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comparison abims_sartools_deseq2.xml @ 4:05c9b1a7f44e draft default tip

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Uploaded new release 1.7.3
author lgueguen
date Thu, 07 Jan 2021 11:12:01 +0000
parents de6d0b7c17af
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3:de6d0b7c17af 4:05c9b1a7f44e
1 <tool id="sartools_deseq2" name="SARTools DESeq2" version="@WRAPPER_VERSION@.0"> 1 <tool id="sartools_deseq2" name="SARTools DESeq2" version="@TOOL_VERSION@+galaxy0">
2 2
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description>Compare two or more biological conditions in a RNA-Seq framework with DESeq2</description> 3 <description>Compare two or more biological conditions in a RNA-Seq framework with DESeq2</description>
5 4
6 <macros> 5 <macros>
7 <import>macros.xml</import> 6 <import>macros.xml</import>
8 </macros> 7 </macros>
9 8
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
11 <expand macro="stdio"/> 10 <expand macro="stdio"/>
12 11
13 <!-- [REQUIRED] The command to execute --> 12 <command><![CDATA[
14 <command interpreter="python"><![CDATA[ 13
15 14 python '$__tool_directory__/abims_sartools_deseq2_wrapper.py'
16 abims_sartools_deseq2_wrapper.py 15 ## parameters
17 ## parameters 16 @COMMAND_BASIC_PARAMETERS@
18 @COMMAND_BASIC_PARAMETERS@ 17 @COMMAND_BATCH_PARAM@
19 #if str( $advanced_parameters.adv_param ) == "show": 18 --fitType '$advanced_parameters.fitType'
20 @COMMAND_BATCH_PARAM@ 19 --cooksCutoff '$advanced_parameters.cooksCutoff'
21 --fitType $advanced_parameters.fitType 20 --independentFiltering '$advanced_parameters.independentFiltering'
22 --cooksCutoff $advanced_parameters.cooksCutoff 21 --alpha '$advanced_parameters.alpha'
23 --independentFiltering $advanced_parameters.independentFiltering 22 --pAdjustMethod '$advanced_parameters.pAdjustMethod'
24 --alpha $advanced_parameters.alpha 23 --typeTrans '$advanced_parameters.typeTrans'
25 --pAdjustMethod $advanced_parameters.pAdjustMethod 24 --locfunc '$advanced_parameters.locfunc'
26 --typeTrans $advanced_parameters.typeTrans 25 --colors "'$advanced_parameters.colors'"
27 --locfunc $advanced_parameters.locfunc 26 --forceCairoGraph '$advanced_parameters.forceCairoGraph'
28 --colors $advanced_parameters.colors 27 ## ouputs
29 --forceCairoGraph $advanced_parameters.forceCairoGraph 28 @COMMAND_OUTPUTS@
30 #end if
31 ## ouputs
32 @COMMAND_OUTPUTS@
33 29
34 ]]></command> 30 ]]></command>
35 31
36 <!-- [REQUIRED] Input files and tool parameters -->
37 <inputs> 32 <inputs>
38 33
39 <expand macro="basic_parameters" /> 34 <expand macro="basic_parameters" />
40 35
41 <conditional name="advanced_parameters" > 36 <section name="advanced_parameters" title="Advanced Parameters" expanded="false">
42 <param name="adv_param" type="select" label="Advanced Parameters" help="" > 37 <expand macro="batch_param" />
43 <option value="hide" selected="true">Hide</option> 38 <param type="select" label="Mean-variance relationship" argument="--fitType" help="Type of model for the mean-dispersion relationship. Parametric by default." >
44 <option value="show">Show</option> 39 <option value="parametric" selected="true">parametric</option>
40 <option value="local">local</option>
41 <option value="mean">mean</option>
45 </param> 42 </param>
46 <when value="hide" /> 43 <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" argument="--cooksCutoff" help="Checked by default."/>
47 <when value="show"> 44 <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" argument="--independentFiltering" help="Checked by default."/>
48 <expand macro="batch_param" /> 45 <expand macro="alpha_param" />
49 <param type="select" label="Mean-variance relationship" argument="--fitType" help="Type of model for the mean-dispersion relationship. Parametric by default." > 46 <expand macro="padjustmethod_param" />
50 <option value="parametric" selected="true">parametric</option> 47 <param type="select" label="Transformation for PCA/clustering" argument="--typeTrans" help="Method of transformation of the counts for the clustering and the PCA: 'VST' (default) for Variance Stabilizing Transformation, or 'rlog' for Regularized Log Transformation." >
51 <option value="local">local</option> 48 <option value="VST" selected="true">VST</option>
52 <option value="mean">mean</option> 49 <option value="rlog">rlog</option>
53 </param> 50 </param>
54 <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" argument="--cooksCutoff" help="Checked by default."/> 51 <param type="select" label="Estimation of the size factors" argument="--locfunc" help="'median' (default) or 'shorth' from the genefilter package." >
55 <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" argument="--independentFiltering" help="Checked by default."/> 52 <option value="median" selected="true">median</option>
56 <expand macro="alpha_param" /> 53 <option value="shorth">shorth</option>
57 <expand macro="padjustmethod_param" /> 54 </param>
58 <param type="select" label="Transformation for PCA/clustering" argument="--typeTrans" help="Method of transformation of the counts for the clustering and the PCA: 'VST' (default) for Variance Stabilizing Transformation, or 'rlog' for Regularized Log Transformation." > 55 <expand macro="colors_param" />
59 <option value="VST" selected="true">VST</option> 56 <expand macro="forceCairoGraph_param" />
60 <option value="rlog">rlog</option> 57 </section>
61 </param>
62 <param type="select" label="Estimation of the size factors" argument="--locfunc" help="'median' (default) or 'shorth' from the genefilter package." >
63 <option value="median" selected="true">median</option>
64 <option value="shorth">shorth</option>
65 </param>
66 <expand macro="colors_param" />
67 <expand macro="forceCairoGraph_param" />
68 </when>
69 </conditional>
70 58
71 </inputs> 59 </inputs>
72 60
73 <!-- [REQUIRED] Output files -->
74 <outputs> 61 <outputs>
75 62
76 <expand macro="outputs" /> 63 <expand macro="outputs" />
77 64
78 </outputs> 65 </outputs>
79 66
80 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
81 <tests> 67 <tests>
82 <!-- [HELP] Test files have to be in the ~/test-data directory -->
83 <test> 68 <test>
84 <!-- Test with 2 conditions, 2 replicates, 8217 features --> 69 <!-- Test with 2 conditions, 2 replicates, 8217 features -->
85 <param name="targetFile" dbkey="?" value="target.txt" /> 70 <param name="targetFile" dbkey="?" value="target.txt" />
86 <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/> 71 <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/>
87 <param name="adv_param" value="show"/>
88 <output name="log"> 72 <output name="log">
89 <assert_contents> 73 <assert_contents>
90 <has_text text="KO vs WT 0.1 171" /> 74 <has_text text="KO vs WT 0.1 171" />
91 <has_text text="KO vs WT 2583 2663 5246" /> 75 <has_text text="KO vs WT 2583 2663 5246" />
92 <has_text text="HTML report created" /> 76 <has_text text="HTML report created" />
93 </assert_contents> 77 </assert_contents>
94 </output> 78 </output>
95 </test> 79 </test>
96 <!-- <test> 80 <!-- <test>
97 --> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect --> 81 --> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect -->
98 <!-- <param name="targetFile" dbkey="?" value="targetT048.txt" /> 82 <!-- <param name="targetFile" dbkey="?" value="targetT048.txt" />
99 <param name="rawDir" value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/> 83 <param name="rawDir" value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/>
100 <param name="condRef" value="T0"/> 84 <param name="condRef" value="T0"/>
101 <param name="adv_param" value="show"/> 85 <param name="condition" value="true"/>
102 <param name="condition" value="true"/>
103 <output name="tables_html" file="SARTools_DESeq2_targetT048_tables.html" lines_diff="14"> 86 <output name="tables_html" file="SARTools_DESeq2_targetT048_tables.html" lines_diff="14">
104 <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_DESeq2_T4vsT0.complete.txt"/> 87 <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_DESeq2_T4vsT0.complete.txt"/>
105 <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_DESeq2_T8vsT0.complete.txt"/> 88 <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_DESeq2_T8vsT0.complete.txt"/>
106 <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_DESeq2_T8vsT4.complete.txt"/> 89 <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_DESeq2_T8vsT4.complete.txt"/>
107 </output> 90 </output>
108 </test> 91 </test>
109 --> </tests> 92 --> </tests>
110 93
111 <!-- [OPTIONAL] Help displayed in Galaxy -->
112 <help><![CDATA[ 94 <help><![CDATA[
113 95
114 @HELP_AUTHORS@ 96 @HELP_AUTHORS@
115 97
116 =============== 98 ===============
133 115
134 ---------- 116 ----------
135 Parameters 117 Parameters
136 ---------- 118 ----------
137 119
138 @HELP_BASIC_PARAMETERS@ 120 @HELP_BASIC_PARAMETERS@
139 * **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); 121 * **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);
140 * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05); 122 * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05);
141 * **fitType:** type of model for the mean-dispersion relationship ("parametric" by default, or "local"); 123 * **fitType:** type of model for the mean-dispersion relationship ("parametric" by default, or "local");
142 * **cooksCutoff:** TRUE (default) of FALSE to execute or not the detection of the outliers [4]; 124 * **cooksCutoff:** TRUE (default) of FALSE to execute or not the detection of the outliers [4];
143 * **independentFiltering:** TRUE (default) of FALSE to execute or not the independent filtering [5]; 125 * **independentFiltering:** TRUE (default) of FALSE to execute or not the independent filtering [5];
144 * **pAdjustMethod:** p-value adjustment method for multiple testing [6, 7] ("BH" by default, "BY" or any value of p.adjust.methods); 126 * **pAdjustMethod:** p-value adjustment method for multiple testing [6, 7] ("BH" by default, "BY" or any value of p.adjust.methods);
145 * **typeTrans:** method of transformation of the counts for the clustering and the PCA (default is "VST" for Variance Stabilizing Transformation, or "rlog" for Regularized Log Transformation); 127 * **typeTrans:** method of transformation of the counts for the clustering and the PCA (default is "VST" for Variance Stabilizing Transformation, or "rlog" for Regularized Log Transformation);
146 * **locfunc:** function used for the estimation of the size factors (default is "median", or "shorth" from the genefilter package); 128 * **locfunc:** function used for the estimation of the size factors (default is "median", or "shorth" from the genefilter package);
147 * **colors:** colors used for the figures (one per biological condition), 8 are given by default. 129 * **colors:** colors used for the figures (one per biological condition), 8 are given by default.
148 * **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo"). 130 * **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo").
149 131
150 132
151 ------------ 133 ------------
152 Output files 134 Output files
153 ------------ 135 ------------
154 136
155 @HELP_OUTPUT_FILES@ 137 @HELP_OUTPUT_FILES@
156 138
157 139
158 --------------------------------------------------- 140 ---------------------------------------------------
159 141
160 [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. 142 [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.
161 143
162 [2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011. 144 [2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011.
170 [6] 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. 152 [6] 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.
171 153
172 [7] Y. Benjamini and D. Yekutieli. The control of the false discovery rate in multiple testing under dependency. Ann. Statist., 29(4):1165–1188, 2001. 154 [7] Y. Benjamini and D. Yekutieli. The control of the false discovery rate in multiple testing under dependency. Ann. Statist., 29(4):1165–1188, 2001.
173 155
174 156
175 ]]></help> 157 ]]></help>
176 158
177 <citations> 159 <citations>
178 <expand macro="common_citations" /> 160 <expand macro="common_citations" />
179 <citation type="bibtex">@ARTICLE{Cook77, 161 <citation type="bibtex">@ARTICLE{Cook77,
180 author = {R.-D. Cook}, 162 author = {R.-D. Cook},
181 title = {Detection of Influential Observation in Linear Regression}, 163 title = {Detection of Influential Observation in Linear Regression},
182 journal = {Technometrics}, 164 journal = {Technometrics},
183 year = {1977}, 165 year = {1977},
184 month = {February} 166 month = {February}
185 }</citation> 167 }</citation>
186 <citation type="bibtex">@ARTICLE{Bourgon10, 168 <citation type="bibtex">@ARTICLE{Bourgon10,
187 author = {R. Bourgon, R. Gentleman, and W. Huber}, 169 author = {R. Bourgon, R. Gentleman, and W. Huber},
188 title = {Independent filtering increases detection power for high-throughput experiments}, 170 title = {Independent filtering increases detection power for high-throughput experiments},
189 journal = {PNAS}, 171 journal = {PNAS},
190 year = {2010}, 172 year = {2010},
191 volume = {107}, 173 volume = {107},
192 number = {21}, 174 number = {21},
193 pages = {9546–9551}, 175 pages = {9546–9551},
194 note = {URL: http://www.pnas.org/content/107/21/9546.long} 176 note = {URL: http://www.pnas.org/content/107/21/9546.long}
195 }</citation> 177 }</citation>
196 </citations> 178 </citations>
197 179
198 </tool> 180 </tool>