Mercurial > repos > iuc > raceid_clustering

comparison raceid_clustering.xml @ 6:a4b734cd253b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
author iuc
date Thu, 15 Apr 2021 18:58:21 +0000
parents 7e014059a88d
children c4f39bf4a068
comparison
equal deleted inserted replaced
5:7e014059a88d 6:a4b734cd253b
1 <tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" > 1 <tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@+galaxy@VERSION_WRAPPER@" >
2 <description>performs clustering, outlier detection, dimensional reduction</description> 2 <description>performs clustering, outlier detection, dimensional reduction</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <import>macros_cheetah.xml</import> 5 <import>macros_cheetah.xml</import>
6 </macros> 6 </macros>
50 <param name="nbtree" type="integer" optional="true" label="Number of trees to be built" /><!-- 0:Null --> 50 <param name="nbtree" type="integer" optional="true" label="Number of trees to be built" /><!-- 0:Null -->
51 <param name="nbfactor" type="integer" min="0" value="5" label="Tree Factor" help="Number of trees based on the number of cells multiplied by this factor. Effective only if the number of trees parameter is set to 0" /> 51 <param name="nbfactor" type="integer" min="0" value="5" label="Tree Factor" help="Number of trees based on the number of cells multiplied by this factor. Effective only if the number of trees parameter is set to 0" />
52 <param name="rfseed" type="integer" value="12345" label="Random Seed" /> 52 <param name="rfseed" type="integer" value="12345" label="Random Seed" />
53 </expand> 53 </expand>
54 </section> 54 </section>
55 <section name="tsne" title="tSNE and FR" expanded="true" > 55 <section name="tsne" title="tSNE, FR and UMAP" expanded="true" >
56 <!-- CompTSNE --> 56 <!-- CompTSNE -->
57 <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" /> 57 <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" />
58 <!-- CompFR --> 58 <!-- CompFR -->
59 <param name="knn" type="integer" min="0" value="10" label="KNN" help="Number of nearest neighbours used for the inference of the Fruchterman-Rheingold layout" /> 59 <param name="knn" type="integer" min="1" value="10" label="KNN" help="Number of nearest neighbours used for the inference of the Fruchterman-Rheingold layout" />
60 <!-- CompUMAP -->
61 <param name="umap_nn" type="integer" min="1" value="15" label="N Neighbours" help="Number of nearest neighbours used for the UMAP connectivity" />
60 <expand macro="use_defaults_no" > 62 <expand macro="use_defaults_no" >
61 <!-- CompTSNE --> 63 <!-- CompTSNE -->
62 <param name="initial_cmd" type="boolean" checked="true" label="tSNE map initialised by classical multidimensional scaling" /> 64 <param name="initial_cmd" type="boolean" checked="true" label="tSNE map initialised by classical multidimensional scaling" />
63 <param name="rseed_tsne" type="integer" value="15555" label="Random Seed (tSNE)" /> 65 <param name="rseed_tsne" type="integer" value="15555" label="Random Seed (tSNE)" />
64 <!-- CompFR --> 66 <!-- CompFR -->
65 <param name="rseed_fr" type="integer" min="0" value="15555" label="Random Seed (FR)" /> 67 <param name="rseed_fr" type="integer" min="0" value="15555" label="Random Seed (FR)" />
68 <!-- CompUMAP -->
69 <param name="umap_epochs" type="integer" min="1" value="200" label="Number Epochs (UMAP)" />
70 <param name="umap_min_dist" type="float" min="0" value="0.1" label="Min Dist (UMAP)" />
66 </expand> 71 </expand>
67 </section> 72 </section>
68 <section name="extra" title="Extra Parameters" expanded="false" > 73 <section name="extra" title="Extra Parameters" expanded="false" >
69 <param name="tablelim" type="integer" min="1" value="25" label="Table Limit" help="Top N genes to print per cluster" /> 74 <param name="tablelim" type="integer" min="1" value="25" label="Table Limit" help="Top N genes to print per cluster" />
70 <param name="plotlim" type="integer" min="1" value="10" label="Plot Limit" help="Top N genes to plot. Must be less than or equal to the Table Limit" /> 75 <param name="plotlim" type="integer" min="1" value="10" label="Plot Limit" help="Top N genes to plot. Must be less than or equal to the Table Limit" />
82 </data> 87 </data>
83 </outputs> 88 </outputs>
84 <tests> 89 <tests>
85 <test> 90 <test>
86 <param name="inputrds" value="matrix.filter.rdat" /> 91 <param name="inputrds" value="matrix.filter.rdat" />
87 <output name="outgenelist" value="matrix2.genelist" compare="re_match"/> 92 <output name="outgenelist" >
88 <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="15" /> 93 <assert_contents>
89 <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="10" /> 94 <has_line_matching expression=".*ENSDARG00000108379\s+1.*" />
95 <has_line_matching expression=".*ENSDARG00000027310\s+8.*" />
96 </assert_contents>
97 </output>
98 <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="500" />
99 <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="100" />
90 <output name="outassignments" > 100 <output name="outassignments" >
91 <assert_contents> 101 <assert_contents>
92 <has_line_matching expression="P1_B1_ATCCAC\s1\s1\sFALSE" /> 102 <has_line_matching expression="P1_B1_ATCCAC\s1\s1\sFALSE" />
93 </assert_contents> 103 </assert_contents>
94 </output> 104 </output>
125 <param name="initial_cmd" value="true" /> 135 <param name="initial_cmd" value="true" />
126 <param name="rseed_tsne" value="15555" /> 136 <param name="rseed_tsne" value="15555" />
127 <param name="rfseed_fr" value="15555" /> 137 <param name="rfseed_fr" value="15555" />
128 </expand> 138 </expand>
129 </section> 139 </section>
130 <output name="outgenelist" value="intestinal.genelist" compare="re_match"/> 140 <output name="outgenelist" >
141 <assert_contents>
142 <has_line_matching expression=".*ENSDARG00000108379\s+1.*" />
143 <has_line_matching expression=".*ENSDARG00000027310\s+8.*" />
144 </assert_contents>
145 </output>
131 <output name="outpdf" value="intestinal.pdf" compare="sim_size" delta="50" /> 146 <output name="outpdf" value="intestinal.pdf" compare="sim_size" delta="50" />
132 </test> 147 </test>
133 <test> 148 <test>
134 <!-- Advanced. Opts, CC used --> 149 <!-- Advanced. Opts, CC used -->
135 <param name="inputrds" value="matrix.filter.rdat" /> 150 <param name="inputrds" value="matrix.filter.rdat" />
166 <param name="initial_cmd" value="false" /> 181 <param name="initial_cmd" value="false" />
167 <param name="rseed_tsne" value="15555" /> 182 <param name="rseed_tsne" value="15555" />
168 <param name="rfseed_fr" value="15555" /> 183 <param name="rfseed_fr" value="15555" />
169 </expand> 184 </expand>
170 </section> 185 </section>
171 <output name="outgenelist" value="intestinal_advanced.genelist" compare="re_match"/> 186 <output name="outgenelist" >
187 <assert_contents>
188 <has_line_matching expression=".*ENSDARG00000107138\s+1.*" />
189 <has_line_matching expression=".*ENSDARG00000016138\s+10.*" />
190 </assert_contents>
191 </output>
172 <output name="outpdf" value="intestinal_advanced.pdf" compare="sim_size" delta="150" /> 192 <output name="outpdf" value="intestinal_advanced.pdf" compare="sim_size" delta="150" />
173 </test> 193 </test>
174 </tests> 194 </tests>
175 <help><![CDATA[ 195 <help><![CDATA[
176 RaceID3 196 RaceID3