Mercurial > repos > ebi-gxa > monocle3_ordercells

annotate monocle3-orderCells.xml @ 3:762c57e35238 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 660486ba0e1ef2f0195e7c6f75448221ba4640f7"
author ebi-gxa
date Tue, 28 Apr 2020 12:34:26 -0400
parents f58c4eb5446d
children
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5520da33a868 "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_orderCells" name="Monocle3 orderCells" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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3 <description>along trajectories</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 orderCells
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10 --reduction-method '${reduction_method}'
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11 #if $root_pr_nodes
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12 --root-pr-nodes '${root_pr_nodes}'
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13 #end if
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14 #if $root_cells
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15 --root-cells '${root_cells}'
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16 #end if
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17 #if $cell_phenotype
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18 --cell-phenotype '${cell_phenotype}'
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19 #end if
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20 #if $root_type
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21 --root-type '${root_type}'
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22 #end if
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23
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24 @INPUT_OPTS@
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25 @OUTPUT_OPTS@
2
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26
0
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27 @VERBOSE@
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28 ]]></command>
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29
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30 <inputs>
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31 <expand macro="input_object_params"/>
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32 <expand macro="output_object_params"/>
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33 <param name="root_pr_nodes" argument="--root-pr-nodes" type="text" optional="true" label="The starting principal points. We learn a principal graph that passes through the middle of the data points and use it to represent the developmental process. Exclusive with the root cell option."/>
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34 <param name="root_cells" argument="--root-cells" type="text" optional="true" label="The starting cells. Each cell corresponds to a principal point and multiple cells can correspond to the same principal point. Exclusive with the root node option."/>
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35 <param name="cell_phenotype" argument="--cell-phenotype" type="text" optional="true" label="The cell phenotype (column in pdata) used to identify root principal nodes."/>
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36 <param name="root_type" argument="--root-type" type="text" optional="true" label="The value in the cell phenotype column used to extract root nodes."/>
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37 <param name="reduction_method" argument="--reduction-method" type="select" label="The dimensionality reduction that was used for clustering.">
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38 <option selected="true" value="UMAP">UMAP</option>
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39 <option value="tSNE">tSNE</option>
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40 <option value="PCA">PCA</option>
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41 <option value="LSI">LSI</option>
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42 </param>
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43 <expand macro="verbose_flag"/>
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44 </inputs>
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45
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46 <outputs>
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47 <data name="output_rds" format="rdata" from_work_dir="output.RDS" label="${tool.name} on ${on_string}: ${output_object_format}"/>
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48 </outputs>
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49
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50 <tests>
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51 <test>
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52 <param name="input_object_file" value="input.RDS"/>
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53 <param name="input_object_format" value="cds3"/>
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54 <param name="reduction_method" value="UMAP"/>
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55 <param name="cell_phenotype" value="embryo.time.bin"/>
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56 <param name="root_type" value="130-170"/>
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57 <param name="output_object_format" value="cds3"/>
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58 <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/>
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59 </test>
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60 </tests>
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61
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62 <help><![CDATA[
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63 ==========================================
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64 Monocle3 ordering of cells (`order_cells`)
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65 ==========================================
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66
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67 Order cells using the inferred graph
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68
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69 @HELP@
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70
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71 @VERSION_HISTORY@
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72 ]]></help>
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73 <expand macro="citations"/>
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74 </tool>