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annotate macros.xml @ 15:464b9243a4a5 draft default tip

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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 01:42:51 +0000
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15
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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1 <macros>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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2 <token name="@TOOL_VERSION@">4.3.0.1</token>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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3 <token name="@FUNCTION_BASE@">function['function_select'] == "base"</token>
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4 <token name="@FUNCTION_CITE@">function['function_select'] == "cite"</token>
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5 <token name="@VARIABLE_CONTINUE@">function['variable_continue']['variable_continue'] == "yes"</token>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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6 <token name="@PCA_CONTINUE@">function['variable_continue']['pca_continue']['pca_continue'] == "yes"</token>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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7 <token name="@CLUSTERS_CONTINUE@">function['variable_continue']['pca_continue']['clusters_continue']['clusters_continue'] == "yes"</token>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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8 <token name="@MARKERS_CONTINUE@">function['variable_continue']['pca_continue']['clusters_continue']['markers_continue']['markers_continue'] == "yes"</token>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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9 <xml name="requirements">
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10 <requirements>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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11 <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement>
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12 <requirement type="package" version="2.22">r-rmarkdown</requirement>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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13 <requirement type="package" version="1.14.2">r-data.table</requirement>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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14 </requirements>
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15 </xml>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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16 <xml name="norm" label="Normalizing data" expanded="true">
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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17 <param name="low_thresholds" type="integer" value="1" min="0" label="Low threshold for filtering cells" />
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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18 <param name="high_thresholds" type="integer" value="20000000" min="1" label="High threshold for filtering cells" />
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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19 <param name="vlnfeat" type="boolean" truevalue="T" falsevalue="F" label="Include violin plot and scatter plot of cell features"/>
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20 <param name="norm_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after data normalization"/>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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21 </xml>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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22 <xml name="variable" label="Variable features" expanded="true">
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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23 <param name="featplot" type="boolean" truevalue="T" falsevalue="F" label="Include plot of variable features"/>
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24 <param name="var_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after data scaling"/>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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25 </xml>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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26 <xml name="pca" label="Principal component analysis" expanded="true">
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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27 <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" />
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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28 <param name="pc_plots" type="boolean" truevalue="T" falsevalue="F" label="Include PCA plots"/>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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29 <param name="pca_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after PCA analysis"/>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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30 </xml>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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31 <xml name="clusters" label="Multidimensional scaling and Clustering" expanded="true">
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32 <param name="perplexity" type="integer" value="" optional="true" label="Perplexity parameter" help="Parameter for the tSNE dimensionality reduction" min="1"/>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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33 <param name="resolution" type="float" value="0.6" min="0" 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" />
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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34 <param name="nmds" type="boolean" truevalue="T" falsevalue="F" label="Include UMAP and TSNE plots"/>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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35 <param name="clusters_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after TSNE and UMAP analysis"/>
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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36 </xml>
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37 <xml name="markers" label="Marker genes" expanded="true">
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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38 <param name="min_pct" type="float" value="0.1" min="0" max="1.0" 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" />
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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39 <param name="logfc_threshold" type="float" min="0" value="0.25" label="Log fold change threshold"
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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40 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" />
464b9243a4a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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41 <param name="heatmaps" type="boolean" truevalue="T" falsevalue="F" label="Include heatmaps of markers"/>
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42 <param name="markers_file" type="boolean" truevalue="T" falsevalue="F" label="Output marker data"/>
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43 </xml>
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44 <xml name="cite-seq" label="Cite-seq analysis" expanded="true">
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45 <param name="cite_markers" type="boolean" truevalue="T" falsevalue="F" label="Output list of cite-seq markers"/>
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46 <conditional name="comparison">
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47 <param name="comparison" type="select" label="Compare specific feature's effect on protein and rna expression?">
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48 <option value="yes">Yes</option>
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49 <option value="no" selected="true">No</option>
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50 </param>
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51 <when value="yes">
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52 <param name="feat_comp" type="text" label="Feature(s) to inspect" help="Comma-separated list of features to directly compare with protein and RNA expression"/>
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53 </when>
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54 <when value="no"/>
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55 </conditional>
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56 <conditional name="marker_compare">
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57 <param name="marker_compare" type="select" label="Compare top RNA and protein features graphically against themselves and one another">
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58 <option value="yes">Yes</option>
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59 <option value="no">No</option>
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60 </param>
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61 <when value="yes">
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62 <param name="top_x" type="integer" min="1" value="5" label="How many of the top features should be shown"/>
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63 </when>
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64 <when value="no"/>
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65 </conditional>
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66 </xml>
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67 </macros>