Mercurial > repos > devteam > cummerbund

comparison cummeRbund.xml @ 0:587c425b4e76 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial commit with version 1.0.0 of the cummeRbund wrapper.
author devteam
date Tue, 23 Dec 2014 15:58:27 -0500
parents
children ac2ebc60ef5d
comparison
equal deleted inserted replaced
-1:000000000000 0:587c425b4e76
1 <?xml version="1.0"?>
2 <tool id="cummeRbund" name="Plot CuffDiff" version="1.0.0">
3 <description>data with cummeRbund</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 Based on the `cummeRbund wrapper <http://toolshed.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute.
355 ]]></help>
356 <citations>
357 <citation type="doi">doi:10.1038/nprot.2012.016</citation>
358 </citations>
359 </tool>