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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:27:38 -0500
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1 <?xml version="1.0"?>
2 <tool id="cummeRbund" name="cummeRbund" version="1.0.1">
3 <description>visualize Cuffdiff output</description>
4 <requirements>
5 <requirement type="set_environment">CUMMERBUND_SCRIPT_PATH</requirement>
6 <requirement type="package" version="3.1.2">R</requirement>
7 <requirement type="package" version="2.8.2">cummeRbund</requirement>
8 </requirements>
9 <expand macro="stdio" />
10 <macros>
11 <import>cummeRbund_macros.xml</import>
12 </macros>
13 <code file="cummeRbund_options.py"/>
14 <command>
15 <![CDATA[
16 #for i, p in enumerate($plots):
17 R --vanilla --no-save -f \$CUMMERBUND_SCRIPT_PATH/cummeRbund.R --args
18 --input "${input_database}" --width $p.width --height $p.height --type "${p.plot.type}"
19 --outfile plot-${p.plot.type}-${i}.png
20 #if $p.plot.type in ["density", "boxplot", "mds", "pca", "dendrogram"]:
21 $p.plot.replicates
22 #elif $p.plot.type == "scatter":
23 $p.plot.smooth --x "$p.plot.x" --y "$p.plot.y" $p.plot.log10
24 #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
25 --features $p.plot.multiple_genes.features --gene_selector
26 #for gene in $p.plot.multiple_genes.genes:
27 --genes ${gene.gene_id}
28 #end for
29 #end if
30 #elif $p.plot.type == "maplot":
31 --x "$p.plot.x" --y "$p.plot.y" $p.plot.count
32 #elif $p.plot.type == "volcano":
33 --x "$p.plot.x" --y "$p.plot.y"
34 #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
35 --features $p.plot.multiple_genes.features --gene_selector
36 #for gene in $p.plot.multiple_genes.genes:
37 --genes ${gene.gene_id}
38 #end for
39 #end if
40 #elif $p.plot.type == "heatmap":
41 --clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10
42 #if len($p.plot.genes) > 0:
43 #for gene in $p.plot.genes:
44 --genes ${gene.gene_id}
45 #end for
46 #end if
47 #elif $p.plot.type == "cluster":
48 --features $p.plot.features --k $p.plot.k --iter_max $p.plot.iter_max
49 #if len($p.plot.genes) > 0:
50 #for gene in $p.plot.genes:
51 --genes ${gene.gene_id}
52 #end for
53 #end if
54 #elif $p.plot.type in [ "expressionplot", "expressionbarplot" ]:
55 #if $p.plot.type == "expressionplot":
56 $p.plot.draw_summary
57 #end if
58 --features $p.plot.features $p.plot.error_bars --genes ${p.plot.gene_id} $p.plot.replicates $p.plot.log10
59 #end if
60 #if $p.plot.type == "density":
61 $p.plot.log10
62 #end if
63 > "${output}" 2>&1 ;
64 #end for
65 ]]></command>
66 <inputs>
67 <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
68 <repeat name="plots" title="Plots">
69 <param name="width" type="integer" value="1280" label="The width of the image"/>
70 <param name="height" type="integer" value="960" label="The height of the image"/>
71 <conditional name="plot">
72 <param name="type" type="select" label="Plot type">
73 <option value="density" selected="true">Density</option>
74 <option value="boxplot">Boxplot</option>
75 <option value="mds">MultiDimentional Scaling (MDS) Plot</option>
76 <option value="pca">Principal Component Analysis (PCA) Plot</option>
77 <option value="dendrogram">Dendrogram</option>
78 <option value="scatter">Scatter</option>
79 <option value="volcano">Volcano</option>
80 <option value="heatmap">Heatmap</option>
81 <option value="dispersion">Dispersion</option>
82 <option value="fpkmSCV">Squared Coefficient of Variation</option>
83 <option value="scatterMatrix">Scatter Matrix</option>
84 <option value="cluster">Cluster</option>
85 <option value="expressionplot">Expression Plot</option>
86 <option value="expressionbarplot">Expression Bar Plot</option>
87 <option value="maplot">Intensity vs Fold-change (MvaA) Plot</option>
88 </param>
89 <when value="density">
90 <expand macro="replicates_checkbox" />
91 <expand macro="log10_checkbox" />
92 </when>
93 <when value="mds">
94 <expand macro="replicates_checkbox" />
95 </when>
96 <when value="pca">
97 <expand macro="replicates_checkbox" />
98 </when>
99 <when value="boxplot">
100 <expand macro="replicates_checkbox" />
101 <expand macro="log10_checkbox" />
102 </when>
103 <when value="dendrogram">
104 <expand macro="replicates_checkbox" />
105 </when>
106 <when value="scatter">
107 <expand macro="xy_selector" />
108 <expand macro="log10_checkbox" />
109 <param name="smooth" type="boolean" truevalue="--smooth" falsevalue="" checked="True" label="Add a smooth-fit regression line"/>
110 <expand macro="multiple_genes_conditional" />
111 </when>
112 <when value="volcano">
113 <param name="x" type="select" label="First sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
114 <param name="y" type="select" label="Second sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
115 <expand macro="multiple_genes_conditional" />
116 </when>
117 <when value="heatmap">
118 <expand macro="features_selector" />
119 <expand macro="genes_selector" />
120 <param name="clustering" type="select" label="Cluster by">
121 <option value="row">Row</option>
122 <option value="column">Column</option>
123 <option value="both" selected="true">Both</option>
124 <option value="none">None</option>
125 </param>
126 <param name="labcol" type="boolean" truevalue="--labcol" falsevalue="" checked="True" label="Display column labels?"/>
127 <param name="labrow" type="boolean" truevalue="--labrow" falsevalue="" checked="True" label="Display column labels?"/>
128 <param name="border" type="boolean" truevalue="--border" falsevalue="" checked="False" label="Draw border around plot?"/>
129 <expand macro="log10_checkbox" />
130 </when>
131 <when value="cluster">
132 <expand macro="features_selector" />
133 <expand macro="genes_selector" />
134 <param name="k" type="integer" value="1" label="Number of pre-defined clusters to attempt to find."/>
135 <param name="iter_max" type="integer" value="100" label="Max iterations"/>
136 </when>
137 <when value="maplot">
138 <expand macro="xy_selector" />
139 <param name="count" type="boolean" truevalue="--count" falsevalue="" checked="False" label="Use Count?"/>
140 </when>
141 <when value="dispersion" />
142 <when value="fpkmSCV" />
143 <when value="scatterMatrix" />
144 <when value="expressionplot">
145 <expand macro="features_selector" />
146 <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
147 <param name="draw_summary" type="boolean" truevalue="--summary" falsevalue="" checked="False" label="Draw a 'summary' line with mean FPKM values for each condition?"/>
148 <param name="error_bars" type="boolean" truevalue="--error_bars" falsevalue="" checked="True" label="Draw error bars?"/>
149 <expand macro="replicates_checkbox" />
150 <expand macro="log10_checkbox" />
151 </when>
152 <when value="expressionbarplot">
153 <expand macro="features_selector" />
154 <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
155 <param name="error_bars" type="boolean" truevalue="--error_bars" falsevalue="" checked="True" label="Draw error bars?"/>
156 <expand macro="replicates_checkbox" />
157 <expand macro="log10_checkbox" />
158 </when>
159 </conditional>
160 </repeat>
161 </inputs>
162 <outputs>
163 <data format="txt" name="output" label="${tool.name} on ${on_string}">
164 <discover_datasets pattern="plot-(?P&lt;designation&gt;.+)\.png" ext="png" visible="true" />
165 </data>
166 </outputs>
167 <tests>
168 <test>
169 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
170 <repeat name="plots">
171 <param name="width" value="1280" />
172 <param name="height" value="960" />
173 <conditional name="plot">
174 <param name="type" value="maplot" />
175 <param name="x" value="q1" />
176 <param name="y" value="q2" />
177 </conditional>
178 </repeat>
179 <output name="output" ftype="txt" file="maplot.txt" lines_diff="2">
180 <discovered_dataset designation="maplot-0" ftype="png" file="maplot.png" />
181 </output>
182 </test>
183 <test>
184 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
185 <repeat name="plots">
186 <param name="width" value="1280" />
187 <param name="height" value="960" />
188 <conditional name="plot">
189 <param name="type" value="scatter" />
190 <param name="x" value="q1" />
191 <param name="y" value="q2" />
192 </conditional>
193 </repeat>
194 <output name="output" ftype="txt" file="scatter.txt" lines_diff="2">
195 <discovered_dataset designation="scatter-0" ftype="png" file="scatter.png" />
196 </output>
197 </test>
198 <test>
199 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
200 <repeat name="plots">
201 <param name="width" value="1280" />
202 <param name="height" value="960" />
203 <conditional name="plot">
204 <param name="type" value="dispersion" />
205 </conditional>
206 </repeat>
207 <output name="output" ftype="txt" file="dispersion.txt" lines_diff="2">
208 <discovered_dataset designation="dispersion-0" ftype="png" file="dispersion.png" />
209 </output>
210 </test>
211 <test>
212 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
213 <repeat name="plots">
214 <param name="width" value="1280" />
215 <param name="height" value="960" />
216 <conditional name="plot">
217 <param name="type" value="scatterMatrix" />
218 </conditional>
219 </repeat>
220 <output name="output" ftype="txt" file="scatterMatrix.txt" lines_diff="2">
221 <discovered_dataset designation="scatterMatrix-0" ftype="png" file="scatterMatrix.png" />
222 </output>
223 </test>
224 <test>
225 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
226 <repeat name="plots">
227 <param name="width" value="1280" />
228 <param name="height" value="960" />
229 <conditional name="plot">
230 <param name="type" value="pca" />
231 </conditional>
232 </repeat>
233 <output name="output" ftype="txt" file="pca.txt" lines_diff="2">
234 <discovered_dataset designation="pca-0" ftype="png" file="pca.png" />
235 </output>
236 </test>
237 <test>
238 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
239 <repeat name="plots">
240 <param name="width" value="1280" />
241 <param name="height" value="960" />
242 <conditional name="plot">
243 <param name="type" value="expressionplot" />
244 <param name="features" value="gene" />
245 <param name="gene_id" value="XLOC_000059" />
246 </conditional>
247 </repeat>
248 <output name="output" ftype="txt" file="expressionplot.txt" lines_diff="2">
249 <discovered_dataset designation="expressionplot-0" ftype="png" file="expressionplot.png" />
250 </output>
251 </test>
252 <test>
253 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
254 <repeat name="plots">
255 <param name="width" value="1280" />
256 <param name="height" value="960" />
257 <conditional name="plot">
258 <param name="features" value="gene" />
259 <param name="type" value="expressionbarplot" />
260 <param name="gene_id" value="XLOC_000039" />
261 </conditional>
262 </repeat>
263 <output name="output" ftype="txt" file="expressionbarplot.txt" lines_diff="2">
264 <discovered_dataset designation="expressionbarplot-0" ftype="png" file="expressionbarplot.png" />
265 </output>
266 </test>
267 <test>
268 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
269 <repeat name="plots">
270 <param name="width" value="1280" />
271 <param name="height" value="960" />
272 <conditional name="plot">
273 <param name="type" value="heatmap" />
274 <repeat name="genes">
275 <param name="gene_id" value="XLOC_000078" />
276 </repeat>
277 </conditional>
278 </repeat>
279 <output name="output" ftype="txt" file="heatmap.txt" lines_diff="2">
280 <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" />
281 </output>
282 </test>
283 <test>
284 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
285 <repeat name="plots">
286 <param name="width" value="1280" />
287 <param name="height" value="960" />
288 <conditional name="plot">
289 <param name="type" value="density" />
290 </conditional>
291 </repeat>
292 <output name="output" ftype="txt" file="density.txt" lines_diff="2">
293 <discovered_dataset designation="density-0" ftype="png" file="density.png" />
294 </output>
295 </test>
296 <test>
297 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
298 <repeat name="plots">
299 <param name="width" value="1280" />
300 <param name="height" value="960" />
301 <conditional name="plot">
302 <param name="type" value="dendrogram" />
303 </conditional>
304 </repeat>
305 <output name="output" ftype="txt" file="dendrogram.txt" lines_diff="2">
306 <discovered_dataset designation="dendrogram-0" ftype="png" file="dendrogram.png" />
307 </output>
308 </test>
309 <test>
310 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
311 <repeat name="plots">
312 <param name="width" value="1280" />
313 <param name="height" value="960" />
314 <conditional name="plot">
315 <param name="type" value="volcano" />
316 <param name="x" value="q1" />
317 <param name="y" value="q2" />
318 </conditional>
319 </repeat>
320 <output name="output" ftype="txt" file="volcano.txt" lines_diff="2">
321 <discovered_dataset designation="volcano-0" ftype="png" file="volcano.png" />
322 </output>
323 </test>
324 <test>
325 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
326 <repeat name="plots">
327 <param name="width" value="1280" />
328 <param name="height" value="960" />
329 <conditional name="plot">
330 <param name="type" value="boxplot" />
331 </conditional>
332 </repeat>
333 <output name="output" ftype="txt" file="boxplot.txt" lines_diff="2">
334 <discovered_dataset designation="boxplot-0" ftype="png" file="boxplot.png" />
335 </output>
336 </test>
337 <test>
338 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
339 <repeat name="plots">
340 <param name="width" value="1280" />
341 <param name="height" value="960" />
342 <conditional name="plot">
343 <param name="type" value="fpkmSCV" />
344 </conditional>
345 </repeat>
346 <output name="output" ftype="txt" file="fpkmSCV.txt" lines_diff="2">
347 <discovered_dataset designation="fpkmSCV-0" ftype="png" file="fpkmSCV.png" />
348 </output>
349 </test>
350 </tests>
351 <help><![CDATA[
352 This tool allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
353
354 ------
355
356 Based on the `cummeRbund wrapper <http://toolshed.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute.
357 ]]></help>
358 <citations>
359 <citation type="doi">doi:10.1038/nprot.2012.016</citation>
360 </citations>
361 </tool>