Mercurial > repos > ebi-gxa > monocle3_create

annotate monocle3-create.xml @ 4:4df9f81262d3 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 18:52:23 +0000
parents 173d87ed3dad
children
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7fb2f5ed06ce "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"?>
2
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2 <tool id="monocle3_create" name="Monocle3 create" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
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3 <description>a Monocle3 object from input data</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 ln -s '${expression_matrix}' expression_matrix.'${expression_matrix_format}' &&
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10 #if $cell_metadata
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11 ln -s '${cell_metadata}' cell_metadata.'${cell_metadata_format}' &&
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12 #end if
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13 #if $gene_annotation
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14 ln -s '${gene_annotation}' gene_annotation.'${gene_annotation_format}' &&
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15 #end if
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16 LANG=en_US.UTF-8 monocle3 create
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17 --expression-matrix expression_matrix.'${expression_matrix_format}'
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18 #if $cell_metadata
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19 --cell-metadata cell_metadata.'${cell_metadata_format}'
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20 #end if
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21 #if $gene_annotation
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22 --gene-annotation gene_annotation.'${gene_annotation_format}'
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23 #end if
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24 @OUTPUT_OPTS@
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25 @VERBOSE@
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26 ]]></command>
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27
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28 <inputs>
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29 <param name="expression_matrix" argument="--expression-matrix" type="data" format="tabular,tsv,csv,rdata" label="Expression matrix, genes as rows, cells as columns. Required input. Provide as TSV, CSV or RDS."/>
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30 <param name="expression_matrix_format" type="select" label="Format of expression matrix">
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31 <option value="rds" selected="true">RDS</option>
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32 <option value="tsv">TSV</option>
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33 <option value="mtx">MTX</option>
0
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34 <option value="csv">CSV</option>
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35 </param>
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36 <param name="cell_metadata" argument="--cell-metadata" optional="true" type="data" format="tabular,tsv,csv,rdata" label="Per-cell annotation, optional. Row names must match the column names of the expression matrix. Provide as TSV, CSV or RDS."/>
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37 <param name="cell_metadata_format" type="select" label="Format of cell metadata">
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38 <option value="rds" selected="true">RDS</option>
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39 <option value="tsv">TSV</option>
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40 <option value="csv">CSV</option>
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41 </param>
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42 <param name="gene_annotation" argument="--gene-annotation" optional="true" type="data" format="tabular,tsv,csv,rdata" label="Per-gene annotation, optional. Row names must match the row names of the expression matrix. Provide as TSV, CSV or RDS."/>
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43 <param name="gene_annotation_format" type="select" label="Format of gene annotation">
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44 <option value="rds" selected="true">RDS</option>
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45 <option value="tsv">TSV</option>
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46 <option value="csv">CSV</option>
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47 </param>
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48 <expand macro="output_object_params"/>
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49 <expand macro="verbose_flag"/>
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50 </inputs>
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51
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52 <outputs>
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53 <data name="output_rds" format="rdata" from_work_dir="output.RDS" label="${tool.name} on ${on_string}: ${output_object_format}"/>
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54 </outputs>
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55
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56 <tests>
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57 <test>
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58 <param name="expression_matrix" value="expression.RDS"/>
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59 <param name="cell_metadata" value="cells.RDS"/>
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60 <param name="gene_annotation" value="genes.RDS"/>
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61 <param name="output_object_format" value="cds3"/>
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62 <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/>
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63 </test>
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64 </tests>
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65
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66 <help><![CDATA[
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67 ===========================================================================
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68 Create Monocle3 object from input expression/metadata (`new_cell_data_set`)
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69 ===========================================================================
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70
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71 Create a Monocle3 cds3 object from input expression data and optional metadata.
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72 The expression matrix, with genes as rows and cells as columns, is the only mandatory
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73 input. The cell metadata (with row names matching the column names of the expression
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74 matrix) and gene annotation (with row names matching the row names of the expression
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75 matrix) are optional. These files can be provided as RDS objects, or CSV/TSV. Select the
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76 format of your input files in the corresponding drop-downs.
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77
7fb2f5ed06ce "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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78 @HELP@
7fb2f5ed06ce "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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79
7fb2f5ed06ce "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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80 @VERSION_HISTORY@
7fb2f5ed06ce "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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81 ]]></help>
7fb2f5ed06ce "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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82 <expand macro="citations"/>
7fb2f5ed06ce "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8ef74a1abb7d22b5c18611b8cdd7a5bf56c51b10"
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83 </tool>