Mercurial > repos > gtrichard > deepstats_dscomparecurves
comparison dsCompareCurves.xml @ 0:cbeae0f83ff8 draft
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author | gtrichard |
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date | Mon, 15 Jul 2019 17:54:31 -0400 |
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children | a2022103f2a2 |
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1 <tool id="deepstats_compare_curves" name="dsCompareCurves" version="@WRAPPER_VERSION@.0" profile="18.01"> | |
2 <description> | |
3 compares multiple bigwigs over multiple region sets with bootstraps and | |
4 Wilcoxon rank-sum test using deepTools computeMatrix output | |
5 </description> | |
6 <macros> | |
7 <token name="@BINARY@">dsCompareCurves</token> | |
8 <import>deepStats_macros.xml</import> | |
9 </macros> | |
10 <expand macro="requirements" /> | |
11 <command> | |
12 <![CDATA[ | |
13 @BINARY@ | |
14 --input '$input' | |
15 --output 'output' | |
16 --comparison '$comparison' | |
17 --signalName '$signalName' | |
18 --scoreLabels '$nameLabels.scoreLabels' | |
19 --regionLabels '$nameLabels.regionLabels' | |
20 | |
21 #if $scaleRegions.showScaleRegionsOpt == "yes": | |
22 --firstRegionName '$scaleRegions.firstRegionName' | |
23 --secondRegionName '$scaleRegions.secondRegionName' | |
24 #else | |
25 --firstRegionName '$scaleRegions.firstRegionName' | |
26 #end if | |
27 | |
28 --bootstraps '$statsOptions.bootstraps' | |
29 --bootstrapsCI '$statsOptions.bootstrapsCI' | |
30 --wilcoxThreshold '$statsOptions.wilcoxThreshold' | |
31 --bootPlotShareY '$plotOptions.bootPlotShareY' | |
32 --bootPlotRatio '$plotOptions.bootPlotRatio' | |
33 --bootPlotWidth '$plotOptions.bootPlotWidth' | |
34 --bootPlotHeight '$plotOptions.bootPlotHeight' | |
35 --wilcoxPlotWidth '$plotOptions.wilcoxPlotWidth' | |
36 --wilcoxPlotHeight '$plotOptions.wilcoxPlotHeight' | |
37 --CPU '$advancedOptions.CPU' | |
38 | |
39 #if $fontOptions.showFontOptions == "yes": | |
40 --font '$fontOptions.font_file' | |
41 #end if | |
42 | |
43 #if $colorsOptions.showColorsOptions == "yes": | |
44 --bootPlotColors '$colorsOptions.bootPlotColors' | |
45 #end if | |
46 ]]> | |
47 </command> | |
48 <inputs> | |
49 <param argument="--input" format="tabular" type="data" | |
50 label="deepTools computeMatrix output file."/> | |
51 | |
52 <param argument="--comparison" type="select" | |
53 label="What do you want to compare?"> | |
54 <option value="scores" selected="true">scores</option> | |
55 <option value="regions">regions</option> | |
56 </param> | |
57 | |
58 <param argument="--signalName" type="text" value= "Normalized ATAC-seq counts" | |
59 label="Name of the genomic signal" help="Name given to the signal on the plots, \n can be added for linebreaks."/> | |
60 | |
61 <conditional name="scaleRegions"> | |
62 <param name="showScaleRegionsOpt" type="select" label="Which mode was used in deepTools computeMatrix?"> | |
63 <option value="reference-point" selected="true">reference-point</option> | |
64 <option value="scale-regions">scale-regions</option> | |
65 </param> | |
66 <when value="scale-regions"> | |
67 <param argument="--firstRegionName" type="text" value="TSS" size="10" | |
68 label="Label for the region start" | |
69 help ="Label shown in the plot | |
70 for the start of the region. Default is TSS (transcription start site), | |
71 but could be changed to anything, e.g. "peak start"." /> | |
72 <param argument="--secondRegionName" type="text" value="TES" size="10" | |
73 label="Label for the region end" | |
74 help ="Label shown in the plot | |
75 for the end of the region. Default is TES (transcription end site), | |
76 but could be changed to anything, e.g. "peak end"." /> | |
77 </when> | |
78 <when value="reference-point"> | |
79 <param argument="--firstRegionName" type="text" value="TSS" | |
80 label="Label for the region start" | |
81 help ="Label shown in the plot | |
82 for the start of the region. Default is TSS (transcription start site), | |
83 but could be changed to anything, e.g. "peak start"." /> | |
84 </when> | |
85 </conditional> | |
86 | |
87 <section name="nameLabels" title="Customize score and region labels" expanded="false"> | |
88 <param argument="--scoreLabels" optional="true" type="text" value= "" | |
89 label="Name of the scores" help="For plot display. It must be provided as text seperated | |
90 by semi-colons, i.e. 'Score A;Score B;Score C' as in the example."> | |
91 <sanitizer> | |
92 <valid initial="string.printable"/> | |
93 </sanitizer> | |
94 </param> | |
95 | |
96 <param argument="--regionLabels" optional="true" type="text" value= "" | |
97 label="Name of the regions" help="For plot display. It must be provided as text seperated | |
98 by semi-colons, i.e. 'Regions A;Regions B;Regions C' as in the example."> | |
99 <sanitizer> | |
100 <valid initial="string.printable"/> | |
101 </sanitizer> | |
102 </param> | |
103 </section> | |
104 | |
105 <section name="statsOptions" title="Statistics options" expanded="false"> | |
106 <param argument="--bootstraps" type="integer" value="1000" | |
107 label="--bootstraps" help="Number of bootstraps to perform. Default is 1000, | |
108 increasing this number will increase the computing time."/> | |
109 <param argument="--bootstrapsCI" type="float" value="0.95" | |
110 label="--bootstrapsCI" help="Bootstraps confidence interval. Default is 0.95, | |
111 increasing this will make the analysis more stringent by increasing the min and max of the shadowed area on the bootstrap plot."/> | |
112 <param argument="--wilcoxThreshold" type="float" value="0.05" | |
113 label="--wilcoxThreshold" help="Threshold used to define significant | |
114 bins on the Wilcoxon rank-sum test plot (grey box). Default is 0.05"/> | |
115 </section> | |
116 | |
117 <section name="plotOptions" title="Plotting options" expanded="false"> | |
118 <param argument="--bootPlotShareY" type="select" label="--bootPlotShareY"> | |
119 <option value="TRUE" selected="true">TRUE</option> | |
120 <option value="FALSE">FALSE</option> | |
121 </param> | |
122 <param argument="--bootPlotRatio" type="float" value="0.85" label="--bootPlotRatio" | |
123 help="Changes the aspect ratio of the plot. A value inferior to 1 results in a wide plot, | |
124 a value above 1 results in a narrow plot. Default: 0.85."/> | |
125 | |
126 <param argument="--bootPlotWidth" type="float" value="5.2" label="--bootPlotWidth" | |
127 help="How large the bootstraps plot should be."/> | |
128 | |
129 <param argument="--bootPlotHeight" type="float" value="3.7" label="--bootPlotHeight" | |
130 help="How tall the bootstraps plot should be."/> | |
131 | |
132 <param argument="--wilcoxPlotWidth" type="float" value="4.6" label="--wilcoxPlotWidth" | |
133 help="How large the Wilcoxon rank-sum test plot should be."/> | |
134 | |
135 <param argument="--wilcoxPlotHeight" type="float" value="4.6" label="--wilcoxPlotHeight" | |
136 help="How tall the Wilcoxon rank-sum test plot should be."/> | |
137 </section> | |
138 | |
139 <section name="advancedOptions" title="Computing options" expanded="false"> | |
140 <param argument="--CPU" type="integer" value="4" label="--CPU" | |
141 help="Number of CPU to use."/> | |
142 </section> | |
143 | |
144 <conditional name="fontOptions"> | |
145 <param name="showFontOptions" type="select" label="Customize font?"> | |
146 <option value="No" selected="true">No</option> | |
147 <option value="Yes">Yes</option> | |
148 </param> | |
149 <when value="No"/> | |
150 <when value="Yes"> | |
151 <param argument="--font" type="file" format="ttf" value=" " label="--font" optional="true" | |
152 help="Font used for plotting, given a TTF file. Default is usually Helvetica."/> | |
153 </when> | |
154 </conditional> | |
155 | |
156 <conditional name="colorsOptions"> | |
157 <param name="showColorsOptions" type="select" label="Customize colors?"> | |
158 <option value="No" selected="true">No</option> | |
159 <option value="Yes">Yes</option> | |
160 </param> | |
161 <when value="No"/> | |
162 <when value="Yes"> | |
163 <param argument="--bootPlotColors" type="file" format="tabular" value=" " label="--bootPlotColors" | |
164 help="Change the bootstraps plot color palette to a user-provided one. The file must | |
165 be tab-delimited and contain for each line two HTML color codes ( #3366CC #769EF2 ). | |
166 The first column corresponds to the mean color, the second column corresponds to the | |
167 color of the bootstrap confidence interval shadowed area. The default color scale | |
168 contains 6 colors that are color blind friendly using the dichromat R package."/> | |
169 </when> | |
170 </conditional> | |
171 | |
172 </inputs> | |
173 <outputs> | |
174 <data format="pdf" name="pdf1" label="${tool.name} on ${on_string}: Bootstrap Plot" from_work_dir="output_bootstraps.pdf"/> | |
175 <data format="pdf" name="pdf2" label="${tool.name} on ${on_string}: Wilcox Plot" from_work_dir="output_wilcoxon.pdf"/> | |
176 </outputs> | |
177 <tests> | |
178 <test> | |
179 </test> | |
180 </tests> | |
181 <help> | |
182 <![CDATA[ | |
183 This tool assesses if multiple genomics signals ( ChIP-seq, ATAC-seq... ) are significantly different or | |
184 not between conditions ( control, KO1, KO2, etc ). `dsCompareCurves` uses bootstraps and corrected | |
185 Wilcoxon Rank-sum tests to do so. The input of this tool corresponds to the output of deepTools | |
186 `computeMatrix --outFileNameMatrix`. If multiple region sets have been used in deepTools, one plot and | |
187 tab-delimited table will be produced for each set of regions. | |
188 | |
189 @REFERENCES@ | |
190 ]]> | |
191 </help> | |
192 <expand macro="citations" /> | |
193 </tool> |