Mercurial > repos > iuc > raceid_clustering
comparison raceid_clustering.xml @ 6:a4b734cd253b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
author | iuc |
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date | Thu, 15 Apr 2021 18:58:21 +0000 |
parents | 7e014059a88d |
children | c4f39bf4a068 |
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5:7e014059a88d | 6:a4b734cd253b |
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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 |