|
2
|
1 <tool id="sartools_edger" name="SARTools edgeR" version="@WRAPPER_VERSION@.0">
|
|
0
|
2
|
|
|
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
|
|
|
4 <description>Compare two or more biological conditions in a RNA-Seq framework with edgeR</description>
|
|
|
5
|
|
|
6 <macros>
|
|
|
7 <import>macros.xml</import>
|
|
|
8 </macros>
|
|
|
9
|
|
|
10 <expand macro="requirements"/>
|
|
|
11 <expand macro="stdio"/>
|
|
|
12
|
|
|
13
|
|
|
14 <!-- [REQUIRED] The command to execute -->
|
|
|
15 <command interpreter="python"><![CDATA[
|
|
|
16
|
|
|
17 abims_sartools_edger_wrapper.py
|
|
|
18 ## parameters
|
|
|
19 @COMMAND_BASIC_PARAMETERS@
|
|
|
20 #if str( $advanced_parameters.adv_param ) == "show":
|
|
|
21 @COMMAND_BATCH_PARAM@
|
|
|
22 --alpha $advanced_parameters.alpha
|
|
|
23 --pAdjustMethod $advanced_parameters.pAdjustMethod
|
|
|
24 --cpmCutoff $advanced_parameters.cpmCutoff
|
|
|
25 --geneSelection $advanced_parameters.geneSelection
|
|
|
26 --normalizationMethod $advanced_parameters.normalizationMethod
|
|
|
27 --colors $advanced_parameters.colors
|
|
|
28 #end if
|
|
|
29 ## ouputs
|
|
|
30 @COMMAND_OUTPUTS@
|
|
|
31
|
|
|
32 ]]></command>
|
|
|
33
|
|
|
34 <!-- [REQUIRED] Input files and tool parameters -->
|
|
|
35 <inputs>
|
|
|
36
|
|
|
37 <expand macro="basic_parameters" />
|
|
|
38
|
|
|
39 <conditional name="advanced_parameters" >
|
|
|
40 <param name="adv_param" type="select" label="Advanced Parameters" help="" >
|
|
|
41 <option value="hide" selected="true">Hide</option>
|
|
|
42 <option value="show">Show</option>
|
|
|
43 </param>
|
|
|
44 <when value="hide" />
|
|
|
45 <when value="show">
|
|
|
46 <expand macro="batch_param" />
|
|
|
47 <expand macro="alpha_param" />
|
|
|
48 <expand macro="padjustmethod_param" />
|
|
|
49 <param name="cpmCutoff" type="integer" value="1" min="0" label="Counts-per-million cut-off to filter low counts" help="(-m, --cpmCutoff) Set to 0 to disable filtering. Default is 1." />
|
|
|
50 <param name="geneSelection" type="select" label="Selection of the features in MDSPlot" help="(-g, --gene.selection) Default is 'pairwise'." >
|
|
|
51 <option value="pairwise" selected="true">pairwise</option>
|
|
|
52 <option value="common">common</option>
|
|
|
53 </param>
|
|
|
54 <param name="normalizationMethod" type="select" label="Normalization method in calcNormFactors" help="(-n, --normalizationMethod) 'TMM' (default), 'RLE' (DESeq method) or 'upperquartile'." >
|
|
|
55 <option value="TMM" selected="true">TMM</option>
|
|
|
56 <option value="RLE">RLE</option>
|
|
|
57 <option value="upperquartile">upperquartile</option>
|
|
|
58 </param>
|
|
|
59 <expand macro="colors_param" />
|
|
|
60 </when>
|
|
|
61 </conditional>
|
|
|
62
|
|
|
63 </inputs>
|
|
|
64
|
|
|
65 <!-- [REQUIRED] Output files -->
|
|
|
66 <outputs>
|
|
|
67
|
|
|
68 <expand macro="outputs" />
|
|
|
69
|
|
|
70 </outputs>
|
|
|
71
|
|
|
72 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
|
|
|
73 <tests>
|
|
|
74 <!-- [HELP] Test files have to be in the ~/test-data directory -->
|
|
|
75 <test>
|
|
|
76 <!-- Test with 2 conditions, 2 replicates, 10 features -->
|
|
|
77 <param name="targetFile" dbkey="?" value="target_small.txt" />
|
|
|
78 <param name="rawDir" value="raw_small.zip" dbkey="?" ftype="zip"/>
|
|
|
79 <param name="adv_param" value="show"/>
|
|
|
80 <output name="log">
|
|
|
81 <assert_contents>
|
|
|
82 <has_text text="KO vs WT 5 4 9" />
|
|
|
83 <has_text text="HTML report created" />
|
|
|
84 </assert_contents>
|
|
|
85 </output>
|
|
|
86 </test>
|
|
|
87 <!-- <test>
|
|
|
88 --> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10 features, with batch effect -->
|
|
|
89 <!-- <param name="targetFile" dbkey="?" value="targetT048_small.txt" />
|
|
|
90 <param name="rawDir" value="rawT048_small.zip" dbkey="?" ftype="no_unzip.zip"/>
|
|
|
91 <param name="condRef" value="T0"/>
|
|
|
92 <param name="adv_param" value="show"/>
|
|
|
93 <param name="condition" value="true"/>
|
|
|
94 <output name="tables_html" file="SARTools_edgeR_targetT048_small_tables.html" lines_diff="12">
|
|
|
95 <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0_small.complete.txt"/>
|
|
|
96 <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0_small.complete.txt"/>
|
|
|
97 <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4_small.complete.txt"/>
|
|
|
98 </output>
|
|
|
99 </test>
|
|
|
100 --> <test>
|
|
|
101 <!-- Test with 2 conditions, 2 replicates, 8217 features -->
|
|
|
102 <param name="targetFile" dbkey="?" value="target.txt" />
|
|
|
103 <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/>
|
|
|
104 <param name="adv_param" value="show"/>
|
|
|
105 <output name="log">
|
|
|
106 <assert_contents>
|
|
|
107 <has_text text="KO vs WT 2691 2713 5404" />
|
|
|
108 <has_text text="HTML report created" />
|
|
|
109 </assert_contents>
|
|
|
110 </output>
|
|
|
111 </test>
|
|
|
112 <!-- <test>
|
|
|
113 --> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect -->
|
|
|
114 <!-- <param name="targetFile" dbkey="?" value="targetT048.txt" />
|
|
|
115 <param name="rawDir" value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/>
|
|
|
116 <param name="condRef" value="T0"/>
|
|
|
117 <param name="adv_param" value="show"/>
|
|
|
118 <param name="condition" value="true"/>
|
|
|
119 <output name="tables_html" file="SARTools_edgeR_targetT048_tables.html" lines_diff="14">
|
|
|
120 <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0.complete.txt"/>
|
|
|
121 <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0.complete.txt"/>
|
|
|
122 <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4.complete.txt"/>
|
|
|
123 </output>
|
|
|
124 </test>
|
|
|
125 --> </tests>
|
|
|
126
|
|
|
127 <!-- [OPTIONAL] Help displayed in Galaxy -->
|
|
|
128 <help><![CDATA[
|
|
|
129
|
|
|
130 @HELP_AUTHORS@
|
|
|
131
|
|
|
132 ==============
|
|
|
133 SARTools edgeR
|
|
|
134 ==============
|
|
|
135
|
|
|
136 -----------
|
|
|
137 Description
|
|
|
138 -----------
|
|
|
139
|
|
|
140 @HELP_DESCRIPTION@
|
|
|
141
|
|
|
142
|
|
|
143 -----------
|
|
|
144 Input files
|
|
|
145 -----------
|
|
|
146
|
|
|
147 @HELP_INPUT_FILES@
|
|
|
148
|
|
|
149
|
|
|
150 ----------
|
|
|
151 Parameters
|
|
|
152 ----------
|
|
|
153
|
|
|
154 @HELP_BASIC_PARAMETERS@
|
|
|
155 * **batch:** adjustment variable to use as a batch effect, must be a column of the target file (NULL if no batch effect needs to be taken into account);
|
|
|
156 * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05);
|
|
|
157 * **pAdjustMethod:** p-value adjustment method for multiple testing [4, 5] ("BH" by default, "BY" or any value of p.adjust.methods);
|
|
|
158 * **cpmCutoff:** counts-per-million cut-off to filter low counts (default is 1, set to 0 to disable filtering);
|
|
|
159 * **gene.selection:** method of selection of the features for the MultiDimensional Scaling plot ("pairwise" by default or common);
|
|
|
160 * **normalizationMethod:** normalization method in calcNormFactors(): "TMM" (default), "RLE" (DESeq method) or "upperquartile";
|
|
|
161 * **colors:** colors used for the figures (one per biological condition), 8 are given by default.
|
|
|
162
|
|
|
163
|
|
|
164 ------------
|
|
|
165 Output files
|
|
|
166 ------------
|
|
|
167
|
|
|
168 @HELP_OUTPUT_FILES@
|
|
|
169
|
|
|
170
|
|
|
171 ---------------------------------------------------
|
|
|
172
|
|
|
173 [1] G.-K. Smyth. Limma: linear models for microarray data. In R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber, editors, Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pages 397–420. Springer, New York, 2005.
|
|
|
174
|
|
|
175 [2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011.
|
|
|
176
|
|
|
177 [3] S. Anders, P.-T. Pyl, and W. Huber. HTSeq - A Python framework to work with high-throughput sequencing data. bioRxiv preprint, 2014. URL: http://dx.doi.org/10.1101/002824.
|
|
|
178
|
|
|
179 [4] Y. Benjamini and Y. Hochberg. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, 57:289–300, 1995.
|
|
|
180
|
|
|
181 [5] Y. Benjamini and D. Yekutieli. The control of the false discovery rate in multiple testing under dependency. Ann. Statist., 29(4):1165–1188, 2001.
|
|
|
182
|
|
|
183
|
|
|
184 ]]></help>
|
|
|
185
|
|
|
186 <citations>
|
|
|
187 <expand macro="common_citations" />
|
|
|
188 </citations>
|
|
|
189
|
|
|
190 </tool>
|
