Mercurial > repos > lgueguen > sartools
comparison abims_sartools_deseq2.xml @ 0:581d217c7337 draft
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author | lgueguen |
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date | Fri, 22 Jul 2016 05:39:13 -0400 |
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children | d86ccac2a660 |
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1 <tool id="sartools_deseq2" name="SARTools DESeq2" 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 DESeq2</description> | |
5 | |
6 <macros> | |
7 <import>macros.xml</import> | |
8 </macros> | |
9 | |
10 <expand macro="requirements"/> | |
11 <expand macro="stdio"/> | |
12 | |
13 <!-- [REQUIRED] The command to execute --> | |
14 <command interpreter="python"><![CDATA[ | |
15 | |
16 abims_sartools_deseq2_wrapper.py | |
17 ## parameters | |
18 @COMMAND_BASIC_PARAMETERS@ | |
19 #if str( $advanced_parameters.adv_param ) == "show": | |
20 @COMMAND_BATCH_PARAM@ | |
21 --fitType $advanced_parameters.fitType | |
22 --cooksCutoff $advanced_parameters.cooksCutoff | |
23 --independentFiltering $advanced_parameters.independentFiltering | |
24 --alpha $advanced_parameters.alpha | |
25 --pAdjustMethod $advanced_parameters.pAdjustMethod | |
26 --typeTrans $advanced_parameters.typeTrans | |
27 --locfunc $advanced_parameters.locfunc | |
28 --colors $advanced_parameters.colors | |
29 #end if | |
30 ## ouputs | |
31 @COMMAND_OUTPUTS@ | |
32 | |
33 ]]></command> | |
34 | |
35 <!-- [REQUIRED] Input files and tool parameters --> | |
36 <inputs> | |
37 | |
38 <expand macro="basic_parameters" /> | |
39 | |
40 <conditional name="advanced_parameters" > | |
41 <param name="adv_param" type="select" label="Advanced Parameters" help="" > | |
42 <option value="hide" selected="true">Hide</option> | |
43 <option value="show">Show</option> | |
44 </param> | |
45 <when value="hide" /> | |
46 <when value="show"> | |
47 <expand macro="batch_param" /> | |
48 <param name="fitType" type="select" label="Mean-variance relationship" help="(-f, --fitType) Type of model for the mean-dispersion relationship. Parametric by default." > | |
49 <option value="parametric" selected="true">parametric</option> | |
50 <option value="local">local</option> | |
51 </param> | |
52 <param name="cooksCutoff" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" help="(-o, --cooksCutoff) Checked by default."/> | |
53 <param name="independentFiltering" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" help="(-i, --independentFiltering) Checked by default."/> | |
54 <expand macro="alpha_param" /> | |
55 <expand macro="padjustmethod_param" /> | |
56 <param name="typeTrans" type="select" label="Transformation for PCA/clustering" help="(-T --typeTrans) Method of transformation of the counts for the clustering and the PCA: 'VST' (default) for Variance Stabilizing Transformation, or 'rlog' for Regularized Log Transformation." > | |
57 <option value="VST" selected="true">VST</option> | |
58 <option value="rlog">rlog</option> | |
59 </param> | |
60 <param name="locfunc" type="select" label="Estimation of the size factors" help="(-l --locfunc) 'median' (default) or 'shorth' from the genefilter package." > | |
61 <option value="median" selected="true">median</option> | |
62 <option value="shorth">shorth</option> | |
63 </param> | |
64 <expand macro="colors_param" /> | |
65 </when> | |
66 </conditional> | |
67 | |
68 </inputs> | |
69 | |
70 <!-- [REQUIRED] Output files --> | |
71 <outputs> | |
72 | |
73 <expand macro="outputs" /> | |
74 | |
75 </outputs> | |
76 | |
77 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | |
78 <tests> | |
79 <!-- [HELP] Test files have to be in the ~/test-data directory --> | |
80 <test> | |
81 <!-- Test with 2 conditions, 2 replicates, 8217 features --> | |
82 <param name="targetFile" dbkey="?" value="target.txt" /> | |
83 <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/> | |
84 <param name="adv_param" value="show"/> | |
85 <output name="log"> | |
86 <assert_contents> | |
87 <has_text text="KO vs WT 0.1 171" /> | |
88 <has_text text="KO vs WT 2584 2665 5249" /> | |
89 <has_text text="HTML report created" /> | |
90 </assert_contents> | |
91 </output> | |
92 </test> | |
93 <!-- <test> | |
94 --> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect --> | |
95 <!-- <param name="targetFile" dbkey="?" value="targetT048.txt" /> | |
96 <param name="rawDir" value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/> | |
97 <param name="condRef" value="T0"/> | |
98 <param name="adv_param" value="show"/> | |
99 <param name="condition" value="true"/> | |
100 <output name="tables_html" file="SARTools_DESeq2_targetT048_tables.html" lines_diff="14"> | |
101 <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_DESeq2_T4vsT0.complete.txt"/> | |
102 <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_DESeq2_T8vsT0.complete.txt"/> | |
103 <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_DESeq2_T8vsT4.complete.txt"/> | |
104 </output> | |
105 </test> | |
106 --> </tests> | |
107 | |
108 <!-- [OPTIONAL] Help displayed in Galaxy --> | |
109 <help><![CDATA[ | |
110 | |
111 @HELP_AUTHORS@ | |
112 | |
113 =============== | |
114 SARTools DESeq2 | |
115 =============== | |
116 | |
117 ----------- | |
118 Description | |
119 ----------- | |
120 | |
121 @HELP_DESCRIPTION@ | |
122 | |
123 | |
124 ----------- | |
125 Input files | |
126 ----------- | |
127 | |
128 @HELP_INPUT_FILES@ | |
129 | |
130 | |
131 ---------- | |
132 Parameters | |
133 ---------- | |
134 | |
135 @HELP_BASIC_PARAMETERS@ | |
136 * **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); | |
137 * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05); | |
138 * **fitType:** type of model for the mean-dispersion relationship ("parametric" by default, or "local"); | |
139 * **cooksCutoff:** TRUE (default) of FALSE to execute or not the detection of the outliers [4]; | |
140 * **independentFiltering:** TRUE (default) of FALSE to execute or not the independent filtering [5]; | |
141 * **pAdjustMethod:** p-value adjustment method for multiple testing [6, 7] ("BH" by default, "BY" or any value of p.adjust.methods); | |
142 * **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); | |
143 * **locfunc:** function used for the estimation of the size factors (default is "median", or "shorth" from the genefilter package); | |
144 * **colors:** colors used for the figures (one per biological condition), 8 are given by default. | |
145 | |
146 | |
147 ------------ | |
148 Output files | |
149 ------------ | |
150 | |
151 @HELP_OUTPUT_FILES@ | |
152 | |
153 | |
154 --------------------------------------------------- | |
155 | |
156 [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. | |
157 | |
158 [2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011. | |
159 | |
160 [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. | |
161 | |
162 [4] R.-D. Cook. Detection of Influential Observation in Linear Regression. Technometrics, February 1977. | |
163 | |
164 [5] R. Bourgon, R. Gentleman, and W. Huber. Independent filtering increases detection power for high-throughput experiments. PNAS, 107(21):9546–9551, 2010. URL: http://www.pnas.org/content/107/21/9546.long. | |
165 | |
166 [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. | |
167 | |
168 [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. | |
169 | |
170 | |
171 ]]></help> | |
172 | |
173 <citations> | |
174 <expand macro="common_citations" /> | |
175 <citation type="bibtex">@ARTICLE{Cook77, | |
176 author = {R.-D. Cook}, | |
177 title = {Detection of Influential Observation in Linear Regression}, | |
178 journal = {Technometrics}, | |
179 year = {1977}, | |
180 month = {February} | |
181 }</citation> | |
182 <citation type="bibtex">@ARTICLE{Bourgon10, | |
183 author = {R. Bourgon, R. Gentleman, and W. Huber}, | |
184 title = {Independent filtering increases detection power for high-throughput experiments}, | |
185 journal = {PNAS}, | |
186 year = {2010}, | |
187 volume = {107}, | |
188 number = {21}, | |
189 pages = {9546–9551}, | |
190 note = {URL: http://www.pnas.org/content/107/21/9546.long} | |
191 }</citation> | |
192 </citations> | |
193 | |
194 </tool> |