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
100 <param name="method_type" value="mean"/>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
101 <param name="exp_design" value="exp_design_file.tabular" ftype="tabular" />
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
102 <param name="correction_method" value="BH"/>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
103 <param name="volcano_with" value="pval"/>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
104 </conditional>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
105 <param name="pe_exp" value="protein_data.tabular" ftype="tabular" />
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
106 <param name="te_exp" value="transcript_data.tabular" ftype="tabular" />
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
107 <param name="cooksd_upper" value="4"/>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
108 <param name="nclust" value="4"/>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
109 <param name="hm_nclust" value="5"/>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
110 <output name="html_file">
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
111 <assert_contents>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
112 <has_text text="SAMPLE DISTRIBUTION" />
1
bcc7a4c4cc29 planemo upload commit 1887dff812162880d66b003a927867cd5000c98f
galaxyp
parents: 0
diff changeset
113 <has_text text="plotly" />
0
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
114 </assert_contents>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
115 </output>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
116 </test>
2
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
117 <test>
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
118 <conditional name="experiment_design_option">
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
119 <param name="sample_type" value="logfold"/>
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
120 <param name="correction_method" value="BH"/>
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
121 <param name="volcano_with" value="pval"/>
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
122 </conditional>
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
123 <param name="pe_exp" value="mouse_protein_log_data.txt" ftype="tabular" />
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
124 <param name="te_exp" value="mouse_transcript_log_data.txt" ftype="tabular" />
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
125 <param name="cooksd_upper" value="4"/>
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
126 <param name="nclust" value="4"/>
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
127 <param name="hm_nclust" value="5"/>
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
128 <output name="html_file">
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
129 <assert_contents>
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
130 <has_text text="SAMPLE DISTRIBUTION" />
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
131 <has_text text="plotly" />
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
132 </assert_contents>
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
133 </output>
ed0bb50d7ffe planemo upload commit bd6bc95760db6832c77d4d2872281772c31f9039
galaxyp
parents: 1
diff changeset
134 </test>
0
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
135 </tests>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
136 <help><![CDATA[
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
137
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
138 **What it does**
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
139
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
140 QuanTP correlates *transcript abundance* and *protein abundance* to examine the association between them.
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
141
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
142 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.
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
143
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
144 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.
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
145
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
146 -----
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
147
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
148 **Input file formats**
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
149
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
150 **Protein data file**
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
151
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
152 First column - Gene
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
153
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
154 Following columns - Abundance values (or log fold-change values)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
155
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
156 Example of Protein input file
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
157
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
158 ====== ========= ========= ========= ========= ========= ========= ========= =========
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
159 Gene sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
160 ------ --------- --------- --------- --------- --------- --------- --------- ---------
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
161 GeneX value value value value value value value value
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
162 GeneY value value value value value value value value
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
163 GeneZ value value value value value value value value
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
164 ====== ========= ========= ========= ========= ========= ========= ========= =========
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
165
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
166
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
167 **Transcript data file**
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
168
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
169 First column - Gene
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
170
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
171 Following columns - Abundance values (or log fold-change values)
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
172
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
173 Example of Transcript input file
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
174
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
175 ====== ========= ========= ========= ========= ========= ========= ========= =========
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
176 Gene sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
177 ------ --------- --------- --------- --------- --------- --------- --------- ---------
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
178 GeneX value value value value value value value value
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
179 GeneY value value value value value value value value
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
180 GeneZ value value value value value value value value
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
181 ====== ========= ========= ========= ========= ========= ========= ========= =========
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
182
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
183
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
184 **Data input type**
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
185
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
186 If data input type is abundance, experiment design file is required.
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
187
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
188 Example of experiment design file
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
189
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
190 ======== =========
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
191 case groupA
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
192 control groupB
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
193 sample1 groupA
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
194 sample2 groupA
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
195 sample3 groupA
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
196 sample4 groupA
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
197 sample5 groupB
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
198 sample6 groupB
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
199 sample7 groupB
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
200 sample8 groupB
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
201 ======== =========
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
202
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
203 Note: No title/header in experiment design file and the first two lines of the experiment design must have keyword "case" and "control"
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
204
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
205 ]]>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
206 </help>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
207 <citations>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
208 <citation type="bibtex">
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
209 @misc{QuanTP: A software resource for quantitative proteo-transcriptomic comparative data analysis and informatics,
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
210 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},
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
211 year={2018},
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
212 title={QuanTP}
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
213 }
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
214 </citation>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
215 </citations>
75faf9a89f5b planemo upload commit a0e968c7bd2b6f7b963baeecb08f3a39e50f52d6
galaxyp
parents:
diff changeset
216 </tool>