Mercurial > repos > lgueguen > sartools

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded new release 1.7.3
author lgueguen
date Thu, 07 Jan 2021 11:12:01 +0000
parents de6d0b7c17af
children
comparison
equal deleted inserted replaced
3:de6d0b7c17af 4:05c9b1a7f44e
1 <tool id="sartools_edger" name="SARTools edgeR" version="@WRAPPER_VERSION@.0"> 1 <tool id="sartools_edger" name="SARTools edgeR" 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 edgeR</description> 3 <description>Compare two or more biological conditions in a RNA-Seq framework with edgeR</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 12
14 <!-- [REQUIRED] The command to execute --> 13 <command><![CDATA[
15 <command interpreter="python"><![CDATA[ 14
16 15 python '$__tool_directory__/abims_sartools_edger_wrapper.py'
17 abims_sartools_edger_wrapper.py 16 ## parameters
18 ## parameters 17 @COMMAND_BASIC_PARAMETERS@
19 @COMMAND_BASIC_PARAMETERS@ 18 @COMMAND_BATCH_PARAM@
20 #if str( $advanced_parameters.adv_param ) == "show": 19 --alpha '$advanced_parameters.alpha'
21 @COMMAND_BATCH_PARAM@ 20 --pAdjustMethod '$advanced_parameters.pAdjustMethod'
22 --alpha $advanced_parameters.alpha 21 --cpmCutoff '$advanced_parameters.cpmCutoff'
23 --pAdjustMethod $advanced_parameters.pAdjustMethod 22 --geneSelection '$advanced_parameters.geneSelection'
24 --cpmCutoff $advanced_parameters.cpmCutoff 23 --normalizationMethod '$advanced_parameters.normalizationMethod'
25 --geneSelection $advanced_parameters.geneSelection 24 --colors "'$advanced_parameters.colors'"
26 --normalizationMethod $advanced_parameters.normalizationMethod 25 --forceCairoGraph '$advanced_parameters.forceCairoGraph'
27 --colors $advanced_parameters.colors 26 ## ouputs
28 --forceCairoGraph $advanced_parameters.forceCairoGraph 27 @COMMAND_OUTPUTS@
29 #end if
30 ## ouputs
31 @COMMAND_OUTPUTS@
32 28
33 ]]></command> 29 ]]></command>
34 30
35 <!-- [REQUIRED] Input files and tool parameters -->
36 <inputs> 31 <inputs>
37 32
38 <expand macro="basic_parameters" /> 33 <expand macro="basic_parameters" />
39 34
40 <conditional name="advanced_parameters" > 35 <section name="advanced_parameters" title="Advanced Parameters" expanded="false" >
41 <param name="adv_param" type="select" label="Advanced Parameters" help="" > 36 <expand macro="batch_param" />
42 <option value="hide" selected="true">Hide</option> 37 <expand macro="alpha_param" />
43 <option value="show">Show</option> 38 <expand macro="padjustmethod_param" />
39 <param type="integer" value="1" min="0" label="Counts-per-million cut-off to filter low counts" argument="--cpmCutoff" help="Set to 0 to disable filtering. Default is 1." />
40 <param name="geneSelection" type="select" label="Selection of the features in MDSPlot" argument="--gene.selection" help="Default is 'pairwise'." >
41 <option value="pairwise" selected="true">pairwise</option>
42 <option value="common">common</option>
44 </param> 43 </param>
45 <when value="hide" /> 44 <param type="select" label="Normalization method in calcNormFactors" argument="--normalizationMethod" help="'TMM' (default), 'RLE' (DESeq method) or 'upperquartile'." >
46 <when value="show"> 45 <option value="TMM" selected="true">TMM</option>
47 <expand macro="batch_param" /> 46 <option value="RLE">RLE</option>
48 <expand macro="alpha_param" /> 47 <option value="upperquartile">upperquartile</option>
49 <expand macro="padjustmethod_param" /> 48 </param>
50 <param type="integer" value="1" min="0" label="Counts-per-million cut-off to filter low counts" argument="--cpmCutoff" help="Set to 0 to disable filtering. Default is 1." /> 49 <expand macro="colors_param" />
51 <param name="geneSelection" type="select" label="Selection of the features in MDSPlot" argument="--gene.selection" help="Default is 'pairwise'." > 50 <expand macro="forceCairoGraph_param" />
52 <option value="pairwise" selected="true">pairwise</option> 51 </section>
53 <option value="common">common</option>
54 </param>
55 <param type="select" label="Normalization method in calcNormFactors" argument="--normalizationMethod" help="'TMM' (default), 'RLE' (DESeq method) or 'upperquartile'." >
56 <option value="TMM" selected="true">TMM</option>
57 <option value="RLE">RLE</option>
58 <option value="upperquartile">upperquartile</option>
59 </param>
60 <expand macro="colors_param" />
61 <expand macro="forceCairoGraph_param" />
62 </when>
63 </conditional>
64 52
65 </inputs> 53 </inputs>
66 54
67 <!-- [REQUIRED] Output files -->
68 <outputs> 55 <outputs>
69 56
70 <expand macro="outputs" /> 57 <expand macro="outputs" />
71 58
72 </outputs> 59 </outputs>
73 60
74 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
75 <tests> 61 <tests>
76 <!-- [HELP] Test files have to be in the ~/test-data directory -->
77 <test> 62 <test>
78 <!-- Test with 2 conditions, 2 replicates, 10 features --> 63 <!-- Test with 2 conditions, 2 replicates, 10 features -->
79 <param name="targetFile" dbkey="?" value="target_small.txt" /> 64 <param name="targetFile" dbkey="?" value="target_small.txt" />
80 <param name="rawDir" value="raw_small.zip" dbkey="?" ftype="zip"/> 65 <param name="rawDir" value="raw_small.zip" dbkey="?" ftype="zip"/>
81 <param name="adv_param" value="show"/>
82 <output name="log"> 66 <output name="log">
83 <assert_contents> 67 <assert_contents>
84 <has_text text="KO vs WT 5 4 9" /> 68 <has_text text="KO vs WT 5 4 9" />
85 <has_text text="HTML report created" /> 69 <has_text text="HTML report created" />
86 </assert_contents> 70 </assert_contents>
87 </output> 71 </output>
88 </test> 72 </test>
89 <!-- <test> 73 <!-- <test>
90 --> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10 features, with batch effect --> 74 --> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10 features, with batch effect -->
91 <!-- <param name="targetFile" dbkey="?" value="targetT048_small.txt" /> 75 <!-- <param name="targetFile" dbkey="?" value="targetT048_small.txt" />
92 <param name="rawDir" value="rawT048_small.zip" dbkey="?" ftype="no_unzip.zip"/> 76 <param name="rawDir" value="rawT048_small.zip" dbkey="?" ftype="no_unzip.zip"/>
93 <param name="condRef" value="T0"/> 77 <param name="condRef" value="T0"/>
94 <param name="adv_param" value="show"/> 78 <param name="condition" value="true"/>
95 <param name="condition" value="true"/>
96 <output name="tables_html" file="SARTools_edgeR_targetT048_small_tables.html" lines_diff="12"> 79 <output name="tables_html" file="SARTools_edgeR_targetT048_small_tables.html" lines_diff="12">
97 <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0_small.complete.txt"/> 80 <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0_small.complete.txt"/>
98 <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0_small.complete.txt"/> 81 <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0_small.complete.txt"/>
99 <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4_small.complete.txt"/> 82 <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4_small.complete.txt"/>
100 </output> 83 </output>
101 </test> 84 </test>
102 --> <test> 85 --> <test>
103 <!-- Test with 2 conditions, 2 replicates, 8217 features --> 86 <!-- Test with 2 conditions, 2 replicates, 8217 features -->
104 <param name="targetFile" dbkey="?" value="target.txt" /> 87 <param name="targetFile" dbkey="?" value="target.txt" />
105 <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/> 88 <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/>
106 <param name="adv_param" value="show"/>
107 <output name="log"> 89 <output name="log">
108 <assert_contents> 90 <assert_contents>
109 <has_text text="KO vs WT 2691 2713 5404" /> 91 <has_text text="KO vs WT 2691 2713 5404" />
110 <has_text text="HTML report created" /> 92 <has_text text="HTML report created" />
111 </assert_contents> 93 </assert_contents>
112 </output> 94 </output>
113 </test> 95 </test>
114 <!-- <test> 96 <!-- <test>
115 --> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect --> 97 --> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect -->
116 <!-- <param name="targetFile" dbkey="?" value="targetT048.txt" /> 98 <!-- <param name="targetFile" dbkey="?" value="targetT048.txt" />
117 <param name="rawDir" value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/> 99 <param name="rawDir" value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/>
118 <param name="condRef" value="T0"/> 100 <param name="condRef" value="T0"/>
119 <param name="adv_param" value="show"/> 101 <param name="condition" value="true"/>
120 <param name="condition" value="true"/>
121 <output name="tables_html" file="SARTools_edgeR_targetT048_tables.html" lines_diff="14"> 102 <output name="tables_html" file="SARTools_edgeR_targetT048_tables.html" lines_diff="14">
122 <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0.complete.txt"/> 103 <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0.complete.txt"/>
123 <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0.complete.txt"/> 104 <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0.complete.txt"/>
124 <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4.complete.txt"/> 105 <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4.complete.txt"/>
125 </output> 106 </output>
126 </test> 107 </test>
127 --> </tests> 108 --> </tests>
128 109
129 <!-- [OPTIONAL] Help displayed in Galaxy -->
130 <help><![CDATA[ 110 <help><![CDATA[
131 111
132 @HELP_AUTHORS@ 112 @HELP_AUTHORS@
133 113
134 ============== 114 ==============
151 131
152 ---------- 132 ----------
153 Parameters 133 Parameters
154 ---------- 134 ----------
155 135
156 @HELP_BASIC_PARAMETERS@ 136 @HELP_BASIC_PARAMETERS@
157 * **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 * **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);
158 * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05); 138 * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05);
159 * **pAdjustMethod:** p-value adjustment method for multiple testing [4, 5] ("BH" by default, "BY" or any value of p.adjust.methods); 139 * **pAdjustMethod:** p-value adjustment method for multiple testing [4, 5] ("BH" by default, "BY" or any value of p.adjust.methods);
160 * **cpmCutoff:** counts-per-million cut-off to filter low counts (default is 1, set to 0 to disable filtering); 140 * **cpmCutoff:** counts-per-million cut-off to filter low counts (default is 1, set to 0 to disable filtering);
161 * **gene.selection:** method of selection of the features for the MultiDimensional Scaling plot ("pairwise" by default or common); 141 * **gene.selection:** method of selection of the features for the MultiDimensional Scaling plot ("pairwise" by default or common);
162 * **normalizationMethod:** normalization method in calcNormFactors(): "TMM" (default), "RLE" (DESeq method) or "upperquartile"; 142 * **normalizationMethod:** normalization method in calcNormFactors(): "TMM" (default), "RLE" (DESeq method) or "upperquartile";
163 * **colors:** colors used for the figures (one per biological condition), 8 are given by default. 143 * **colors:** colors used for the figures (one per biological condition), 8 are given by default.
164 * **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo"). 144 * **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo").
165 145
166 146
167 ------------ 147 ------------
168 Output files 148 Output files
169 ------------ 149 ------------
170 150
171 @HELP_OUTPUT_FILES@ 151 @HELP_OUTPUT_FILES@
172 152
173 153
174 --------------------------------------------------- 154 ---------------------------------------------------
175 155
176 [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. 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.
177 157
178 [2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011. 158 [2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011.
182 [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. 162 [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.
183 163
184 [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. 164 [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.
185 165
186 166
187 ]]></help> 167 ]]></help>
188 168
189 <citations> 169 <citations>
190 <expand macro="common_citations" /> 170 <expand macro="common_citations" />
191 </citations> 171 </citations>
192 172