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comparison cpm_tpm_rpk.xml @ 4:be358a1ebf67 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit a8486c89b7ddabfb1e814c2c42f6c04d3896904c
author artbio
date Thu, 05 Oct 2023 13:50:22 +0000
parents 8b1020c25f0f
children bcff1eb6fdb5
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3:8b1020c25f0f 4:be358a1ebf67
1 <tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.4.0"> 1 <tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.5.0">
2 <description>from raw counts expression values</description> 2 <description>from raw counts expression values</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> 4 <requirement type="package" version="1.7.1">r-optparse</requirement>
5 <requirement type="package" version="0.13=r3.3.2_0">r-rtsne</requirement> 5 <requirement type="package" version="0.16">r-rtsne</requirement>
6 <requirement type="package" version="2.2.1=r3.3.2_0">r-ggplot2</requirement> 6 <requirement type="package" version="3.3.6">r-ggplot2</requirement>
7 <requirement type="package" version="0.4.1=r3.3.2_0">r-ggfortify</requirement> 7 <requirement type="package" version="0.4.14">r-ggfortify</requirement>
8 <requirement type="package" version="1.4.4">r-reshape2</requirement>
8 </requirements> 9 </requirements>
9 <stdio> 10 <stdio>
10 <exit_code range="1:" level="fatal" description="Tool exception" /> 11 <exit_code range="1:" level="fatal" description="Tool exception" />
11 </stdio> 12 </stdio>
12 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
136 <filter>visu_option['visualisation'] == 'yes'</filter> 137 <filter>visu_option['visualisation'] == 'yes'</filter>
137 </data> 138 </data>
138 </outputs> 139 </outputs>
139 <tests> 140 <tests>
140 <!-- test t-SNE --> 141 <!-- test t-SNE -->
141 <test> 142 <test expect_num_outputs="3">
142 <param name="input" value="none.tab" ftype="tabular"/> 143 <param name="input" value="none.tab" ftype="tabular"/>
143 <param name="type_transfo" value="none"/> 144 <param name="type_transfo" value="none"/>
144 <param name="log" value="FALSE"/> 145 <param name="log" value="FALSE"/>
145 <param name="visualisation" value="yes"/> 146 <param name="visualisation" value="yes"/>
146 <param name="seed" value="49"/> 147 <param name="seed" value="49"/>
147 <param name="perp" value="10"/> 148 <param name="perp" value="10"/>
148 <param name="theta" value="1" /> 149 <param name="theta" value="1" />
149 <param name="tsne_labels" value="yes" /> 150 <param name="tsne_labels" value="yes" />
150 <output name="output" file="none.tab" ftype="tabular"/> 151 <output name="output" file="none.tab" ftype="tabular" />
151 <output name="tsne_out" file="none_tsne.pdf" ftype="pdf"/> 152 <output name="tsne_out" file="none_tsne.pdf" ftype="pdf" compare="sim_size" delta="1000" />
152 <output name="pca_out" file="none_pca.pdf" ftype="pdf"/> 153 <output name="pca_out" file="none_pca.pdf" ftype="pdf" />
153 </test> 154 </test>
154 <test> 155 <test expect_num_outputs="3">
155 <param name="input" value="counts.tab" ftype="tabular"/> 156 <param name="input" value="counts.tab" ftype="tabular"/>
156 <param name="type_transfo" value="cpm"/> 157 <param name="type_transfo" value="cpm"/>
157 <param name="log" value="TRUE"/> 158 <param name="log" value="TRUE"/>
158 <param name="visualisation" value="yes"/> 159 <param name="visualisation" value="yes"/>
159 <param name="seed" value="49"/> 160 <param name="seed" value="49"/>
160 <param name="perp" value="2"/> 161 <param name="perp" value="2"/>
161 <param name="theta" value="1" /> 162 <param name="theta" value="1" />
162 <param name="tsne_labels" value="yes" /> 163 <param name="tsne_labels" value="yes" />
163 <output name="output" file="logcpm.tab" ftype="tabular"/> 164 <output name="output" file="logcpm.tab" ftype="tabular" />
164 <output name="tsne_out" file="tsne.pdf" ftype="pdf"/> 165 <output name="tsne_out" file="tsne.pdf" ftype="pdf" compare="sim_size" delta="1000" />
165 <output name="pca_out" file="pca.pdf" ftype="pdf"/> 166 <output name="pca_out" file="pca.pdf" ftype="pdf" />
166 </test> 167 </test>
167 <test> 168 <test expect_num_outputs="3">
168 <param name="input" value="counts.tab" ftype="tabular"/> 169 <param name="input" value="counts.tab" ftype="tabular"/>
169 <param name="type_transfo" value="tpm"/> 170 <param name="type_transfo" value="tpm"/>
170 <param name="gene_file" value="gene_length.tab" ftype="tabular"/> 171 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
171 <param name="log" value="TRUE"/> 172 <param name="log" value="TRUE"/>
172 <param name="visualisation" value="yes"/> 173 <param name="visualisation" value="yes"/>
173 <param name="seed" value="49"/> 174 <param name="seed" value="49"/>
174 <param name="perp" value="2"/> 175 <param name="perp" value="2"/>
175 <param name="theta" value="1" /> 176 <param name="theta" value="1" />
176 <param name="tsne_labels" value="no" /> 177 <param name="tsne_labels" value="no" />
177 <output name="output" file="logtpm.tab" ftype="tabular"/> 178 <output name="output" file="logtpm.tab" ftype="tabular" />
178 <output name="tsne_out" file="tsne.nolab.pdf" ftype="pdf"/> 179 <output name="tsne_out" file="tsne.nolab.pdf" ftype="pdf" compare="sim_size" delta="1000" />
179 <output name="pca_out" file="pca.nolab.pdf" ftype="pdf"/> 180 <output name="pca_out" file="pca.nolab.pdf" ftype="pdf" />
180 </test> 181 </test>
181 <!-- test without t-SNE --> 182 <!-- test without t-SNE -->
182 <test> 183 <test expect_num_outputs="1">
183 <param name="input" value="counts.tab" ftype="tabular"/> 184 <param name="input" value="counts.tab" ftype="tabular"/>
184 <param name="type_transfo" value="cpm"/> 185 <param name="type_transfo" value="cpm"/>
185 <output name="output" file="cpm.tab" ftype="tabular"/> 186 <output name="output" file="cpm.tab" ftype="tabular"/>
186 </test> 187 </test>
187 <test> 188 <test expect_num_outputs="1">
188 <param name="input" value="counts.tab" ftype="tabular"/> 189 <param name="input" value="counts.tab" ftype="tabular"/>
189 <param name="type_transfo" value="cpm"/> 190 <param name="type_transfo" value="cpm"/>
190 <param name="log" value="TRUE"/> 191 <param name="log" value="TRUE"/>
191 <output name="output" file="logcpm.tab" ftype="tabular"/> 192 <output name="output" file="logcpm.tab" ftype="tabular" />
192 </test> 193 </test>
193 <test> 194 <test expect_num_outputs="1">
194 <param name="input" value="counts.tab" ftype="tabular"/> 195 <param name="input" value="counts.tab" ftype="tabular"/>
195 <param name="type_transfo" value="tpm"/> 196 <param name="type_transfo" value="tpm"/>
196 <param name="gene_file" value="gene_length.tab" ftype="tabular"/> 197 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
197 <param name="gene_header" value="TRUE"/> 198 <param name="gene_header" value="TRUE"/>
198 <output name="output" file="tpm.tab" ftype="tabular"/> 199 <output name="output" file="tpm.tab" ftype="tabular"/>
199 </test> 200 </test>
200 <test> 201 <test expect_num_outputs="1">
201 <param name="input" value="counts.tab" ftype="tabular"/> 202 <param name="input" value="counts.tab" ftype="tabular"/>
202 <param name="type_transfo" value="tpm"/> 203 <param name="type_transfo" value="tpm"/>
203 <param name="gene_file" value="gene_length.tab" ftype="tabular"/> 204 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
204 <param name="gene_header" value="TRUE"/> 205 <param name="gene_header" value="TRUE"/>
205 <param name="log" value="TRUE"/> 206 <param name="log" value="TRUE"/>
206 <output name="output" file="logtpm.tab" ftype="tabular"/> 207 <output name="output" file="logtpm.tab" ftype="tabular" />
207 </test> 208 </test>
208 <test> 209 <test expect_num_outputs="1">
209 <param name="input" value="counts.tab" ftype="tabular"/> 210 <param name="input" value="counts.tab" ftype="tabular"/>
210 <param name="type_transfo" value="rpk"/> 211 <param name="type_transfo" value="rpk"/>
211 <param name="gene_file" value="gene_length.tab" ftype="tabular"/> 212 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
212 <param name="gene_header" value="TRUE"/> 213 <param name="gene_header" value="TRUE"/>
213 <output name="output" file="rpk.tab" ftype="tabular"/> 214 <output name="output" file="rpk.tab" ftype="tabular" />
214 </test> 215 </test>
215 <test> 216 <test expect_num_outputs="1">
216 <param name="input" value="counts.tab" ftype="tabular"/> 217 <param name="input" value="counts.tab" ftype="tabular"/>
217 <param name="type_transfo" value="rpk"/> 218 <param name="type_transfo" value="rpk"/>
218 <param name="gene_file" value="gene_length.tab" ftype="tabular"/> 219 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
219 <param name="gene_header" value="TRUE"/> 220 <param name="gene_header" value="TRUE"/>
220 <param name="log" value="TRUE"/> 221 <param name="log" value="TRUE"/>
221 <output name="output" file="logrpk.tab" ftype="tabular"/> 222 <output name="output" file="logrpk.tab" ftype="tabular" />
222 </test> 223 </test>
223 </tests> 224 </tests>
224 <help> 225 <help>
225 226
226 **What it does** 227 **What it does**
238 Note: do not comment you header line if you have header line in you tabular input (ie do not start the header line with a '#' character) 239 Note: do not comment you header line if you have header line in you tabular input (ie do not start the header line with a '#' character)
239 240
240 Computed values may be log-transformed (log2([CPM or RPK or TPM]+1)) 241 Computed values may be log-transformed (log2([CPM or RPK or TPM]+1))
241 242
242 </help> 243 </help>
244 <citations>
245 <citation type="bibtex">@Article{,
246 title = {Visualizing High-Dimensional Data Using t-SNE},
247 volume = {9},
248 pages = {2579-2605},
249 year = {2008},
250 author = {L.J.P. {van der Maaten} and G.E. Hinton},
251 journal = {Journal of Machine Learning Research},
252 }
253 </citation>
254 <citation type="bibtex">@Manual{,
255 title = {{ClusterR}: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans,
256 K-Medoids and Affinity Propagation Clustering},
257 author = {Lampros Mouselimis},
258 year = {2019},
259 note = {R package version 1.1.9},
260 url = {https://github.com/mlampros/ClusterR},
261 }
262 </citation>
263 </citations>
243 </tool> 264 </tool>