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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
author iuc
date Mon, 02 Oct 2023 13:23:00 +0000
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-1:000000000000 0:852e3f4321d4
1 <tool id="baredsc_1d" name="baredSC 1d" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2 <description>Compute distribution for a single gene</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam_topics"/>
7 <edam_operations>
8 <edam_operation>operation_2495</edam_operation>
9 </edam_operations>
10 <xrefs>
11 <xref type="bio.tools">baredsc</xref>
12 </xrefs>
13 <expand macro="requirements"/>
14 <command detect_errors="exit_code"><![CDATA[
15 baredSC_1d
16 ## Required inputs:
17 @REQUIRED_INPUTS_1D@
18
19 ## Filter cells
20 @FILTER_CELLS@
21 ## MCMC
22 @MCMC_1D@
23 @BAREDSC_COMMON@
24 ## Plots
25 @PLOTS@
26 @PRETTYBINS_1D@
27 ## Advanced
28 @ADVANCED_COMMON_X@
29 @ADVANCED_BAREDSC_COMMON@
30 ## Outputs
31 --output output
32 --figure baredSC.$plots.image_file_format
33 --logevidence logevidence.txt &&
34 mkdir QC output &&
35 mv baredSC_convergence.* QC &&
36 mv baredSC_p.$plots.image_file_format QC &&
37 mv baredSC_corner.* QC &&
38 mv baredSC_neff.txt output &&
39 @ORDER_OUTPUTS_1D@
40 ]]></command>
41 <inputs>
42 <expand macro="macro_input_counts"/>
43 <expand macro="macro_single_gene"/>
44 <expand macro="macro_filter_cells"/>
45 <section name="MCMC" title="MCMC parameters">
46 <expand macro="macro_MCMC_params_common_axis" axis="x" />
47 <expand macro="macro_scale_seed"/>
48 <expand macro="macro_MCMC_common_baredSC"/>
49 </section>
50 <section name="plots" title="Customize plots">
51 <expand macro="macro_plots"/>
52 <expand macro="macro_prettybins_1d"/>
53 </section>
54 <section name="advanced" title="Advanced parameters" expanded="false">
55 <expand macro="macro_advanced_common_axis" axis="x"/>
56 <expand macro="macro_advanced_evidence"/>
57 <expand macro="macro_advanced_common_baredSC"/>
58 </section>
59 </inputs>
60 <outputs>
61 <data format="npz" name="output" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: Numpy archive" from_work_dir="output.npz"/>
62 <data format="txt" name="neff" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: Neff" from_work_dir="output/baredSC_neff.txt"/>
63 <collection type="list" name="qc_plots" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: QC plots">
64 <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)" directory="QC"/>
65 </collection>
66 <data format="tabular" name="pdf" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: PDF with error bar" from_work_dir="output/baredSC_pdf.txt">
67 <actions>
68 <action name="column_names" type="metadata" default="x,low,mean,high,median" />
69 </actions>
70 </data>
71 <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: plot" from_work_dir="baredSC">
72 <change_format>
73 <when input="plots.image_file_format" value="png" format="png" />
74 <when input="plots.image_file_format" value="svg" format="svg" />
75 <when input="plots.image_file_format" value="pdf" format="pdf" />
76 </change_format>
77 </data>
78 <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: plots and txt">
79 <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)"/>
80 </collection>
81 <data format="txt" name="logevidence" label="${tool.name} on $getVar('input_counts.input', 'input_counts.inputAnnData') for ${geneColName}: Log evidence" from_work_dir="logevidence.txt"/>
82 </outputs>
83 <tests>
84 <!-- First test -->
85 <test>
86 <conditional name="input_counts">
87 <param name="filetype" value="tabular"/>
88 <param name="input" value="nih3t3_generated_2d_2.txt"/>
89 </conditional>
90 <param name="geneColName" value="0.5_0_0_0.5_x"/>
91 <section name="MCMC">
92 <param name="nnorm" value="1"/>
93 </section>
94 <section name="plots">
95 <param name="title" value="first gene 1 gauss"/>
96 </section>
97 <output name="output">
98 <assert_contents>
99 <has_size value="1257974" delta="100000"/>
100 </assert_contents>
101 </output>
102 <output name="neff">
103 <assert_contents>
104 <has_text_matching expression="^80[0-9][0-9]\."/>
105 </assert_contents>
106 </output>
107 <output_collection name="qc_plots" count="3" type="list">
108 <element name="convergence" ftype="png">
109 <assert_contents>
110 <has_size value="23021" delta="2000"/>
111 </assert_contents>
112 </element>
113 <element name="p" ftype="png">
114 <assert_contents>
115 <has_size value="45302" delta="4000"/>
116 </assert_contents>
117 </element>
118 <element name="corner" ftype="png">
119 <assert_contents>
120 <has_size value="66254" delta="6000"/>
121 </assert_contents>
122 </element>
123 </output_collection>
124 <!--In the next output pdf means probability density function-->
125 <output name="pdf" ftype="tabular">
126 <assert_contents>
127 <has_text_matching expression="x\s+low\s+mean\s+high\s+median"/>
128 <has_n_lines n="101"/>
129 <has_line_matching expression="0\.0125\s+0\.2[0-9]+\s+0\.2[0-9]+\s+0\.2[0-9]+\s+0\.2[0-9]+"/>
130 </assert_contents>
131 </output>
132 <output name="plot" ftype="png">
133 <assert_contents>
134 <has_size value="239991" delta="20000"/>
135 </assert_contents>
136 </output>
137 <output_collection name="other_outputs" count="7" type="list">
138 <element name="individuals" ftype="png">
139 <assert_contents>
140 <has_size value="54420" delta="5000"/>
141 </assert_contents>
142 </element>
143 <element name="p" ftype="txt">
144 <assert_contents>
145 <has_line_matching expression="name\s+low\s+median\s+high"/>
146 <has_line_matching expression="mu0\s+0\.6[0-9]+\s+0\.6[0-9]+\s+0\.6[0-9]+"/>
147 <has_text_matching expression="scale0\s+0\.3[0-9]+\s+0\.3[0-9]+\s+0\.3[0-9]+" />
148 <has_n_lines n="3"/>
149 </assert_contents>
150 </element>
151 <element name="with_posterior" ftype="png">
152 <assert_contents>
153 <has_size value="243443" delta="20000"/>
154 </assert_contents>
155 </element>
156 <element name="posterior_per_cell" ftype="txt">
157 <assert_contents>
158 <has_n_lines n="2362"/>
159 <has_line_matching expression="mu\s+sd"/>
160 </assert_contents>
161 </element>
162 <element name="posterior_andco" ftype="png">
163 <assert_contents>
164 <has_size value="194143" delta="10000"/>
165 </assert_contents>
166 </element>
167 <element name="posterior_individuals" ftype="png">
168 <assert_contents>
169 <has_size value="135293" delta="10000"/>
170 </assert_contents>
171 </element>
172 <element name="means" ftype="txt">
173 <assert_contents>
174 <has_n_lines n="75001"/>
175 </assert_contents>
176 </element>
177 </output_collection>
178 <output name="logevidence">
179 <assert_contents>
180 <has_text_matching expression="^-42[0-9][0-9]\."/>
181 </assert_contents>
182 </output>
183 </test>
184 <!-- Second test pdf filtering cells pretty log scale-->
185 <test>
186 <conditional name="input_counts">
187 <param name="filetype" value="tabular"/>
188 <param name="input" value="nih3t3_generated_2d_2.txt"/>
189 </conditional>
190 <param name="geneColName" value="0.5_0_0_0.5_x"/>
191 <conditional name="filter">
192 <param name="nb" value="1"/>
193 <param name="metadata1ColName" value="0_0.5_0.5_0_group"/>
194 <param name="metadata1Values" value="1.0"/>
195 </conditional>
196 <section name="MCMC">
197 <param name="xmin" value="-15"/>
198 <param name="xmax" value="-7"/>
199 <param name="nx" value="25"/>
200 <param name="nnorm" value="2"/>
201 <param name="nsampMCMC" value="20000"/>
202 <conditional name="automaticRestart">
203 <param name="set_minNeff" value="yes"/>
204 <param name="minNeff" value="400"/>
205 </conditional>
206 <conditional name="scale">
207 <param name="type" value="log"/>
208 </conditional>
209 </section>
210 <section name="plots">
211 <param name="image_file_format" value="pdf"/>
212 <param name="prettyBins" value="200"/>
213 </section>
214 <output name="output">
215 <assert_contents>
216 <has_size value="3198024" delta="300000"/>
217 </assert_contents>
218 </output>
219 <output name="neff">
220 <assert_contents>
221 <has_text_matching expression="^317[56]\."/>
222 </assert_contents>
223 </output>
224 <output_collection name="qc_plots" count="3" type="list">
225 <element name="convergence" ftype="pdf">
226 <assert_contents>
227 <has_size value="25976" delta="2000"/>
228 </assert_contents>
229 </element>
230 <element name="p" ftype="pdf">
231 <assert_contents>
232 <has_size value="479327" delta="20000"/>
233 </assert_contents>
234 </element>
235 <element name="corner" ftype="pdf">
236 <assert_contents>
237 <has_size value="223275" delta="20000"/>
238 </assert_contents>
239 </element>
240 </output_collection>
241 <!--In the next output pdf means probability density function-->
242 <output name="pdf" ftype="tabular">
243 <assert_contents>
244 <has_text_matching expression="x\s+low\s+mean\s+high\s+median"/>
245 <has_n_lines n="201"/>
246 <has_line_matching expression="-8\.5\s+0\.4[0-9]+\s+0\.5[0-9]+\s+0\.6[0-9]+\s+0\.5[0-9]+"/>
247 </assert_contents>
248 </output>
249 <output name="plot" ftype="pdf">
250 <assert_contents>
251 <has_size value="111517" delta="10000"/>
252 </assert_contents>
253 </output>
254 <output_collection name="other_outputs" count="7" type="list">
255 <element name="individuals" ftype="pdf">
256 <assert_contents>
257 <has_size value="95638" delta="10000"/>
258 </assert_contents>
259 </element>
260 <element name="p" ftype="txt">
261 <assert_contents>
262 <has_line_matching expression="name\s+low\s+median\s+high"/>
263 <has_line_matching expression="mu[01]\s+-8\.8[0-9]+\s+-8\.7[0-9]+\s+-8\.6[0-9]+"/>
264 <has_text_matching expression="scale[01]\s+0\.1[0-9]+\s+0\.2[0-9]+\s+0\.2[0-9]+" />
265 <has_n_lines n="6"/>
266 </assert_contents>
267 </element>
268 <element name="with_posterior" ftype="pdf">
269 <assert_contents>
270 <has_size value="112356" delta="10000"/>
271 </assert_contents>
272 </element>
273 <element name="posterior_per_cell" ftype="txt">
274 <assert_contents>
275 <has_n_lines n="1164"/>
276 <has_line_matching expression="mu\s+sd"/>
277 </assert_contents>
278 </element>
279 <element name="posterior_andco" ftype="pdf">
280 <assert_contents>
281 <has_size value="66922" delta="6000"/>
282 </assert_contents>
283 </element>
284 <element name="posterior_individuals" ftype="pdf">
285 <assert_contents>
286 <has_size value="77887" delta="7000"/>
287 </assert_contents>
288 </element>
289 <element name="means" ftype="txt">
290 <assert_contents>
291 <has_n_lines n="100000"/>
292 </assert_contents>
293 </element>
294 </output_collection>
295 <output name="logevidence">
296 <assert_contents>
297 <has_text_matching expression="^-20[78][0-9]\."/>
298 </assert_contents>
299 </output>
300 </test>
301 </tests>
302 <expand macro="helpcitations"/>
303 </tool>