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comparison abims_sartools_edger.xml @ 0:581d217c7337 draft

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author lgueguen
date Fri, 22 Jul 2016 05:39:13 -0400
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-1:000000000000 0:581d217c7337
1 <tool id="sartools_edger" name="SARTools edgeR" version="1.0.0">
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>