annotate seurat_read10x.xml @ 6:f5db0e853f57 draft default tip

planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:42:53 +0000
parents 301cf1b4b43d
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1 <tool id="seurat_read10x" name="Seurat Read10x" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
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2 <description>Loads Tabular or 10x data into a serialized seurat R object</description>
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3 <macros>
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4 <import>seurat_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command><![CDATA[
2
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12 #if str($input.format) == "mtx":
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13 ln -s "$matrix" matrix.mtx;
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14 ln -s "$genes" genes.tsv;
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15 ln -s "$barcodes" barcodes.tsv;
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16 #end if
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17
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18 seurat-read-10x.R
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19 #if str($input.format) == "mtx":
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20 -d ./
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21 #else
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22 -f $input.file
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23 #end if
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24 #if $metadata
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25 --metadata '$metadata'
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26 #end if
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27 #if $min_cells
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28 --min-cells '$min_cells'
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29 #end if
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30 #if $min_features
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31 --min-features '$min_features'
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32 #end if
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33
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34 @OUTPUT_OBJECT@
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35
0
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36 ]]></command>
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37 <inputs>
2
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38 <conditional name="input" label="Input expression data">
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39 <param type="select" name="format" label="Choose the format of the input" help="10X MTX or tabular">
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40 <option value="mtx" selected="true">10X-type MTX</option>
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41 <option value="tab" selected="true">tab-delimited text</option>
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42 </param>
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43 <when value="tab">
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44 <param type="data" name="file" label="Expression table" help="Tab-delimted expression table" format="tabular"/>
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45 </when>
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46 <when value="mtx">
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47 <param type="data" name="matrix" help="Raw expression quantification as a sparse matrix in Matrix Market format, where each column is a gene and each row is a barcode/cell." format="txt" label="Expression matrix in sparse matrix format (.mtx)" />
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48 <param type="data" name="genes" help="Matrix market column file for genes" label="Gene table" format="tsv,tabular"/>
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49 <param type="data" name="barcodes" help="Matrix market row file for genes" label="Barcode/cell table" format="tsv,tabular"/>
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50 </when>
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51 </conditional>
1
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52 <param label="Cell Metadata" optional="true" name="metadata" argument="--metadata" type="data" format="tsv,tabular" help="File with metdata for the cells, first column should be cell identifiers as used in the cells 10x file."/>
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53 <param label="Minimum cells to include features" optional="true" name="min_cells" argument="--min-cells" type="integer" help="Include features detected in at least this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff."/>
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54 <param label="Minimum features to include cells" optional="true" name="min_features" argument="--min-features" type="integer" help="Include cells where at least this many features are detected."/>
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55 <expand macro="output_object_params"/>
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56 </inputs>
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57 <outputs>
1
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58 <expand macro="output_files"/>
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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 <conditional name="input">
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64 <param name="format" value="mtx"/>
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65 </conditional>
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66 <param name="matrix" ftype="txt" value="E-MTAB-6077_3k_features_90_cells_matrix.txt"/>
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67 <param name="genes" ftype="txt" value="E-MTAB-6077_3k_features_90_cells_genes.tsv"/>
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68 <param name="barcodes" ftype="txt" value="E-MTAB-6077_3k_features_90_cells_barcodes.tsv"/>
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69 <output name="rds_seurat_file" ftype="rdata">
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70 <assert_contents>
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71 <has_size value="2260044" delta="200000"/>
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72 </assert_contents>
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73 </output>
0
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74 </test>
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75 </tests>
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76
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77
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78 <help><![CDATA[
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79 .. class:: infomark
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80
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81 **What it does**
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82
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83 @SEURAT_INTRO@
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84
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85 **Read expression data from a tabular file or a 10x-Genomics-formatted mtx directory (`read_10x_mtx`)**
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86
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87 For mtx, the directory should contain:
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88
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89 1) Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell.
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90
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91 2) A gene table of at least two columns where the first column gives the gene IDs.
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92
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93 3) A barcode/cell table of at least one column giving the barcode/cell IDs.
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94
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95 The above-mentioned files can be obtained by running `EBI SCXA Data Retrieval`
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96 with a dataset accession. Otherwise, they need to be provided as separate Galaxy
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97 datasets.
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98
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99 **Inputs**
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100 * A tabular file of expression data OR
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101 * Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell.
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102 * A gene table of at least two columns where the first column gives the gene IDs.
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103 * A barcode/cell table of at least one column giving the barcode/cell IDs.
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104 * Optionally, a file with cell metadata.
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105
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106 **Outputs**
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107 * R object for Seurat
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108
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109 .. _Seurat: https://www.nature.com/articles/nbt.4096
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110 .. _Satija Lab: https://satijalab.org/seurat/
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111 .. _Seurat Guided Clustering tutorial: https://satijalab.org/seurat/pbmc3k_tutorial.html
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112
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113 @VERSION_HISTORY@
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114 ]]></help>
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115 <expand macro="citations"/>
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116 </tool>