Mercurial > repos > ebi-gxa > monocle3_reducedim

annotate monocle3-reduceDim.xml @ 1:004a86dffd79 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb
author ebi-gxa
date Wed, 29 Jan 2020 10:39:45 -0500
parents 9e59e242ed63
children 98f4918eee70
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9e59e242ed63 "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"?>
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2 <tool id="monocle3_reduceDim" name="Monocle3 reduceDim" version="@TOOL_VERSION@+galaxy0">
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3 <description>for downstream analysis</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 reduceDim
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10 #if $max_components
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11 --max-components '${max_components}'
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12 #end if
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13 --reduction-method '${reduction_method}'
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14 --preprocess-method '${preprocess_method}'
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15
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16 @INPUT_OPTS@
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17 @OUTPUT_OPTS@
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18
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19 @VERBOSE@
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20 ]]></command>
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21
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22 <inputs>
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23 <expand macro="input_object_params"/>
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24 <expand macro="output_object_params"/>
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25 <param name="max_components" argument="--max-components" optional="true" type="integer" value="2" label="The dimensionality of the reduced space."/>
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26 <param name="reduction_method" argument="--reduction-method" type="select" label="The algorithm to use for dimensionality reduction.">
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27 <option selected="true" value="UMAP">UMAP</option>
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28 <option value="tSNE">tSNE</option>
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29 <option value="PCA">PCA</option>
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30 <option value="LSI">LSI</option>
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31 </param>
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32 <param name="preprocess_method" argument="--preprocess-method" type="select" label="The preprocessing method used on the data.">
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33 <option value="PCA" selected="true">PCA</option>
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34 <option value="LSI">LSI</option>
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35 </param>
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36 <expand macro="verbose_flag"/>
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37 </inputs>
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38
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39 <outputs>
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40 <data name="output_rds" format="rdata" from_work_dir="output.RDS" label="${tool.name} on ${on_string}: ${output_object_format}"/>
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41 </outputs>
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42
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43 <tests>
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44 <test>
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45 <param name="input_object_file" value="input.RDS"/>
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46 <param name="input_object_format" value="cds3"/>
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47 <param name="max_components" value="2"/>
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48 <param name="reduction_method" value="UMAP"/>
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49 <param name="preprocess_method" value="PCA"/>
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50 <param name="output_object_format" value="cds3"/>
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51 <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/>
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52 </test>
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53 </tests>
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54
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55 <help><![CDATA[
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56 ==============================================================
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57 Primary Monocle3 dimensionality reduction (`reduce_dimension`)
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58 ==============================================================
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59
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60 Use the results of preprocessing to propose a primary dimensionally reduced space for use
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61 in downstream analysis.
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62
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63 @HELP@
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64
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65 @VERSION_HISTORY@
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66 ]]></help>
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67 <expand macro="citations"/>
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68 </tool>