Mercurial > repos > ebi-gxa > monocle3_partition

annotate monocle3-partition.xml @ 5:d98b4705eb4c draft default tip

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b28c91675a0a90e45c65f275fc2fd596b431aa45"
author ebi-gxa
date Wed, 03 Jun 2020 14:55:56 -0400
parents 92ca41fbc123
children
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be84f9c3a2dd "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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1 <?xml version="1.0" encoding="utf-8"?>
2
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2 <tool id="monocle3_partition" name="Monocle3 partition" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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3 <description>of cells into groups</description>
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4 <macros>
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5 <import>monocle3-macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 LANG=en_US.UTF-8 monocle3 partition
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10 --reduction-method '${reduction_method}'
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11 #if $knn
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12 --knn '${knn}'
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13 #end if
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14 #if $weight
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15 --weight
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16 #end if
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17 #if $louvain_iter
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18 --louvain-iter '${louvain_iter}'
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19 #end if
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20 #if $resolution
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21 --resolution '${resolution}'
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22 #end if
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23 #if $partition_qval
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24 --partition-qval '${partition_qval}'
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25 #end if
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26
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27 @INPUT_OPTS@
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28 @OUTPUT_OPTS@
2
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29
0
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30 @VERBOSE@
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31 ]]></command>
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32
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33 <inputs>
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34 <expand macro="input_object_params"/>
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35 <expand macro="output_object_params"/>
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36 <param name="reduction_method" argument="--reduction-method" type="select" label="The dimensionality reduction to base the clustering on.">
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37 <option selected="true" value="UMAP">UMAP</option>
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38 <option value="tSNE">tSNE</option>
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39 <option value="PCA">PCA</option>
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40 <option value="LSI">LSI</option>
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41 </param>
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42 <param name="knn" argument="--knn" optional="true" type="integer" value="20" label="Number of nearest neighbours used for Louvain clustering."/>
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43 <param name="weight" argument="--weight" type="boolean" checked="false" label="When this option is set, calculate the weight for each edge in the kNN graph."/>
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44 <param name="louvain_iter" argument="--louvain-iter" optional="true" type="integer" value="1" label="The number of iterations for Louvain clustering."/>
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45 <param name="resolution" argument="--resolution" optional="true" type="float" label="Resolution of clustering result, specifying the granularity of clusters. Not used by default and the standard igraph louvain clustering algorithm will be used."/>
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46 <param name="partition_qval" argument="--partition-qval" optional="true" type="float" value="0.05" label="The q-value threshold used to determine the partition of cells."/>
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47 <expand macro="verbose_flag"/>
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48 </inputs>
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49
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50 <outputs>
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51 <data name="output_rds" format="rdata" from_work_dir="output.RDS" label="${tool.name} on ${on_string}: ${output_object_format}"/>
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52 </outputs>
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53
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54 <tests>
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55 <test>
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56 <param name="input_object_file" value="input.RDS"/>
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57 <param name="input_object_format" value="cds3"/>
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58 <param name="reduction_method" value="UMAP"/>
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59 <param name="knn" value="20"/>
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60 <param name="louvain_iter" value="1"/>
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61 <param name="partition_qval" value="0.05"/>
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62 <param name="output_object_format" value="cds3"/>
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63 <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/>
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64 </test>
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65 </tests>
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66
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67 <help><![CDATA[
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68 ==============================================
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69 Monocle3 clustering of cells (`cluster_cells`)
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70 ==============================================
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71
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72 Cluster the primary dimensionality reduced space
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73
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74 @HELP@
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75
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76 @VERSION_HISTORY@
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77 ]]></help>
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78 <expand macro="citations"/>
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79 </tool>