Mercurial > repos > artbio > gsc_high_dimensions_visualisation

comparison high_dim_visu.xml @ 9:58aa18e1fe14 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization commit 7343be2d3b1b8cb1ba0c4c55767b60dbce8f8b22
author artbio
date Thu, 07 Nov 2024 22:43:01 +0000
parents fe6f76030168
children
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8:fe6f76030168 9:58aa18e1fe14
1 <tool id="high_dimensions_visualisation" name="Generate PCA, tSNE and HCPC" version="4.3+galaxy0" profile="20.01"> 1 <tool id="high_dimensions_visualisation" name="Generate PCA, tSNE and HCPC" version="4.3+galaxy1" profile="20.01">
2 <description>from highly dimensional expression data</description> 2 <description>from highly dimensional expression data</description>
3 <xrefs>
4 <xref type="bio.tools">galaxy_single_cell_suite</xref>
5 </xrefs>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="1.7.3=r43hc72bb7e_2">r-optparse</requirement> 7 <requirement type="package" version="1.7.3=r43hc72bb7e_2">r-optparse</requirement>
5 <requirement type="package" version="2.9=r43h57805ef_0">r-factominer</requirement> 8 <requirement type="package" version="2.9=r43h57805ef_0">r-factominer</requirement>
6 <requirement type="package" version="1.0.7=r43hc72bb7e_3">r-factoextra</requirement> 9 <requirement type="package" version="1.0.7=r43hc72bb7e_3">r-factoextra</requirement>
7 <requirement type="package" version="0.16=r43h7ce84a7_2">r-rtsne</requirement> 10 <requirement type="package" version="0.16=r43h7ce84a7_2">r-rtsne</requirement>
234 <param name="input" value="cpm_input.tsv" ftype="txt"/> 237 <param name="input" value="cpm_input.tsv" ftype="txt"/>
235 <param name="labels" value="yes" /> 238 <param name="labels" value="yes" />
236 <param name="visu_choice" value="PCA" /> 239 <param name="visu_choice" value="PCA" />
237 <param name="factor_choice" value="No" /> 240 <param name="factor_choice" value="No" />
238 <param name="item_size" value="0.5" /> 241 <param name="item_size" value="0.5" />
239 <output name="pdf_out" file="pca.1.pdf" ftype="pdf"/> 242 <output name="pdf_out" file="pca.1.pdf" ftype="pdf" compare="sim_size" delta="1000"/>
240 </test> 243 </test>
241 <!-- test PCA PC2 vs PC3 --> 244 <!-- test PCA PC2 vs PC3 -->
242 <test expect_num_outputs="1"> 245 <test expect_num_outputs="1">
243 <param name="input" value="cpm_input.tsv" ftype="txt"/> 246 <param name="input" value="cpm_input.tsv" ftype="txt"/>
244 <param name="labels" value="no" /> 247 <param name="labels" value="no" />
245 <param name="visu_choice" value="PCA" /> 248 <param name="visu_choice" value="PCA" />
246 <param name="factor_choice" value="No" /> 249 <param name="factor_choice" value="No" />
247 <param name="x_axis" value="2" /> 250 <param name="x_axis" value="2" />
248 <param name="y_axis" value="3" /> 251 <param name="y_axis" value="3" />
249 <output name="pdf_out" file="pca.2.pdf" ftype="pdf"/> 252 <output name="pdf_out" file="pca.2.pdf" ftype="pdf" compare="sim_size" delta="1000"/>
250 </test> 253 </test>
251 <!-- test factor contrasting on PCA --> 254 <!-- test factor contrasting on PCA -->
252 <test expect_num_outputs="1"> 255 <test expect_num_outputs="1">
253 <param name="input" value="cpm_input.tsv" ftype="txt"/> 256 <param name="input" value="cpm_input.tsv" ftype="txt"/>
254 <param name="labels" value="no" /> 257 <param name="labels" value="no" />
255 <param name="visu_choice" value="PCA" /> 258 <param name="visu_choice" value="PCA" />
256 <param name="factor_choice" value="Yes" /> 259 <param name="factor_choice" value="Yes" />
257 <param name="factor" value="factor.tsv" ftype="txt"/> 260 <param name="factor" value="factor.tsv" ftype="txt"/>
258 <output name="pdf_out" file="pca.3.pdf" ftype="pdf"/> 261 <output name="pdf_out" file="pca.3.pdf" ftype="pdf" compare="sim_size" delta="1000"/>
259 </test> 262 </test>
260 <!-- test numerical factor contrasting on PCA --> 263 <!-- test numerical factor contrasting on PCA -->
261 <test expect_num_outputs="1"> 264 <test expect_num_outputs="1">
262 <param name="input" value="cpm_input.tsv" ftype="txt"/> 265 <param name="input" value="cpm_input.tsv" ftype="txt"/>
263 <param name="labels" value="no" /> 266 <param name="labels" value="no" />