Mercurial > repos > ebi-gxa > monocle3_preprocess

annotate monocle3-preprocess.xml @ 1:0869b0264af1 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 10:38:23 -0500
parents 384b9bcf2807
children 273d11a83e42
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="monocle3_preprocess" name="Monocle3 preprocess" version="@TOOL_VERSION@+galaxy0">
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3 <description>a Monocle3 object to an initially dimensionally reduced space</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 preprocess
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10 --method '${method}'
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11 #if $num_dim
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12 --num-dim '${num_dim}'
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13 #end if
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14 --norm-method '${norm_method}'
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15 #if $use_genes
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16 --use-genes '${use_genes}'
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17 #end if
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18 #if $residual_model_formula_str
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19 --residual-model-formula-str '${residual_model_formula_str}'
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20 #end if
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21 #if $pseudo_count
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22 --pseudo-count '${pseudo_count}'
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23 #end if
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24 #if $no_scaling
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25 --no-scaling
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26 #end if
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28 @INPUT_OPTS@
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29 @OUTPUT_OPTS@
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30
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31 @VERBOSE@
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32 ]]></command>
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33
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34 <inputs>
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35 <expand macro="input_object_params"/>
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36 <expand macro="output_object_params"/>
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37 <param name="method" argument="--method" type="select" label="Initial dimensionality reduction to perform.">
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38 <option value="PCA" selected="true">PCA</option>
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39 <option value="LSI">LSI</option>
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40 </param>
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41 <param name="num_dim" argument="--num-dim" optional="true" type="integer" value="50" label="The dimensionality of the reduced space."/>
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42 <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values prior to reducing dimensionality.">
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43 <option value="log" selected="true">Size factor correction and log transformation</option>
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44 <option value="size_only">Size factor correction only</option>
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45 </param>
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46 <param name="use_genes" argument="--use-genes" type="text" optional="true" label="Manually subset the gene pool to these genes for dimensionality reduction."/>
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47 <param name="residual_model_formula_str" argument="--residual-model-formula-str" type="text" optional="true" label="A string model formula specifying effects to subtract from the data.">
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48 <sanitizer>
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49 <valid initial="string.printable"/>
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50 </sanitizer>
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51 </param>
0
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52 <param name="pseudo_count" argument="--pseudo-count" optional="true" type="float" value="1" label="Amount to increase expression values before dimensionality reduction."/>
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53 <param name="no_scaling" argument="--no-scaling" type="boolean" checked="false" label="When this option is NOT set, scale each gene before running trajectory reconstruction."/>
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54 <expand macro="verbose_flag"/>
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55 </inputs>
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56
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57 <outputs>
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58 <data name="output_rds" format="rdata" from_work_dir="output.RDS" label="${tool.name} on ${on_string}: ${output_object_format}"/>
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59 </outputs>
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60
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61 <tests>
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62 <test>
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63 <param name="input_object_file" value="input.RDS"/>
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64 <param name="input_object_format" value="cds3"/>
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65 <param name="method" value="PCA"/>
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66 <param name="num_dim" value="50"/>
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67 <param name="norm_method" value="log"/>
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68 <param name="pseudo_count" value="1"/>
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69 <param name="output_object_format" value="cds3"/>
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70 <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/>
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71 </test>
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72 </tests>
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73
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74 <help><![CDATA[
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75 ====================================================================================
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76 Preprocess Monocle3 object up to initial dimensionality reduction (`preprocess_cds`)
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77 ====================================================================================
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78
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79 Preprocess a Monocle3 object with size factor scaling of the count data, optionally
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80 log transforming, and computing an initial dimensionality reduction. This space is
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81 used as a starting point for a number of subsequent analyses.
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82
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83 @HELP@
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84
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85 @VERSION_HISTORY@
384b9bcf2807 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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86 ]]></help>
384b9bcf2807 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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87 <expand macro="citations"/>
384b9bcf2807 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 815e36252846236124957052433572f1c1247114"
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88 </tool>