Mercurial > repos > iuc > scanpy_normalize

comparison normalize.xml @ 6:3bcd5445cd7a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
author iuc
date Thu, 20 Feb 2020 08:24:54 -0500
parents ec32793ce1dd
children a407e7f8bdc1
comparison
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5:ec32793ce1dd 6:3bcd5445cd7a
113 </when> 113 </when>
114 <when value="pp.recipe_seurat"> 114 <when value="pp.recipe_seurat">
115 <expand macro="param_log"/> 115 <expand macro="param_log"/>
116 </when> 116 </when>
117 </conditional> 117 </conditional>
118 <expand macro="inputs_common_advanced"/>
118 </inputs> 119 </inputs>
119 <outputs> 120 <outputs>
120 <expand macro="anndata_outputs"/> 121 <expand macro="anndata_outputs"/>
121 </outputs> 122 </outputs>
122 <tests> 123 <tests>
123 <test> 124 <test>
124 <!-- test 1 --> 125 <!-- test 0 -->
125 <param name="adata" value="krumsiek11.h5ad" /> 126 <param name="adata" value="krumsiek11.h5ad" />
126 <conditional name="method"> 127 <conditional name="method">
127 <param name="method" value="pp.normalize_total"/> 128 <param name="method" value="pp.normalize_total"/>
128 <conditional name="exclude_highly_expressed"> 129 <conditional name="exclude_highly_expressed">
129 <param name="exclude_highly_expressed" value="False"/> 130 <param name="exclude_highly_expressed" value="False"/>
130 </conditional> 131 </conditional>
131 <param name="key_added" value="n_counts"/> 132 <param name="key_added" value="n_counts"/>
132 <param name="layers" value="all"/> 133 <param name="layers" value="all"/>
133 <param name="layer_norm" value="None"/> 134 <param name="layer_norm" value="None"/>
134 </conditional> 135 </conditional>
135 <assert_stdout> 136 <section name="advanced_common">
136 <has_text_matching expression="sc.pp.normalize_total"/> 137 <param name="show_log" value="true" />
137 <has_text_matching expression="exclude_highly_expressed=False"/> 138 </section>
138 <has_text_matching expression="key_added='n_counts'"/> 139 <output name="hidden_output">
139 <has_text_matching expression="layers='all'"/> 140 <assert_contents>
140 </assert_stdout> 141 <has_text_matching expression="sc.pp.normalize_total"/>
142 <has_text_matching expression="exclude_highly_expressed=False"/>
143 <has_text_matching expression="key_added='n_counts'"/>
144 <has_text_matching expression="layers='all'"/>
145 </assert_contents>
146 </output>
141 <output name="anndata_out" file="pp.normalize_total.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 147 <output name="anndata_out" file="pp.normalize_total.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
142 </test> 148 </test>
143 <test> 149 <test>
144 <!-- test 2 --> 150 <!-- test 1 -->
145 <param name="adata" value="random-randint.h5ad"/> 151 <param name="adata" value="random-randint.h5ad"/>
146 <conditional name="method"> 152 <conditional name="method">
147 <param name="method" value="pp.recipe_zheng17"/> 153 <param name="method" value="pp.recipe_zheng17"/>
148 <param name="n_top_genes" value="1000"/> 154 <param name="n_top_genes" value="1000"/>
149 <param name="log" value="True"/> 155 <param name="log" value="True"/>
150 </conditional> 156 </conditional>
151 <assert_stdout> 157 <section name="advanced_common">
152 <has_text_matching expression="sc.pp.recipe_zheng17"/> 158 <param name="show_log" value="true" />
153 <has_text_matching expression="n_top_genes=1000"/> 159 </section>
154 <has_text_matching expression="log=True"/> 160 <output name="hidden_output">
155 </assert_stdout> 161 <assert_contents>
162 <has_text_matching expression="sc.pp.recipe_zheng17"/>
163 <has_text_matching expression="n_top_genes=1000"/>
164 <has_text_matching expression="log=True"/>
165 </assert_contents>
166 </output>
156 <output name="anndata_out" file="pp.recipe_zheng17.random-randint.h5ad" ftype="h5ad" compare="sim_size"/> 167 <output name="anndata_out" file="pp.recipe_zheng17.random-randint.h5ad" ftype="h5ad" compare="sim_size"/>
157 </test> 168 </test>
158 <test> 169 <test>
159 <!-- test 3 --> 170 <!-- test 2 -->
160 <param name="adata" value="paul15_subsample.h5ad" /> 171 <param name="adata" value="paul15_subsample.h5ad" />
161 <conditional name="method"> 172 <conditional name="method">
162 <param name="method" value="pp.recipe_weinreb17"/> 173 <param name="method" value="pp.recipe_weinreb17"/>
163 <param name="log" value="True"/> 174 <param name="log" value="True"/>
164 <param name="mean_threshold" value="0.01"/> 175 <param name="mean_threshold" value="0.01"/>
165 <param name="cv_threshold" value="2.0"/> 176 <param name="cv_threshold" value="2.0"/>
166 <param name="n_pcs" value="50"/> 177 <param name="n_pcs" value="50"/>
167 <param name="svd_solver" value="randomized"/> 178 <param name="svd_solver" value="randomized"/>
168 <param name="random_state" value="0"/> 179 <param name="random_state" value="0"/>
169 </conditional> 180 </conditional>
170 <assert_stdout> 181 <section name="advanced_common">
171 <has_text_matching expression="sc.pp.recipe_weinreb17"/> 182 <param name="show_log" value="true" />
172 <has_text_matching expression="log=True"/> 183 </section>
173 <has_text_matching expression="mean_threshold=0.01"/> 184 <output name="hidden_output">
174 <has_text_matching expression="cv_threshold=2.0"/> 185 <assert_contents>
175 <has_text_matching expression="n_pcs=50"/> 186 <has_text_matching expression="sc.pp.recipe_weinreb17"/>
176 <has_text_matching expression="svd_solver='randomized'"/> 187 <has_text_matching expression="log=True"/>
177 <has_text_matching expression="random_state=0"/> 188 <has_text_matching expression="mean_threshold=0.01"/>
178 </assert_stdout> 189 <has_text_matching expression="cv_threshold=2.0"/>
190 <has_text_matching expression="n_pcs=50"/>
191 <has_text_matching expression="svd_solver='randomized'"/>
192 <has_text_matching expression="random_state=0"/>
193 </assert_contents>
194 </output>
179 <output name="anndata_out" file="pp.recipe_weinreb17.paul15_subsample.updated.h5ad" ftype="h5ad" compare="sim_size"/> 195 <output name="anndata_out" file="pp.recipe_weinreb17.paul15_subsample.updated.h5ad" ftype="h5ad" compare="sim_size"/>
180 </test> 196 </test>
181 <test> 197 <test>
182 <!-- test 4 --> 198 <!-- test 3 -->
183 <param name="adata" value="pp.recipe_zheng17.random-randint.h5ad" /> 199 <param name="adata" value="pp.recipe_zheng17.random-randint.h5ad" />
184 <conditional name="method"> 200 <conditional name="method">
185 <param name="method" value="pp.recipe_seurat"/> 201 <param name="method" value="pp.recipe_seurat"/>
186 <param name="log" value="True"/> 202 <param name="log" value="True"/>
187 </conditional> 203 </conditional>
188 <assert_stdout> 204 <section name="advanced_common">
189 <has_text_matching expression="sc.pp.recipe_seurat"/> 205 <param name="show_log" value="true" />
190 <has_text_matching expression="log=True"/> 206 </section>
191 </assert_stdout> 207 <output name="hidden_output">
208 <assert_contents>
209 <has_text_matching expression="sc.pp.recipe_seurat"/>
210 <has_text_matching expression="log=True"/>
211 </assert_contents>
212 </output>
192 <output name="anndata_out" file="pp.recipe_seurat.recipe_zheng17.h5ad" ftype="h5ad" compare="sim_size"/> 213 <output name="anndata_out" file="pp.recipe_seurat.recipe_zheng17.h5ad" ftype="h5ad" compare="sim_size"/>
193 </test> 214 </test>
194
195 </tests> 215 </tests>
196 <help><![CDATA[ 216 <help><![CDATA[
197 Normalize total counts per cell (`pp.normalize_per_cell`) 217 Normalize total counts per cell (`pp.normalize_per_cell`)
198 ========================================================= 218 =========================================================
199 219