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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
author iuc
date Fri, 07 Jul 2023 01:43:02 +0000
parents c0fd285eb553
children
comparison
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14:c0fd285eb553 15:fab6ff46e019
1 <tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="seurat" name="Seurat" version="@TOOL_VERSION@+galaxy1">
2 <description>- toolkit for exploration of single-cell RNA-seq data</description> 2 <description>- toolkit for exploration of single-cell RNA-seq data</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">4.3.0</token> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <expand macro="requirements"/>
7 <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement>
8 <requirement type="package" version="2.18">r-rmarkdown</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
11 #if "vln" in $meta.plots: 8 #if $function.function_select == "base":
12 #set $vln = 'T' 9 Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\",
13 #else 10 params = list(counts = \"${function.input}\",
14 #set $vln = 'F' 11 min_cells = \"${function.min_cells}\",
15 #end if 12 min_genes = \"${function.min_genes}\",
16 #if "feat" in $meta.plots: 13 low_thresholds = \"${function.low_thresholds}\",
17 #set $feat = 'T' 14 high_thresholds = \"${function.high_thresholds}\",
18 #else 15 vlnfeat = \"${function.vlnfeat}\",
19 #set $feat = 'F' 16 norm_out = \"${function.norm_file}\",
20 #end if 17 #if $function.variable_continue.variable_continue == "yes":
21 #if "PCs" in $meta.plots: 18 featplot = \"${function.variable_continue.featplot}\",
22 #set $PCs = 'T' 19 variable_out = \"${function.variable_continue.var_file}\",
23 #else 20 #if $function.variable_continue.pca_continue.pca_continue == "yes":
24 #set $PCs = 'F' 21 numPCs = \"${function.variable_continue.pca_continue.num_PCs}\",
25 #end if 22 PCplots = \"${function.variable_continue.pca_continue.pc_plots}\",
26 #if "tsne" in $meta.plots: 23 pca_out = \"${function.variable_continue.pca_continue.pca_file}\",
27 #set $tsne = 'T' 24 #if $function.variable_continue.pca_continue.clusters_continue.clusters_continue == "yes":
28 #else 25 perplexity = \"${function.variable_continue.pca_continue.clusters_continue.perplexity}\",
29 #set $tsne = 'F' 26 resolution = \"${function.variable_continue.pca_continue.clusters_continue.resolution}\",
30 #end if 27 nmds = \"${function.variable_continue.pca_continue.clusters_continue.nmds}\",
31 #if "heat" in $meta.plots: 28 clusters_out = \"${function.variable_continue.pca_continue.clusters_continue.clusters_file}\",
32 #set $heatmaps = 'T' 29 #if $function.variable_continue.pca_continue.clusters_continue.markers_continue.markers_continue == "yes":
33 #else 30 min_pct = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.min_pct}\",
34 #set $heatmaps = 'F' 31 logfc_threshold = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.logfc_threshold}\",
35 #end if 32 heatmaps = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.heatmaps}\",
36 #if not str($adv.perplexity): 33 markers_out = \"${function.variable_continue.pca_continue.clusters_continue.markers_continue.markers_file}\",
37 #set $adv_perplexity = -1 34 end_step="\"5"\",
38 #else: 35 #else:
39 #set $adv_perplexity = $adv.perplexity 36 end_step="\"4"\",
40 #end if 37 #end if
41 Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/Seurat.R\", 38 #else:
42 params = list(counts = \"${counts}\", 39 end_step="\"3"\",
43 min_cells = \"${adv.min_cells}\", 40 #end if
44 min_genes = \"${adv.min_genes}\", 41 #else:
45 low_thresholds = \"${adv.low_thresholds}\", 42 end_step="\"2"\",
46 high_thresholds = \"${adv.high_thresholds}\", 43 #end if
47 numPCs = \"${adv.num_PCs}\", 44 #else:
48 cells_use = \"${adv.cells_use}\", 45 end_step="\"1"\",
49 resolution = \"${adv.resolution}\", 46 #end if
50 perplexity = \"${adv_perplexity}\", 47 varstate = \"${meta.varstate}\",
51 min_pct = \"${adv.min_pct}\",
52 logfc_threshold = \"${adv.logfc_threshold}\",
53 warn = \"${meta.warn}\", 48 warn = \"${meta.warn}\",
49 showcode = \"${meta.showcode}\"),
50 intermediates_dir = \".\",
51 output_format = html_document(),
52 output_dir = \".\",
53 output_file = \"out.html\")"
54 #else:
55 Rscript -e "library(\"rmarkdown\"); render(\"$__tool_directory__/citeseq_Seurat.R\",
56 params = list(rna = \"${function.rna}\",
57 prot = \"${function.prot}\",
58 cite_markers = \"${function.cite_markers}\",
59
60
61 #if $function.comparison.comparison == "yes"
62 comparison="\"T"\",
63 feat_comp=\"${function.comparison.feat_comp}\",
64 #else:
65 comparison="\"F"\",
66 feat_comp="\""\",
67 #end if
68 #if $function.marker_compare.marker_compare == "yes"
69 marker_compare="\"T"\",
70 top_x=\"${function.marker_compare.top_x}\",
71 #else:
72 marker_compare="\"F"\",
73 top_x="\""\",
74 #end if
75 min_cells = \"${function.min_cells}\",
76 min_genes = \"${function.min_genes}\",
77 low_thresholds = \"${function.low_thresholds}\",
78 high_thresholds = \"${function.high_thresholds}\",
79 vlnfeat = \"${function.vlnfeat}\",
80 norm_out = \"${function.norm_file}\",
81 featplot = \"${function.featplot}\",
82 variable_out = \"${function.var_file}\",
83 numPCs = \"${function.num_PCs}\",
84 PCplots = \"${function.pc_plots}\",
85 pca_out = \"${function.pca_file}\",
86 perplexity = \"${function.perplexity}\",
87 resolution = \"${function.resolution}\",
88 nmds = \"${function.nmds}\",
89 clusters_out = \"${function.clusters_file}\",
90 min_pct = \"${function.min_pct}\",
91 logfc_threshold = \"${function.logfc_threshold}\",
92 heatmaps = \"${function.heatmaps}\",
93 markers_out = \"${function.markers_file}\",
54 varstate = \"${meta.varstate}\", 94 varstate = \"${meta.varstate}\",
55 showcode = \"${meta.showcode}\", 95 warn = \"${meta.warn}\",
56 vlnfeat = \"$vln\", 96 showcode = \"${meta.showcode}\"),
57 featplot = \"$feat\", 97 intermediates_dir = \".\",
58 PCplots = \"$PCs\", 98 output_format = html_document(),
59 tsne = \"$tsne\", 99 output_dir = \".\",
60 heatmaps = \"$heatmaps\"), 100 output_file = \"out.html\")"
61 intermediates_dir = \".\", 101 #end if
62 output_format = html_document(),
63 output_dir = \".\",
64 output_file = \"out.html\")"
65 ]]></command> 102 ]]></command>
66 <inputs> 103 <inputs>
67 <param name="counts" type="data" format="tabular,tsv" label="Counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/> 104 <conditional name="function">
68 <section name="adv" title="Advanced Options" expanded="true"> 105 <param name="function_select" type="select" label="Which Seurat method should be run?">
69 <param name="num_PCs" type="integer" min="0" value="10" label="Number of PCs to use in plots" help="Uses this number of PCs in PCHEatmap, JackStrawPlot, FindClusters, RunTSNE" /> 106 <option value="base">Base</option>
70 <param name="min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells" /> 107 <option value="cite">Cite-seq</option>
71 <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected" /> 108 </param>
72 <param name="low_thresholds" type="integer" value="1" label="Low threshold for filtering cells" /> 109 <when value="base">
73 <param name="high_thresholds" type="integer" value="20000000" label="High threshold for filtering cells" /> 110 <param name="input" type="data" format="tabular,tsv" label="Counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/>
74 <param name="cells_use" type="integer" min="1" value="500" label="Cells to use for PCHeatmap" help="Plots this number of top ‘extreme’ cells on both ends of the spectrum, which dramatically speeds plotting for large datasets" /> 111 <param name="min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells" />
75 <param name="resolution" type="float" value="0.6" label="Resolution parameter" help="Value of the resolution parameter used in FindClusters, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities" /> 112 <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected"/>
76 <param name="perplexity" type="integer" value="" optional="true" label="Perplexity parameter" help="Parameter for the tSNE dimensionality reduction" /> 113 <expand macro="norm"/>
77 <param name="min_pct" type="float" value="0.1" label="Minimum percent cells" help="With FindMarkers, only test genes that are detected in at least this percentage of cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed" /> 114 <conditional name="variable_continue">
78 <param name="logfc_threshold" type="float" min="0" value="0.25" label="Log fold change threshold" 115 <param name="variable_continue" type="select" label="Continue workflow after Normalization step?">
79 help="With FindMarkers, limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Increasing this parameter speeds up the function, but can miss weaker signals" /> 116 <option value="yes">Yes</option>
80 </section> 117 <option value="no" selected="true">No</option>
118 </param>
119 <when value="yes">
120 <expand macro="variable"/>
121 <conditional name="pca_continue">
122 <param name="pca_continue" type="select" label="Continue workflow after scaling step?">
123 <option value="yes">Yes</option>
124 <option value="no" selected="true">No</option>
125 </param>
126 <when value="yes">
127 <expand macro="pca"/>
128 <conditional name="clusters_continue">
129 <param name="clusters_continue" type="select" label="Continue workflow after PCA step?">
130 <option value="yes">Yes</option>
131 <option value="no" selected="true">No</option>
132 </param>
133 <when value="yes">
134 <expand macro="clusters"/>
135 <conditional name="markers_continue">
136 <param name="markers_continue" type="select" label="Continue workflow after TSNE and UMAP step?">
137 <option value="yes">Yes</option>
138 <option value="no" selected="true">No</option>
139 </param>
140 <when value="yes">
141 <expand macro="markers"/>
142 </when>
143 <when value="no"/>
144 </conditional>
145 </when>
146 <when value="no"/>
147 </conditional>
148 </when>
149 <when value="no"/>
150 </conditional>
151 </when>
152 <when value="no"/>
153 </conditional>
154 </when>
155 <when value="cite">
156 <param name="rna" type="data" format="tabular,tsv" label="RNA counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/>
157 <param name="prot" type="data" format="tabular,tsv" label="Protein counts file" help="The should be a TAB-separated count matrix with gene identifers in the first column and a header row"/>
158 <param name="min_cells" type="integer" min="0" value="0" label="Minimum cells" help="Include genes with detected expression in at least this many cells" />
159 <param name="min_genes" type="integer" min="0" value="0" label="Minimum genes" help="Include cells where at least this many genes are detected"/>
160 <expand macro="norm"/>
161 <expand macro="variable"/>
162 <expand macro="pca"/>
163 <expand macro="clusters"/>
164 <expand macro="markers"/>
165 <expand macro="cite-seq"/>
166 </when>
167 </conditional>
81 <section name="meta" title="Output options" expanded="true"> 168 <section name="meta" title="Output options" expanded="true">
82 <param name="showcode" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Show code alongside outputs?"/> 169 <param name="showcode" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Show code alongside outputs?"/>
83 <param name="warn" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Include warnings in the output file (Yes) or pipe to stdout (No)"/> 170 <param name="warn" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Include warnings in the output file (Yes) or pipe to stdout (No)"/>
84 <param name="varstate" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Display variable values used in code at the beginning of output file?"/> 171 <param name="varstate" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Display variable values used in code at the beginning of output file?"/>
85 <param name="plots" type="select" optional="true" multiple="true" display="checkboxes" label="Which plots should be output?">
86 <option value="vln" selected="true">Violin and Scatter plots</option>
87 <option value="feat" selected="true">Feature counts plots</option>
88 <option value="PCs" selected="true">PC plots</option>
89 <option value="tsne" selected="true">tSNE plots</option>
90 <option value="heat" selected="true">Heatmap plots</option>
91 </param>
92 </section> 172 </section>
93 </inputs> 173 </inputs>
94 <outputs> 174 <outputs>
95 <data name="out_html" format="html" from_work_dir="out.html" label="${tool.name} on ${on_string}" /> 175 <data name="out_html" format="html" from_work_dir="out.html" label="${tool.name} on ${on_string}" />
176 <data name="norm_out" format="rdata" from_work_dir="norm_out.rds" label="${tool.name} on ${on_string}: normalization intermediate output">
177 <filter>@FUNCTION_BASE@</filter>
178 <filter>function['norm_file']</filter>
179 </data>
180 <data name="var_out" format="rdata" from_work_dir="var_out.rds" label="${tool.name} on ${on_string}: normalization and scaling intermediate output">
181 <filter>@FUNCTION_BASE@</filter>
182 <filter>@VARIABLE_CONTINUE@</filter>
183 <filter>function['variable_continue']['var_file']</filter>
184 </data>
185 <data name="pca_out" format="rdata" from_work_dir="pca_out.rds" label="${tool.name} on ${on_string}: PCA embedding data">
186 <filter>@FUNCTION_BASE@</filter>
187 <filter>@VARIABLE_CONTINUE@</filter>
188 <filter>@PCA_CONTINUE@</filter>
189 <filter>function['variable_continue']['pca_continue']['pca_file']</filter>
190 </data>
191 <data name="cluters_out" format="rdata" from_work_dir="tsne_out.rds" label="${tool.name} on ${on_string}: TSNE embedding data">
192 <filter>@FUNCTION_BASE@</filter>
193 <filter>@VARIABLE_CONTINUE@</filter>
194 <filter>@PCA_CONTINUE@</filter>
195 <filter>@CLUSTERS_CONTINUE@</filter>
196 <filter>function['variable_continue']['pca_continue']['clusters_continue']['clusters_file']</filter>
197 </data>
198 <data name="umap_out" format="rdata" from_work_dir="umap_out.rds" label="${tool.name} on ${on_string}: UMAP embedding data">
199 <filter>@FUNCTION_BASE@</filter>
200 <filter>@VARIABLE_CONTINUE@</filter>
201 <filter>@PCA_CONTINUE@</filter>
202 <filter>@CLUSTERS_CONTINUE@</filter>
203 <filter>function['variable_continue']['pca_continue']['clusters_continue']['clusters_file']</filter>
204 </data>
205 <data name="markers_out" format="rdata" from_work_dir="markers_out.rds" label="${tool.name} on ${on_string}: Markers data">
206 <filter>@FUNCTION_BASE@</filter>
207 <filter>@VARIABLE_CONTINUE@</filter>
208 <filter>@PCA_CONTINUE@</filter>
209 <filter>@CLUSTERS_CONTINUE@</filter>
210 <filter>@MARKERS_CONTINUE@</filter>
211 <filter>function['variable_continue']['pca_continue']['clusters_continue']['markers_continue']['markers_file']</filter>
212 </data>
213 <data name="markers_tabular" format="tabular" from_work_dir="markers_out.tsv" label="${tool.name} on ${on_string}: Markers list">
214 <filter>@FUNCTION_BASE@</filter>
215 <filter>@VARIABLE_CONTINUE@</filter>
216 <filter>@PCA_CONTINUE@</filter>
217 <filter>@CLUSTERS_CONTINUE@</filter>
218 <filter>@MARKERS_CONTINUE@</filter>
219 <filter>function['variable_continue']['pca_continue']['clusters_continue']['markers_continue']['markers_file']</filter>
220 <actions>
221 <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" />
222 <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" />
223 </actions>
224 </data>
225 <!-- cite-seq out -->
226 <data name="protmarkerst" format="tabular" from_work_dir="protein_out.tsv" label="${tool.name} cite-seq on ${on_string}: Protein markers">
227 <filter>@FUNCTION_CITE@</filter>
228 <filter>function['cite_markers']</filter>
229 <actions>
230 <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" />
231 <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" />
232 </actions>
233 </data>
234 <data name="rnamarkerst" format="tabular" from_work_dir="rna_out.tsv" label="${tool.name} cite-seq on ${on_string}: RNA markers">
235 <filter>@FUNCTION_CITE@</filter>
236 <filter>function['cite_markers']</filter>
237 <actions>
238 <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" />
239 <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" />
240 </actions>
241 </data>
242 <data name="cite_graps" format="pdf" from_work_dir="citeseq_out.pdf" label="${tool.name} cite-seq on ${on_string}: Citeseq graphs">
243 <filter>@FUNCTION_CITE@</filter>
244 <filter>function['marker_compare']['marker_compare'] == "yes"</filter>
245 </data>
246 <data name="norm_cite" format="rdata" from_work_dir="norm_out.rds" label="${tool.name} cite-seq on ${on_string}: normalization intermediate output">
247 <filter>@FUNCTION_CITE@</filter>
248 <filter>function['norm_file']</filter>
249 </data>
250 <data name="var_cite" format="rdata" from_work_dir="var_out.rds" label="${tool.name} cite-seq on ${on_string}: normalization and scaling intermediate output">
251 <filter>@FUNCTION_CITE@</filter>
252 <filter>function['var_file']</filter>
253 </data>
254 <data name="pca_cite" format="rdata" from_work_dir="pca_out.rds" label="${tool.name} cite-seq on ${on_string}: PCA embedding data">
255 <filter>@FUNCTION_CITE@</filter>
256 <filter>function['pca_file']</filter>
257 </data>
258 <data name="cluters_cite" format="rdata" from_work_dir="tsne_out.rds" label="${tool.name} cite-seq on ${on_string}: TSNE embedding data">
259 <filter>@FUNCTION_CITE@</filter>
260 <filter>function['clusters_file']</filter>
261 </data>
262 <data name="umap_cite" format="rdata" from_work_dir="umap_out.rds" label="${tool.name} cite-seq on ${on_string}: UMAP embedding data">
263 <filter>@FUNCTION_CITE@</filter>
264
265 <filter>function['clusters_file']</filter>
266 </data>
267 <data name="markers_cite" format="rdata" from_work_dir="markers_out.rds" label="${tool.name} cite-seq on ${on_string}: Markers data">
268 <filter>@FUNCTION_CITE@</filter>
269 <filter>function['markers_file']</filter>
270 </data>
271 <data name="markers_cite_tabular" format="tabular" from_work_dir="markers_out.tsv" label="${tool.name} cite-seq on ${on_string}: Markers list">
272 <filter>@FUNCTION_CITE@</filter>
273 <filter>function['markers_file']</filter>
274 <actions>
275 <action name="column_names" type="metadata" default="\\,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,gene" />
276 <action name="column_types" type="metadata" default="str,float,float,float,float,float,int,str" />
277 </actions>
278 </data>
96 </outputs> 279 </outputs>
97
98 <tests> 280 <tests>
99 <test> 281 <test expect_num_outputs="8">
100 <param name="counts" ftype="tabular" value="counts.tab.gz"/> 282 <conditional name="function">
101 <section name="adv"> 283 <param name="function_select" value="base"/>
102 <param name="numPCs" value="10" /> 284 <param name="input" ftype="tabular" value="counts.tab.gz"/>
103 <param name="min_cells" value="3"/> 285 <param name="min_cells" value="3"/>
104 <param name="min_genes" value="200"/> 286 <param name="min_genes" value="200"/>
105 <param name="low_thresholds" value="1" /> 287 <param name="low_thresholds" value="1" />
106 <param name="high_thresholds" value="20000000" /> 288 <param name="high_thresholds" value="20000000" />
107 <param name="cells_use" value="500"/> 289 <param name="vlnfeat" value="T"/>
108 <param name="resolution" value="0.6" /> 290 <param name="norm_file" value="T"/>
109 <param name="min_pct" value="0.25" /> 291 <conditional name="variable_continue">
110 <param name="logfc_threshold" value="0.25" /> 292 <param name="variable_continue" value="yes"/>
111 </section> 293 <param name="featplot" value="T"/>
294 <param name="var_file" value="T"/>
295 <conditional name="pca_continue">
296 <param name="pca_continue" value="yes"/>
297 <param name="numPCs" value="10" />
298 <param name="pc_plots" value="T"/>
299 <param name="pca_file" value="T"/>
300 <conditional name="clusters_continue">
301 <param name="clusters_continue" value="yes"/>
302 <param name="resolution" value="0.6" />
303 <param name="nmds" value="T"/>
304 <param name="clusters_file" value="T"/>
305 <conditional name="markers_continue">
306 <param name="markers_continue" value="yes"/>
307 <param name="min_pct" value="0.25" />
308 <param name="logfc_threshold" value="0.25" />
309 <param name="heatmaps" value="T"/>
310 <param name="markers_file" value="T"/>
311 </conditional>
312 </conditional>
313 </conditional>
314 </conditional>
315 </conditional>
112 <section name="meta"> 316 <section name="meta">
113 <param name="showcode" value="T"/> 317 <param name="showcode" value="T"/>
114 <param name="warn" value="F"/> 318 <param name="warn" value="F"/>
115 <param name="varstate" value="F"/> 319 <param name="varstate" value="F"/>
116 <param name="plots" value="feat"/>
117 </section> 320 </section>
118 <output name="out_html" ftype="html"> 321 <output name="out_html" ftype="html">
119 <assert_contents> 322 <assert_contents>
120 <has_text text="Seurat Analysis" /> 323 <has_text text="Seurat Analysis" />
121 <has_text text="Performed using Galaxy" /> 324 <has_text text="Performed using Galaxy" />
122 <has_text text="img src=&quot;data:image/png;base64" /> 325 <has_text text="img src=&quot;data:image/png;base64" />
123 </assert_contents> 326 </assert_contents>
124 </output> 327 </output>
328 <output name="markers_tabular" file="markers.tsv" compare="sim_size" delta="500"/>
125 </test> 329 </test>
126 <test> <!-- perplexity test --> 330 <test expect_num_outputs="1">
127 <param name="counts" ftype="tabular" value="counts.tab.gz"/> 331 <!-- test perplexity and output filters -->
128 <section name="adv"> 332 <conditional name="function">
129 <param name="numPCs" value="10" /> 333 <param name="function_select" value="base"/>
334 <param name="input" ftype="tabular" value="counts.tab.gz"/>
130 <param name="min_cells" value="3"/> 335 <param name="min_cells" value="3"/>
131 <param name="min_genes" value="200"/> 336 <param name="min_genes" value="200"/>
132 <param name="low_thresholds" value="1" /> 337 <param name="low_thresholds" value="1" />
133 <param name="high_thresholds" value="20000000" /> 338 <param name="high_thresholds" value="20000000" />
134 <param name="cells_use" value="500"/> 339 <param name="vlnfeat" value="T"/>
135 <param name="resolution" value="0.6" /> 340 <param name="norm_file" value="F"/>
136 <param name="perplexity" value="16" /> 341 <conditional name="variable_continue">
137 <param name="min_pct" value="0.25" /> 342 <param name="variable_continue" value="yes"/>
138 <param name="logfc_threshold" value="0.25" /> 343 <param name="featplot" value="T"/>
139 </section> 344 <param name="var_file" value="F"/>
345 <conditional name="pca_continue">
346 <param name="pca_continue" value="yes"/>
347 <param name="numPCs" value="10" />
348 <param name="pc_plots" value="T"/>
349 <param name="pca_file" value="F"/>
350 <conditional name="clusters_continue">
351 <param name="clusters_continue" value="yes"/>
352 <param name="perplexity" value="16"/>
353 <param name="resolution" value="0.6" />
354 <param name="nmds" value="T"/>
355 <param name="clusters_file" value="F"/>
356 <conditional name="markers_continue">
357 <param name="markers_continue" value="yes"/>
358 <param name="min_pct" value="0.25" />
359 <param name="logfc_threshold" value="0.25" />
360 <param name="heatmaps" value="T"/>
361 <param name="markers_file" value="F"/>
362 </conditional>
363 </conditional>
364 </conditional>
365 </conditional>
366 </conditional>
140 <section name="meta"> 367 <section name="meta">
141 <param name="showcode" value="T"/> 368 <param name="showcode" value="T"/>
142 <param name="warn" value="F"/> 369 <param name="warn" value="F"/>
143 <param name="varstate" value="F"/> 370 <param name="varstate" value="F"/>
144 <param name="plots" value="feat"/>
145 </section> 371 </section>
146 <output name="out_html" ftype="html"> 372 <output name="out_html" ftype="html">
147 <assert_contents> 373 <assert_contents>
148 <has_text text="Seurat Analysis" /> 374 <has_text text="Seurat Analysis" />
149 <has_text text="Performed using Galaxy" /> 375 <has_text text="Performed using Galaxy" />
150 <has_text text="img src=&quot;data:image/png;base64" /> 376 <has_text text="img src=&quot;data:image/png;base64" />
151 </assert_contents> 377 </assert_contents>
152 </output> 378 </output>
379 </test>
380 <test expect_num_outputs="4">
381 <conditional name="function">
382 <param name="function_select" value="cite"/>
383 <param name="rna" ftype="tabular" value="rna.tab.gz"/>
384 <param name="prot" ftype="tabular" value="adt.tab.gz"/>
385 <param name="min_cells" value="0"/>
386 <param name="min_genes" value="0"/>
387 <param name="low_thresholds" value="1" />
388 <param name="high_thresholds" value="20000000" />
389 <param name="vlnfeat" value="F"/>
390 <param name="norm_file" value="F"/>
391 <param name="featplot" value="T"/>
392 <param name="var_file" value="F"/>
393 <param name="num_PCs" value="20" />
394 <param name="pc_plots" value="T"/>
395 <param name="pca_file" value="F"/>
396 <param name="resolution" value="0.6" />
397 <param name="nmds" value="F"/>
398 <param name="clusters_file" value="F"/>
399 <param name="min_pct" value="0.25" />
400 <param name="logfc_threshold" value="0.25" />
401 <param name="heatmaps" value="T"/>
402 <param name="markers_file" value="F"/>
403 <param name="cite_markers" value="T"/>
404 <conditional name="comparison">
405 <param name="comparison" value="yes"/>
406 <param name="feat_comp" value="CD4,CD19"/>
407 </conditional>
408 <conditional name="marker_compare">
409 <param name="marker_compare" value="yes"/>
410 <param name="top_x" value="3"/>
411 </conditional>
412 </conditional>
413 <section name="meta">
414 <param name="showcode" value="T"/>
415 <param name="warn" value="F"/>
416 <param name="varstate" value="F"/>
417 </section>
418 <output name="rnamarkerst" ftype="tabular" file="rna_out.tsv" compare="sim_size" delta="500" />
419 <output name="protmarkerst" ftype="tabular" file="protein_out.tsv" compare="sim_size" delta="500" />
420 </test>
421 <test expect_num_outputs="9">
422 <conditional name="function">
423 <param name="function_select" value="cite"/>
424 <param name="rna" ftype="tabular" value="rna.tab.gz"/>
425 <param name="prot" ftype="tabular" value="adt.tab.gz"/>
426 <param name="min_cells" value="0"/>
427 <param name="min_genes" value="0"/>
428 <param name="low_thresholds" value="1" />
429 <param name="high_thresholds" value="20000000" />
430 <param name="vlnfeat" value="F"/>
431 <param name="norm_file" value="T"/>
432 <param name="featplot" value="T"/>
433 <param name="var_file" value="T"/>
434 <param name="num_PCs" value="20" />
435 <param name="pc_plots" value="T"/>
436 <param name="pca_file" value="T"/>
437 <param name="resolution" value="0.6" />
438 <param name="nmds" value="T"/>
439 <param name="clusters_file" value="T"/>
440 <param name="min_pct" value="0.25" />
441 <param name="logfc_threshold" value="0.25" />
442 <param name="heatmaps" value="T"/>
443 <param name="markers_file" value="T"/>
444 <param name="cite_markers" value="F"/>
445 <conditional name="comparison">
446 <param name="comparison" value="yes"/>
447 <param name="feat_comp" value="CD4,CD19"/>
448 </conditional>
449 <conditional name="marker_compare">
450 <param name="marker_compare" value="yes"/>
451 <param name="top_x" value="3"/>
452 </conditional>
453 </conditional>
454 <section name="meta">
455 <param name="showcode" value="T"/>
456 <param name="warn" value="F"/>
457 <param name="varstate" value="F"/>
458 </section>
153 </test> 459 </test>
154 </tests> 460 </tests>
155 <help><![CDATA[ 461 <help><![CDATA[
156 .. class:: infomark 462 .. class:: infomark
157 463
165 ----- 471 -----
166 472
167 **Inputs** 473 **Inputs**
168 474
169 * Gene count matrix in TAB-separated format 475 * Gene count matrix in TAB-separated format
476 or
477 * RNA and Protein count matrices in TAB-separated formats
170 478
171 ----- 479 -----
172 480
173 **Outputs** 481 **Outputs**
174 482