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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:50:41 -0400
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1 <tool id="expressions" name="TEA" version="1.0.0">
2 <description>Tiling Expression Analizer</description>
3 <command interpreter="perl">calcolo_p_v4_norm_intron.pl -opt ${ann_choice.type1} -log ${ann_choice.type_data} -ann ${ann_choice.ann} -wt ${ann_choice.wt} -treat ${ann_choice.treat} -out $output -fdr ${ann_choice.fdr} -pv ${ann_choice.pv} -norm ${ann_choice.norm} -rc ${ann_choice.rc} -fc ${ann_choice.summary_choice.fc} -exon ${ann_choice.type} -sum_met ${ann_choice.summary_choice.fc_output}</command>
4 <inputs>
5 <conditional name="ann_choice">
6 <param name="type1" type="select" label="Analysis type">
7 <option value="comp">comparison</option>
8 <option value="expr">expression</option>
9 </param>
10
11 <when value="comp">
12 <param format="tabular" name="ann" type="data" label="annotation file"/>
13 <param format="tabular" name="wt" type="data" label="expression chip condition A"/>
14 <param format="tabular" name="treat" type="data" label="expression chip condition B"/>
15 <param name="type_data" type="select" label="Data type">
16 <option value="log">log2 value</option>
17 <option value="no_log">raw value</option>
18 </param>
19 <param name="norm" type="select" label="Normalization">
20 <option value="yes">quantile-normalization</option>
21 <option value="no">no normalization</option>
22 </param>
23 <param name="type" type="select" label="probes selection">
24 <option value="internal_exon">internal exon</option>
25 <option value="all_exon">all exon</option>
26 <option value="last_exon">last exon</option>
27 </param>
28 <conditional name="summary_choice">
29 <param name="fc_output" type="select" label="summary method">
30 <option value="mean">mean</option>
31 <option value="median">median</option>
32 <option value="both">both</option>
33 </param>
34 <when value="mean">
35 <param name="fc" size="3" type="text" value="1.5" label="Fold change cutoff"/>
36 </when>
37 <when value="median">
38 <param name="fc" size="3" type="text" value="1.5" label="Fold change cutoff"/>
39 </when>
40 <when value="both">
41 <param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/>
42 </when>
43 </conditional>
44 <param name="rc" size="2" type="text" value="7" label="raw value cutoff (log2)"/>
45 <param name="fdr" type="select" label="FDR correction">
46 <option value="yes">yes</option>
47 <option value="no">no</option>
48 </param>
49 <param name="pv" size="4" type="text" value="0.05" label="p-value cutoff"/>
50
51
52
53 </when>
54 <when value="expr">
55 <param format="tabular" name="ann" type="data" label="annotation file"/>
56 <param format="tabular" name="wt" type="data" label="expression chip"/>
57 <param format="tabular" name="treat" type="data" label="NOT NEEDED"/>
58 <param name="type_data" type="select" label="Data type">
59 <option value="log">log2 value</option>
60 <option value="no_log">raw value</option>
61 </param>
62 <param name="type" type="select" label="probes selection">
63 <option value="internal_exon">internal exon</option>
64 <option value="all_exon">all exon</option>
65 <option value="last_exon">last exon</option>
66 </param>
67 <conditional name="summary_choice">
68 <param name="fc_output" type="select" label="summary method">
69 <option value="mean">mean</option>
70 <option value="median">median</option>
71 <option value="both">both</option>
72 </param>
73 <when value="mean">
74 <param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/>
75 </when>
76 <when value="median">
77 <param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/>
78 </when>
79 <when value="both">
80 <param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/>
81 </when>
82 </conditional>
83 <param name="norm" size="12" type="text" value="NOT-NEEDED" label="Normalization"/>
84 <param name="pv" size="12" type="text" value="NOT-NEEDED" label="p-value cutoff"/>
85 <param name="fdr" size="12" type="text" value="NOT-NEEDED" label="FDR correction"/>
86 <param name="rc" size="12" type="text" value="NOT-NEEDED" label="raw value cutoff (log2)"/>
87 </when>
88 </conditional>
89
90
91 </inputs>
92 <outputs>
93 <data format="tabular" name="output" />
94 </outputs>
95
96 <help>
97 .. class:: infomark
98
99 **What it does**
100
101 TEA utilizes NimbleGen expression files in gff format and annotated table by ENO as INPUT FILES and generates a table with the expression value. When comparing two different conditions a Fold Change and a p-value are calculated.
102
103 PLEASE, for more detailed information refer to the CARPET user Manual:
104 click to download_ it.
105
106 .. _download: /static/example_file/CARPET_userManual.zip
107
108 --------
109
110 **Parameters:**
111
112 - **Analysis type:**
113 - **expression** analysis calculates an expression value for each transcript coming from the mean or the median of all matching probes
114 - **comparison** analysis calculate an expression value for each transcript in both conditions, then calculates a Fold Change for each transcript and a p-value based on t-Test distribution.
115 - **Data type:**
116 - **log2 value:** the data is not converted in log2
117 - **raw value:** the data is converted in log2
118 - **Normalization:** quantile normalization between the two chips (not necessary if analysis type is "expression")
119 - **probe selection:**
120 - **internal exon:** only probes annotated as exons are used to calculate expression value.
121 - **all exon:** also probes annotated at the boundaries of introns/exons are used to calculate the expression value. (probes in intronexon position usually have lower signal)
122 - **last exon:** only probes in the last exon are used to calculate expression value. This analysis can be preferred for cDNA generated by oligo-dT RT, since 3' of transcripts are generally better represented.
123 - **summary method:**
124 - **mean:** fold change for each gene is calculated based on the mean value
125 - **median:** fold change for each gene is calculated based on the median value
126 - **both:** both are used
127 - **Fold change cutoff:** only transcripts with FC higher than cutoff are kept
128 - **FDR:**
129 - **yes:** False Discovery Rate correction is applied (as described in Storie et al. 2002)
130 - **no:** No correction --> raw p-value
131 - **p-value cutoff:** only transcripts with p-value less than cutoff are kept
132 - **raw value cutoff (log2):** only transcripts with raw value higher than cutoff at least in one experiment are kept
133
134 --------
135
136
137 **INPUT FILE**
138
139 Nimblegen gives you back a GFF file with the coordinates of each probe and the signal raw value.
140
141 Click here_ to download a GFF file example.
142
143 .. _here: /static/example_file/Expression_analysis_files.zip
144
145
146 Example of Nimblegen Expression GFF format::
147
148 chr19 Nimblegen tiling_array 100000 1000051 20459 + . probe_name
149 chr19 Nimblegen tiling_array 100100 1000151 1394 + . probe_name
150
151 .. class:: warningmark
152
153 The sixth column **must** contain the raw signal (**NOT** log2) that Nimblegen gives you back after the experiment
154
155 The annotation table **MUST** be created usign ENO tool, before running TEA.
156
157 ---------
158
159 .. class:: infomark
160
161 **How does it work?**
162
163 For each gene is built the signal distibution of the probes matching Exon.
164
165 -In an expression experiment, the mean or the median of the distribution represents the result of Tea.
166
167 -In a comparison experiment the distibution of the gene exon signal is compared between the two conditions (1 and 2) and a t-test is performed with the possibility to introduce FDR correction.
168
169 .. image:: static/images/CARPET/Tea.png
170
171
172
173
174 **OUTPUT**
175
176 - **expresion**
177
178 .. image:: static/images/CARPET/expression.png
179
180 - **comparison**
181
182 .. image:: static/images/CARPET/comparison.png
183
184 </help>
185
186
187 </tool>