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comparison integrate.xml @ 1:74fa68f4e579 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit 566984b588e88225f0b3f2dae88c6fd084315e7c
author iuc
date Tue, 05 Nov 2024 11:55:09 +0000
parents 4341b8ff2a46
children
comparison
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0:4341b8ff2a46 1:74fa68f4e579
1 <tool id="seurat_integrate" name="Seurat Integrate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="seurat_integrate" name="Seurat Integrate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> and manipulate layers </description> 2 <description> and manipulate layers </description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 @CMD@ 10 @CMD@
10 ]]></command> 11 ]]></command>
13 @CMD_imports@ 14 @CMD_imports@
14 @CMD_read_inputs@ 15 @CMD_read_inputs@
15 16
16 #if $method.method == 'SplitLayers' 17 #if $method.method == 'SplitLayers'
17 seurat_obj[['$method.assay']]<-split( 18 seurat_obj[['$method.assay']]<-split(
18 seurat_obj[['$method.assay']], 19 seurat_obj[['$method.assay']],
19 f = seurat_obj[['$method.factor', drop = TRUE]] 20 f = seurat_obj[['$method.factor', drop = TRUE]]
20 ) 21 )
21 22
22 #else if $method.method == 'IntegrateLayers' 23 #else if $method.method == 'IntegrateLayers'
23 24
24 #if $method.features 25 #if $method.features
25 features_list<-paste(readLines('$method.features'), collapse=",") 26 features_list<-paste(readLines('$method.features'), collapse=",")
26 #end if 27 #end if
27 28
28 seurat_obj<-IntegrateLayers( 29 seurat_obj<-IntegrateLayers(
29 seurat_obj, 30 seurat_obj,
30 method = $method.integration.integration_method, 31 method = $method.integration.integration_method,
31 #if $method.integration.integration_method == 'CCAIntegration' 32 #if $method.integration.integration_method == 'CCAIntegration'
32 #if $method.integration.adv.k_filter 33 #if $method.integration.adv.k_filter
33 k.filter = $method.integration.adv.k_filter, 34 k.filter = $method.integration.adv.k_filter,
34 #else 35 #else
35 k.filter = NA, 36 k.filter = NA,
36 #end if 37 #end if
37 dims = 1:$method.integration.adv.dims, 38 dims = 1:$method.integration.adv.dims,
38 #if $method.integration.adv.dims_to_integrate 39 #if $method.integration.adv.dims_to_integrate
39 dims.to.integrate = $method.integration.adv.dims_to_integrate, 40 dims.to.integrate = $method.integration.adv.dims_to_integrate,
71 sd.weight = $method.integration.adv.sd_weight, 72 sd.weight = $method.integration.adv.sd_weight,
72 preserve.order = $method.integration.adv.preserve_order, 73 preserve.order = $method.integration.adv.preserve_order,
73 #else if $method.integration.integration_method == 'RPCAIntegration' 74 #else if $method.integration.integration_method == 'RPCAIntegration'
74 #if $method.integration.adv.k_filter 75 #if $method.integration.adv.k_filter
75 k.filter = $method.integration.adv.k_filter, 76 k.filter = $method.integration.adv.k_filter,
76 #else 77 #else
77 k.filter = NA, 78 k.filter = NA,
78 #end if 79 #end if
79 dims = 1:$method.integration.adv.dims, 80 dims = 1:$method.integration.adv.dims,
80 #if $method.integration.adv.dims_to_integrate 81 #if $method.integration.adv.dims_to_integrate
81 dims.to.integrate = $method.integration.adv.dims_to_integrate, 82 dims.to.integrate = $method.integration.adv.dims_to_integrate,
85 weight.reduction = c(unlist(strsplit(gsub(" ", "", '$method.integration.adv.weight_reduction'), ","))), 86 weight.reduction = c(unlist(strsplit(gsub(" ", "", '$method.integration.adv.weight_reduction'), ","))),
86 #end if 87 #end if
87 sd.weight = $method.integration.adv.sd_weight, 88 sd.weight = $method.integration.adv.sd_weight,
88 preserve.order = $method.integration.adv.preserve_order, 89 preserve.order = $method.integration.adv.preserve_order,
89 #end if 90 #end if
90 orig.reduction = '$method.orig_reduction', 91 orig.reduction = '$method.orig_reduction',
91 new.reduction = '$method.new_reduction', 92 new.reduction = '$method.new_reduction',
92 #if $method.assay != '' 93 #if $method.assay != ''
93 assay = '$method.assay', 94 assay = '$method.assay',
94 #end if 95 #end if
95 #if $method.features 96 #if $method.features
217 <!-- test1: SplitLayers --> 218 <!-- test1: SplitLayers -->
218 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/added_metadata.rds"/> 219 <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/added_metadata.rds"/>
219 <conditional name="method"> 220 <conditional name="method">
220 <param name="method" value="SplitLayers"/> 221 <param name="method" value="SplitLayers"/>
221 <param name="assay" value="RNA"/> 222 <param name="assay" value="RNA"/>
222 <param name="factor" value="Group"/> 223 <param name="factor" value="Group"/>
223 </conditional> 224 </conditional>
224 <section name="advanced_common"> 225 <section name="advanced_common">
225 <param name="show_log" value="true"/> 226 <param name="show_log" value="true"/>
226 </section> 227 </section>
227 <output name="hidden_output"> 228 <output name="hidden_output">
259 <param name="method" value="IntegrateLayers"/> 260 <param name="method" value="IntegrateLayers"/>
260 <conditional name="integration"> 261 <conditional name="integration">
261 <param name="integration_method" value="HarmonyIntegration"/> 262 <param name="integration_method" value="HarmonyIntegration"/>
262 </conditional> 263 </conditional>
263 <param name="orig_reduction" value="pca"/> 264 <param name="orig_reduction" value="pca"/>
264 <param name="new_reduction" value="integrated.harm"/> 265 <param name="new_reduction" value="integrated.harm"/>
265 </conditional> 266 </conditional>
266 <section name="advanced_common"> 267 <section name="advanced_common">
267 <param name="show_log" value="true"/> 268 <param name="show_log" value="true"/>
268 </section> 269 </section>
269 <output name="hidden_output"> 270 <output name="hidden_output">
308 </tests> 309 </tests>
309 <help><![CDATA[ 310 <help><![CDATA[
310 Seurat 311 Seurat
311 ====== 312 ======
312 313
313 Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. 314 Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.
314 315
315 Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. 316 Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.
316 317
317 318
318 Split 319 Split
325 326
326 327
327 Integrate 328 Integrate
328 ========= 329 =========
329 330
330 Multiple layers are integrated to enable them to be analysed together. 331 Multiple layers are integrated to enable them to be analysed together.
331 332
332 Available methods are: CCA, Harmony, JointPCA, RPCA, FastMNN and scVI. 333 Available methods are: CCA, Harmony, JointPCA, RPCA, FastMNN and scVI.
333 334
334 More details on the `seurat documentation 335 More details on the `seurat documentation
335 <https://satijalab.github.io/seurat-object/reference/CreateSeuratObject.html>`__ 336 <https://satijalab.github.io/seurat-object/reference/CreateSeuratObject.html>`__
343 <https://satijalab.github.io/seurat-object/reference/SplitLayers.html>`__ 344 <https://satijalab.github.io/seurat-object/reference/SplitLayers.html>`__
344 345
345 PrepSCTFindMarkers 346 PrepSCTFindMarkers
346 ================== 347 ==================
347 348
348 Given a merged object with multiple SCT models, this function uses minimum of the median UMI (calculated using the raw UMI counts) of individual objects to reverse the individual SCT regression model using minimum of median UMI as the sequencing depth covariate. 349 Given a merged object with multiple SCT models, this function uses minimum of the median UMI (calculated using the raw UMI counts) of individual objects to reverse the individual SCT regression model using minimum of median UMI as the sequencing depth covariate.
349 The counts slot of the SCT assay is replaced with recorrected counts and the data slot is replaced with log1p of recorrected counts. 350 The counts slot of the SCT assay is replaced with recorrected counts and the data slot is replaced with log1p of recorrected counts.
350 351
351 More details on the `seurat documentation 352 More details on the `seurat documentation
352 <https://satijalab.org/seurat/reference/prepsctfindmarkers>`__ 353 <https://satijalab.org/seurat/reference/prepsctfindmarkers>`__
353 354