Mercurial > repos > ebi-gxa > monocle3_diffexp

annotate monocle3-diffExp.xml @ 0:9261eff5cd98 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
author ebi-gxa
date Tue, 03 Mar 2020 22:58:02 +0000
parents
children 05f1ad42d728
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9261eff5cd98 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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1 <?xml version="1.0" encoding="utf-8"?>
9261eff5cd98 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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2 <tool id="monocle3_diffExp" name="Monocle3 diffExp" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
9261eff5cd98 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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3 <description> of genes along a trajectory</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 diffExp
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10 --neighbor-graph '$(neighbor_graph)'
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11 --reduction-method '$(reduction_method)'
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12 #if $knn
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13 --knn '$(knn)'
9261eff5cd98 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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14 #end if
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15 --method '$(method)'
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16 --alternative '$(alternative)'
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17
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18 @INPUT_OPTS@
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19 output.tsv
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20
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21 @VERBOSE@
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22 ]]></command>
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23
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24 <inputs>
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25 <expand macro="input_object_params"/>
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26 <param name="neighbor_graph" argument="--neighbor-graph" type="select" label="What neighbor graph to use, principal graph recommended for trajectory analysis.">
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27 <option value="knn" selected="true">KNN</option>
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28 <option value="principal_graph">Principal graph</option>
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29 </param>
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30 <param name="reduction_method" argument="--reduction-method" type="select" label="The reduction method to base the analysis on.">
9261eff5cd98 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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31 <option value="UMAP" selected="true">UMAP</option>
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32 </param>
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33 <param name="knn" argument="--knn" optional="true" type="integer" value="20" label="Number of nearest neighbors used for building the kNN graph which is passed to knn2nb function during the Moran's I (Geary's C) test procedure."/>
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34 <param name="method" argument="--method" type="select" label="A character string specifying the method for detecting significant genes showing correlated expression along the principal graph embedded in the low dimensional space.">
9261eff5cd98 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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35 <option value="Moran_I" selected="true">Moran_I</option>
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36 </param>
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37 <param name="alternative" argument="--alternative" type="select" label="A character string specifying the alternative hypothesis.">
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38 <option value="greater" selected="true">greater</option>
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39 <option value="less">less</option>
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40 <option value="two.sided">two-sided</option>
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41 </param>
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42 <expand macro="verbose_flag"/>
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43 </inputs>
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44
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45 <outputs>
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46 <data name="output_tsv" format="tsv" from_work_dir="output.tsv" label="${tool.name} on ${on_string}: tsv"/>
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47 </outputs>
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48
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49 <tests>
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50 <test>
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51 <param name="input_object_file" value="input.RDS"/>
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52 <param name="input_object_format" value="cds3"/>
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53 <param name="neighbor_graph" value="knn"/>
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54 <param name="reduction_method" value="UMAP"/>
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55 <param name="knn" value="20"/>
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56 <param name="method" value="Moran_I"/>
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57 <param name="alternative" value="greater"/>
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58 <output name="output_tsv" file="output.tsv" ftype="tsv" 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 differential expression testing along trajectory (`graph_test`)
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65 ========================================================================
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66
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67 Identify differentially expressed genes along the inferred trajectory.
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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>