Mercurial > repos > iuc > raceid_inspectclusters

comparison raceid_inspectclusters.xml @ 8:2b0d3e2f402a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 455bad7eca54164f95755174904842907846bb42"
author iuc
date Mon, 20 Dec 2021 10:13:54 +0000
parents be4646256624
children c7ddb719554d
comparison
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7:be4646256624 8:2b0d3e2f402a
1 <tool id="raceid_inspectclusters" name="Cluster Inspection using RaceID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > 1 <tool id="raceid_inspectclusters" name="Cluster Inspection using RaceID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>examines gene expression within clusters</description> 2 <description>examines gene expression within clusters</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 <macro name="select_cells" token_sectionname="@SECTIONNAME@" token_sectiontitle="@SECTIONTITLE@" > 6 <macro name="select_cells" token_sectionname="@SECTIONNAME@" token_sectiontitle="@SECTIONTITLE@" >
35 </macro> 35 </macro>
36 </macros> 36 </macros>
37 <expand macro="requirements" /> 37 <expand macro="requirements" />
38 <expand macro="version_command_config" prog="clusterinspect.R" cheetah="INSPECTCLUSTERS_CHEETAH" out="&#38;&#62; '$outlog'" /> 38 <expand macro="version_command_config" prog="clusterinspect.R" cheetah="INSPECTCLUSTERS_CHEETAH" out="&#38;&#62; '$outlog'" />
39 <inputs> 39 <inputs>
40 <param name="inputrds" type="data" format="rdata" label="Input RaceID RDS" help="Requires the RDS output from the cluster analysis" /> 40 <param name="inputrds" type="data" format="rds" label="Input RaceID RDS" help="Requires the RDS output from the cluster analysis" />
41 <conditional name="plotgen"> 41 <conditional name="plotgen">
42 <param name="do_opt" type="select" label="Plot Clusters?" help="Generates tSNE and F-R plots" > 42 <param name="do_opt" type="select" label="Plot Clusters?" help="Generates tSNE and F-R plots" >
43 <option value="yes" selected="true" >Yes</option> 43 <option value="yes" selected="true" >Yes</option>
44 <option value="no" >No</option> 44 <option value="no" >No</option>
45 </param> 45 </param>
291 RaceID3 291 RaceID3
292 ========= 292 =========
293 293
294 RaceID is a clustering algorithm for the identification of cell types from single-cell RNA-sequencing data. It was specifically designed for the detection of rare cells which correspond to outliers in conventional clustering methods. 294 RaceID is a clustering algorithm for the identification of cell types from single-cell RNA-sequencing data. It was specifically designed for the detection of rare cells which correspond to outliers in conventional clustering methods.
295 295
296 This module inspects the clusters generated from the previous clustering step (and requires the output RData file from it as input). 296 This module inspects the clusters generated from the previous clustering step (and requires the output RDS file from it as input).
297 297
298 The tool offers three modes of inspection which can all be activated at the same time, resulting in a single PDF report: 298 The tool offers three modes of inspection which can all be activated at the same time, resulting in a single PDF report:
299 299
300 * Plot All Clusters: 300 * Plot All Clusters:
301 * Produces a tSNE of all clusters, as well as a force-directed Fruchterman-Reingold (F-R) layout which may have tidier plots. 301 * Produces a tSNE of all clusters, as well as a force-directed Fruchterman-Reingold (F-R) layout which may have tidier plots.
311 * A list of the most differentially expressed genes in each cluster 311 * A list of the most differentially expressed genes in each cluster
312 * An output PDF that provides heatmaps for: 312 * An output PDF that provides heatmaps for:
313 * The initial and final clustering (as determined using random forest) 313 * The initial and final clustering (as determined using random forest)
314 * Heatmaps for each of the most differentially expressed genes in each cluster 314 * Heatmaps for each of the most differentially expressed genes in each cluster
315 315
316 The tool requires the RData input from the previous filtering / normalisation / confounder removal step to work. 316 The tool requires the RDS input from the previous filtering / normalisation / confounder removal step to work.
317 317
318 318
319 319
320 ]]></help> 320 ]]></help>
321 <expand macro="citations" /> 321 <expand macro="citations" />