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annotate macros.xml @ 15:fab6ff46e019 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 01:43:02 +0000
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15
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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1 <macros>
fab6ff46e019 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>
fab6ff46e019 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>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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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>
fab6ff46e019 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>
fab6ff46e019 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>
fab6ff46e019 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>
fab6ff46e019 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>
fab6ff46e019 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>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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12 <requirement type="package" version="2.22">r-rmarkdown</requirement>
fab6ff46e019 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>
fab6ff46e019 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>
fab6ff46e019 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">
fab6ff46e019 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" />
fab6ff46e019 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" />
fab6ff46e019 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"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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20 <param name="norm_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after data normalization"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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21 </xml>
fab6ff46e019 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">
fab6ff46e019 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"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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24 <param name="var_file" type="boolean" truevalue="T" falsevalue="F" label="Output seurat object after data scaling"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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25 </xml>
fab6ff46e019 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">
fab6ff46e019 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" />
fab6ff46e019 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"/>
fab6ff46e019 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"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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30 </xml>
fab6ff46e019 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">
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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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"/>
fab6ff46e019 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" />
fab6ff46e019 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"/>
fab6ff46e019 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"/>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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36 </xml>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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37 <xml name="markers" label="Marker genes" expanded="true">
fab6ff46e019 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" />
fab6ff46e019 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"
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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" />
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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>
fab6ff46e019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat commit b437a46efb50e543b6d7c9988f954efe2caa9046
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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>