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planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:42:13 +0000
parents 970696a7ae0b
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0:970696a7ae0b 1:834f7d8e5b4c
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@VERSION@">0.3.0</token> 3 <token name="@VERSION@">4.0.0</token>
4 <token name="@SEURAT_VERSION@">3.2.3</token> 4 <token name="@SEURAT_VERSION@">4.0.4</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@VERSION@">seurat-scripts</requirement> 7 <requirement type="package" version="@VERSION@">seurat-scripts</requirement>
8 </requirements> 8 </requirements>
9 </xml> 9 </xml>
11 <version_command><![CDATA[ 11 <version_command><![CDATA[
12 echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 12 echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
13 ]]></version_command> 13 ]]></version_command>
14 </xml> 14 </xml>
15 15
16 <xml name="input_object_params"> 16 <xml name="input_object_params" token_multiple="False" token_varname="input" token_optional="False">
17 <conditional name="input" label="Input format"> 17 <conditional name="@VARNAME@" label="Input format">
18 <param type="select" name="format" label="Choose the format of the input" help="RData, Loom or AnnData"> 18 <param type="select" name="format" label="Choose the format of the @VARNAME@" help="Seurat RDS, Seurat H5, Single Cell Experiment RDS, Loom or AnnData">
19 <option value="rds_seurat" selected="true">RDS with a Seurat object</option> 19 <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
20 <option value="loom">Loom</option> 20 <option value="loom">Loom</option>
21 <option value="h5seurat">Seurat HDF5</option>
21 <option value="anndata">AnnData</option> 22 <option value="anndata">AnnData</option>
22 <option value="rds_sce">RDS with a Single Cell Experiment object</option> 23 <option value="rds_sce">RDS with a Single Cell Experiment object</option>
23 </param> 24 </param>
24 <when value="anndata"> 25 <when value="anndata">
25 <param type="data" name="anndata_file" label="AnnData file" help="The AnnData format provided by Scanpy" format="h5,h5ad"/> 26 <param type="data" name="anndata_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="AnnData file" help="Select AnnData files for @VARNAME@" format="h5,h5ad"/>
26 </when> 27 </when>
27 <when value="loom"> 28 <when value="loom">
28 <param type="data" name="loom_file" label="Loom file" help="Input as Loom v? file" format="h5,h5loom"/> 29 <param type="data" name="loom_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="Loom file" help="Select Loom file(s) for @VARNAME@" format="h5,h5loom"/>
29 </when> 30 </when>
30 <when value="rds_seurat"> 31 <when value="rds_seurat">
31 <param type="data" name="rds_seurat_file" label="RDS file" help="Input as RDS file with Seurat 3 object" format="rdata"/> 32 <param type="data" name="rds_seurat_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="RDS file" help="Select RDS file(s) with Seurat object for @VARNAME@" format="rdata"/>
32 </when> 33 </when>
33 <when value="rds_sce"> 34 <when value="rds_sce">
34 <param type="data" name="rds_sce_file" label="RDS file" help="Input as RDS file with Single Cell Experiment object" format="rdata"/> 35 <param type="data" name="rds_sce_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="RDS file" help="Select RDS file(s) with Single Cell Experiment object for @VARNAME@" format="rdata"/>
36 </when>
37 <when value="h5seurat">
38 <param type="data" name="h5seurat_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="Seurat HDF5" help="Select Seurat HDF5 file(s) for @VARNAME" format="h5"/>
35 </when> 39 </when>
36 </conditional> 40 </conditional>
37 </xml> 41 </xml>
38 42
43 <token name="@INPUT_OBJ_PREAMBLE@">
44 #if $input.format == 'loom'
45 ln -s '$input.loom_file' input.loom;
46 #else if $input.format == 'h5seurat'
47 ln -s '$input.h5seurat_file' input.h5seurat;
48 #else if $input.format == 'anndata'
49 ## it complains when using links for AnnData...
50 cp '$input.anndata_file' input.h5ad;
51 #end if
52 </token>
53
39 <token name="@INPUT_OBJECT@"> 54 <token name="@INPUT_OBJECT@">
40 #if $input.format == "anndata" 55 #if $input.format == "anndata"
41 --input-object-file '$input.anndata_file' --input-format anndata 56 --input-object-file input.h5ad --input-format anndata
42 #else if $input.format == "loom" 57 #else if $input.format == "loom"
43 --input-object-file '$input.loom_file' --input-format loom 58 --input-object-file input.loom --input-format loom
44 #else if $input.format == "rds_seurat" 59 #else if $input.format == "rds_seurat"
45 --input-object-file '$input.rds_seurat_file' --input-format seurat 60 --input-object-file '$input.rds_seurat_file' --input-format seurat
46 #else if $input.format == "rds_sce" 61 #else if $input.format == "rds_sce"
47 --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment 62 --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment
63 #else if $input.format == "h5seurat"
64 --input-object-file input.h5seurat --input-format h5seurat
65 #end if
66 </token>
67
68 <token name="@QUERY_OBJ_PREAMBLE@">
69 #if $query.format == 'loom'
70 ln -s '$query.loom_file' query.loom;
71 #else if $query.format == 'h5seurat'
72 ln -s '$query.h5seurat_file' query.h5seurat;
73 #else if $query.format == 'anndata'
74 ## it complains when using links for AnnData...
75 cp '$query.anndata_file' query.h5ad;
76 #end if
77 </token>
78
79 <token name="@QUERY_OBJECT@">
80 #if $query.format == "anndata"
81 --query-object-file query.h5ad --query-format anndata
82 #else if $query.format == "loom"
83 --query-object-file query.loom --query-format loom
84 #else if $query.format == "rds_seurat"
85 --query-object-file '$query.rds_seurat_file' --query-format seurat
86 #else if $query.format == "rds_sce"
87 --query-object-file '$query.rds_sce_file' --query-format singlecellexperiment
88 #else if $query.format == "h5seurat"
89 --query-object-file query.h5seurat --query-format h5seurat
90 #end if
91 </token>
92
93 <token name="@ANCHORS_OBJ_PREAMBLE@">
94 #if $anchors.format == 'loom'
95 ln -s '$anchors.loom_file' anchors.loom;
96 #else if $anchors.format == 'h5seurat'
97 ln -s '$anchors.h5seurat_file' anchors.h5seurat;
98 #else if $anchors.format == 'anndata'
99 ## it complains when using links for AnnData...
100 cp '$anchors.anndata_file' anchors.h5ad;
101 #end if
102 </token>
103
104 <token name="@ANCHORS_OBJECT@">
105 #if $anchors.format == "anndata"
106 --anchors-object-file anchors.h5ad --anchors-format anndata
107 #else if $anchors.format == "loom"
108 --anchors-object-file anchors.loom --anchors-format loom
109 #else if $anchors.format == "rds_seurat"
110 --anchors-object-file '$anchors.rds_seurat_file' --anchors-format seurat
111 #else if $anchors.format == "rds_sce"
112 --anchors-object-file '$anchors.rds_sce_file' --anchors-format singlecellexperiment
113 #else if $anchors.format == "h5seurat"
114 --anchors-object-file anchors.h5seurat --anchors-format h5seurat
115 #end if
116 </token>
117
118 <token name="@REFERENCE_OBJ_PREAMBLE@">
119 #if $reference.format == 'loom'
120 ln -s '$reference.loom_file' reference.loom;
121 #else if $reference.format == 'h5seurat'
122 ln -s '$reference.h5seurat_file' reference.h5seurat;
123 #else if $reference.format == 'anndata'
124 ## it complains when using links for AnnData...
125 cp '$reference.anndata_file' reference.h5ad;
126 #end if
127 </token>
128
129 <token name="@REFERENCE_OBJECT@">
130 #if $reference.format == "anndata"
131 --reference-object-file reference.h5ad --reference-format anndata
132 #else if $reference.format == "loom"
133 --reference-object-file reference.loom --reference-format loom
134 #else if $reference.format == "rds_seurat"
135 --reference-object-file '$reference.rds_seurat_file' --reference-format seurat
136 #else if $reference.format == "rds_sce"
137 --reference-object-file '$reference.rds_sce_file' --reference-format singlecellexperiment
138 #else if $reference.format == "h5seurat"
139 --reference-object-file reference.h5seurat --reference-format h5seurat
140 #end if
141 </token>
142
143 <token name="@INPUT_OBJS_PREAMBLE@">
144 #if $input.format == 'loom'
145 #for $i, $fh in enumerate($input.loom_file):
146 ln -s '$fh' input.${i}.loom;
147 #end for
148 #else if $input.format == 'h5seurat'
149 #for $i, $fh in enumerate($input.h5seurat_file):
150 ln -s '$fh' input.${i}.h5seurat;
151 #end for
152 #else if $input.format == 'anndata'
153 ## it complains when using links for AnnData...
154 #for $i, $fh in enumerate($input.anndata_file):
155 cp '$fh' input.${i}.h5ad;
156 #end for
157 #end if
158 </token>
159
160 <token name="@INPUT_OBJECTS@">
161 #if $input.format == "anndata"
162 --input-object-files
163 #set file_array = [ "input."+str($i)+".h5ad" for $i, $fh in enumerate($input.anndata_file)]
164 #set files = ",".join($file_array)
165 ${files}
166 --input-format anndata
167 #else if $input.format == "loom"
168 --input-object-files
169 #set file_array = [ "input."+str($i)+".loom" for $i, $fh in enumerate($input.loom_file)]
170 #set files = ",".join($file_array)
171 ${files}
172 --input-format loom
173 #else if $input.format == "rds_seurat"
174 --input-object-files
175 #set file_array = $input.rds_seurat_file
176 #set files = ",".join([ str($fh) for $fh in $file_array ])
177 ${files}
178 --input-format seurat
179 #else if $input.format == "rds_sce"
180 --input-object-files
181 #set file_array = $input.rds_sce_file
182 #set files = ",".join([ str($fh) for $fh in $file_array ])
183 ${files}
184 --input-format singlecellexperiment
185 #else if $input.format == "h5seurat"
186 --input-object-files
187 #set file_array = [ "input."+str($i)+".h5seurat" for $i, $fh in enumerate($input.h5seurat)]
188 #set files = ",".join($file_array)
189 ${files}
190 --input-format h5seurat
191 #end if
192 </token>
193
194 <token name="@REFERENCE_OBJS_PREAMBLE@">
195 #if $reference.format == 'loom'
196 #for $i, $fh in enumerate($reference.loom_file):
197 ln -s '$fh' reference.${i}.loom;
198 #end for
199 #else if $reference.format == 'h5seurat'
200 #for $i, $fh in enumerate($reference.h5seurat_file):
201 ln -s '$fh' reference.${i}.h5seurat;
202 #end for
203 #else if $reference.format == 'anndata'
204 ## it complains when using links for AnnData...
205 #for $i, $fh in enumerate($reference.anndata_file):
206 cp '$fh' reference.${i}.h5ad;
207 #end for
208 #end if
209 </token>
210
211 <token name="@REFERENCE_OBJECTS@">
212 #if $reference.format == "anndata" and $reference.anndata_file:
213 --reference-object-files
214 #set file_array = [ "reference."+str($i)+".h5ad" for $i, $fh in enumerate($reference.anndata_file)]
215 #set files = ",".join($file_array)
216 ${files}
217 --reference-format anndata
218 #else if $reference.format == "loom" and $reference.loom_file:
219 --reference-object-files
220 #set file_array = [ "reference."+str($i)+".loom" for $i, $fh in enumerate($reference.loom_file)]
221 #set files = ",".join($file_array)
222 ${files}
223 --reference-format loom
224 #else if $reference.format == "rds_seurat" and $reference.rds_seurat_file:
225 --reference-object-files
226 #set files = ",".join([ str($fh) for $fh in $reference.rds_seurat_file ])
227 ${files}
228 --reference-format seurat
229 #else if $reference.format == "rds_sce" and $reference.rds_sce_file:
230 --reference-object-files
231 #set files = ",".join([ str($fh) for $fh in $reference.rds_sce_file ])
232 ${files}
233 --reference-format singlecellexperiment
234 #else if $reference.format == "h5seurat" and $reference.h5seurat:
235 --reference-object-files
236 #set file_array = [ "reference."+str($i)+".h5seurat" for $i, $fh in enumerate($reference.h5seurat)]
237 #set files = ",".join($file_array)
238 ${files}
239 --reference-format h5seurat
48 #end if 240 #end if
49 </token> 241 </token>
50 242
51 <xml name="output_object_params"> 243 <xml name="output_object_params">
52 <param type="select" name="format" label="Choose the format of the output" help="Seurat, Single Cell Experiment or Loom"> 244 <param type="select" name="format" label="Choose the format of the output" help="Seurat, Single Cell Experiment, AnnData or Loom">
53 <option value="rds_seurat" selected="true">RDS with a Seurat object</option> 245 <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
246 <option value="anndata">AnnData written by Seurat</option>
54 <option value="loom">Loom</option> 247 <option value="loom">Loom</option>
55 <option value="rds_sce">RDS with a Single Cell Experiment object</option> 248 <option value="rds_sce">RDS with a Single Cell Experiment object</option>
56 </param> 249 </param>
57 </xml> 250 </xml>
58 251
60 <data name="loom_file" from_work_dir="seurat_obj.loom" format="h5" label="${tool.name} on ${on_string}: Seurat Loom"> 253 <data name="loom_file" from_work_dir="seurat_obj.loom" format="h5" label="${tool.name} on ${on_string}: Seurat Loom">
61 <filter>format == 'loom'</filter> 254 <filter>format == 'loom'</filter>
62 </data> 255 </data>
63 <data name="rds_seurat_file" format="rdata" label="${tool.name} on ${on_string}: Seurat RDS"> 256 <data name="rds_seurat_file" format="rdata" label="${tool.name} on ${on_string}: Seurat RDS">
64 <filter>format == 'rds_seurat'</filter> 257 <filter>format == 'rds_seurat'</filter>
258 </data>
259 <data name="anndata_file" format="h5ad" label="${tool.name} on ${on_string}: AnnData from Seurat">
260 <filter>format == 'anndata'</filter>
65 </data> 261 </data>
66 <data name="rds_sce_file" format="rdata" label="${tool.name} on ${on_string}: Seurat Single Cell Experiment RDS"> 262 <data name="rds_sce_file" format="rdata" label="${tool.name} on ${on_string}: Seurat Single Cell Experiment RDS">
67 <filter>format == 'rds_sce'</filter> 263 <filter>format == 'rds_sce'</filter>
68 </data> 264 </data>
69 </xml> 265 </xml>
78 #else if $format == "rds_sce" 274 #else if $format == "rds_sce"
79 --output-object-file '$rds_sce_file' --output-format singlecellexperiment 275 --output-object-file '$rds_sce_file' --output-format singlecellexperiment
80 #end if 276 #end if
81 </token> 277 </token>
82 278
279 <xml name="plot_output_files_format" token_format="png">
280 <data label="Seurat ${plot_type.plot_type_selector} on ${on_string}: @FORMAT@ plot" name="plot_out_@FORMAT@" format='@FORMAT@' >
281 <filter>plot_format == '@FORMAT@'</filter>
282 </data>
283 </xml>
284
285 <token name="@OUTPUT_PLOT@">
286 #if $plot_format == "png"
287 --plot-out '$plot_out_png'
288 #else if $plot_format == "pdf"
289 --plot-out '$plot_out_pdf'
290 #else if $plot_format == "eps"
291 --plot-out '$plot_out_eps'
292 #else if $plot_format == "ps"
293 --plot-out '$plot_out_ps'
294 #else if $plot_format == "jpg"
295 --plot-out '$plot_out_jpg'
296 #else if $plot_format == "tiff"
297 --plot-out '$plot_out_tiff'
298 #else if $plot_format == "svg"
299 --plot-out '$plot_out_svg'
300 #end if
301 </token>
302
83 <xml name="genes-use-input"> 303 <xml name="genes-use-input">
84 <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv,txt,tabular" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/> 304 <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv,txt,tabular" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/>
85 </xml> 305 </xml>
86 <xml name="dims-use-input"> 306 <xml name="dims-use-input">
87 <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/> 307 <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/>
94 types of single cell data. 314 types of single cell data.
95 ]]></token> 315 ]]></token>
96 316
97 <token name="@VERSION_HISTORY@"><![CDATA[ 317 <token name="@VERSION_HISTORY@"><![CDATA[
98 **Version history** 318 **Version history**
319 4.0.0: Moves to Seurat 4.0.0, introducing a number of methods for merging datasets, plus the whole suite of Seurat plots. Pablo Moreno with funding from AstraZeneca.
99 320
100 3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support. 321 3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support.
101 322
102 3.1.2_0.0.8: Update metadata parsing 323 3.1.2_0.0.8: Update metadata parsing
103 324
106 3.1.1_0.0.6+galaxy0: Moved to Seurat 3. 327 3.1.1_0.0.6+galaxy0: Moved to Seurat 3.
107 328
108 Find clusters: removed dims-use, k-param, prune-snn. 329 Find clusters: removed dims-use, k-param, prune-snn.
109 330
110 2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at 331 2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
111 EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(github.com/drosofff) and Lea Bellenger(github.com/bellenger-l). 332 EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski (GitHub drosofff) and Lea Bellenger (GitHub bellenger-l).
112 333
113 0.0.1: Initial contribution. Maria Doyle (github.com/mblue9). 334 0.0.1: Initial contribution. Maria Doyle (GitHub mblue9).
114 ]]></token> 335 ]]></token>
115 336
116 337
117 <xml name="citations"> 338 <xml name="citations">
118 <citations> 339 <citations>
340 <citation type="doi">10.1038/s41592-021-01102-w</citation>
119 <citation type="doi">10.1038/nbt.4096</citation> 341 <citation type="doi">10.1038/nbt.4096</citation>
120 <citation type="bibtex"> 342 <citation type="bibtex">
121 @misc{r-seurat-scripts.git, 343 @misc{r-seurat-scripts.git,
122 author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team}, 344 author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team},
123 year = {2018}, 345 year = {2018},
125 publisher = {GitHub}, 347 publisher = {GitHub},
126 journal = {GitHub repository}, 348 journal = {GitHub repository},
127 url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git}, 349 url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
128 } 350 }
129 </citation> 351 </citation>
130 <citation type="doi">10.1038/s41592-021-01102-w</citation>
131 </citations> 352 </citations>
132 </xml> 353 </xml>
133 </macros> 354 </macros>