Mercurial > repos > iuc > anndata_import

annotate import.xml @ 16:56e4b2d882ad draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata commit 7511ac8af2d638d0ad54f196b5ab3657c7577aa5
author iuc
date Wed, 10 Dec 2025 16:58:27 +0000
parents bfac01f0393b
children
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1 <tool id="anndata_import" name="Import Anndata" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
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2 <description>from different formats</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="params_10x">
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6 <param name="barcodes" type="data" format="tabular,txt" label="Barcodes (whitelist) file with one barcode per line"/>
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7 <param name="var_names" type="select" label="Variables index">
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8 <option value="gene_symbols">gene_symbols</option>
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9 <option value="gene_ids">gene_ids</option>
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10 </param>
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11 <param name="make_unique" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Make the variable index unique by appending '-1', '-2'?"/>
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12 <param name="gex_only" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Keep only 'Gene Expression' data and ignore other feature types?"/>
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13 </xml>
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14 </macros>
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15 <expand macro="bio_tools"/>
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16 <expand macro="requirements">
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17 <requirement type="package" version="1.10.2">scanpy</requirement>
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18 </expand>
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19 <expand macro="version_command"/>
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20 <command detect_errors="exit_code"><![CDATA[
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21 #if $in.adata_format == 'mtx'
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22 mkdir mtx
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23 #if $in.tenx.use == 'legacy_10x'
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24 && cp '$in.matrix' 'mtx/matrix.mtx'
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25 && cp '$in.tenx.genes' 'mtx/genes.tsv'
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26 && cp '$in.tenx.barcodes' 'mtx/barcodes.tsv'
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27 #else if $in.tenx.use == 'v3_10x'
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28 && cp '$in.matrix' 'mtx/matrix.mtx'
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29 && gzip 'mtx/matrix.mtx'
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30 && cp '$in.tenx.features' 'mtx/features.tsv'
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31 && gzip 'mtx/features.tsv'
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32 && cp '$in.tenx.barcodes' 'mtx/barcodes.tsv'
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33 && gzip 'mtx/barcodes.tsv'
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34 #end if
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35 &&
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36 #else if $in.adata_format == 'umi_tools'
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37 ## avoid gzipping in the inputdir
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38 gzip -c '$in.input' > umi_tools_input.gz
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39 &&
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40 #end if
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41
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42 @CMD@
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43 ]]></command>
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44 <configfiles>
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45 <configfile name="script_file"><![CDATA[
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46 @CMD_imports@
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47 #if $in.adata_format == 'loom'
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48 adata = ad.read_loom(
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49 '$in.input',
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50 sparse=$in.sparse,
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51 cleanup=$in.cleanup,
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52 X_name='$in.x_name',
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53 obs_names='$in.obs_names',
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54 var_names='$in.var_names')
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55
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56 #else if $in.adata_format == 'tabular'
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57 #set delimiter=$in.input.metadata.delimiter
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58 #if $delimiter != ','
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59 #set delimiter='\\t'
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60 #end if
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61 adata = ad.read_csv(
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62 '$in.input',
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63 delimiter='$delimiter',
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64 first_column_names=$in.first_column_names)
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65 ## convert into sparse matrix. Dense matrix needs large disk space and higher access times
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66 from scipy.sparse import csr_matrix
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67 adata.X = csr_matrix(adata.X)
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68
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69 #else if $in.adata_format == '10x_h5'
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70 import scanpy as sc
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71 adata = sc.read_10x_h5('$in.input')
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72
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73 #else if $in.adata_format == 'mtx'
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74 #if $in.tenx.use == 'no'
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75 adata = ad.read_mtx(filename='$in.matrix')
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76 #else
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77 import scanpy as sc
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78 adata = sc.read_10x_mtx(
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79 'mtx',
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80 var_names='$in.tenx.var_names',
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81 make_unique=$in.tenx.make_unique,
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82 cache=False,
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83 gex_only=$in.tenx.gex_only)
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84 #end if
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85
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86 #else if $in.adata_format == 'umi_tools'
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87 adata = ad.read_umi_tools('umi_tools_input.gz')
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88
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89 #else if $in.adata_format == 'custom'
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90 import pandas as pd
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91
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92 adata = ad.read_mtx(filename='$in.mtx')
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93 adata = adata.transpose().copy()
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94
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95 obs = pd.read_csv('$in.obs', sep='\t', index_col=0)
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96 var = pd.read_csv('$in.var', sep='\t', index_col=0)
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97
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98 if adata.shape[0] != obs.shape[0]:
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99 raise ValueError(f"Mismatch: adata has {adata.shape[0]} cells, but obs has {obs.shape[0]} rows.")
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100
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101 if adata.shape[1] != var.shape[0]:
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102 raise ValueError(f"Mismatch: adata has {adata.shape[1]} genes, but var has {var.shape[0]} rows.")
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103
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104
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105 adata.obs = obs
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106 adata.var = var
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107
3
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108 #end if
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109 adata.write('anndata.h5ad', compression='gzip')
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110 print(adata)
0
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111 ]]></configfile>
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112 </configfiles>
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113 <inputs>
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114 <conditional name="in">
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115 <param name="adata_format" type="select" label="Create annadata from">
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116 <option value="loom">Loom data</option>
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117 <option value="tabular">Tabular, CSV, TSV</option>
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118 <option value="10x_h5">H5 format from Cell ranger or not</option>
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119 <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option>
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120 <option value="umi_tools">UMI tools count matrix</option>
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121 <option value="custom">custom (with annotated cells and genes tables)</option>
0
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122 </param>
12
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123 <when value="loom">
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124 <param name="input" type="data" format="loom" label="Annotated data matrix"/>
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125 <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/>
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126 <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/>
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127 <param name="x_name" type="text" value="spliced" label="X_name"/>
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128 <param name="obs_names" type="text" value="CellID" label="obs_names"/>
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129 <param name="var_names" type="text" value="Gene" label="var_names"/>
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130 </when>
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131 <when value="tabular">
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132 <param name="input" type="data" format="tabular,csv,tsv" label="Annotated data matrix"/>
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133 <param name="first_column_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Does the first column store the row names?"/>
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134 </when>
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135 <when value="10x_h5" >
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136 <param name="input" type="data" format="h5" label="Data matrix"/>
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137 </when>
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138 <when value="mtx">
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139 <param name="matrix" type="data" format="mtx" label="Matrix in Matrix Market format"/>
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140 <conditional name="tenx">
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141 <param name="use" type="select" label="Use 10x Genomics formatted mtx">
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142 <option value="no">No</option>
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143 <option value="legacy_10x">Output from Cell Ranger v2 or earlier versions</option>
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144 <option value="v3_10x">Output from Cell Ranger v3 or later versions</option>
0
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145 </param>
12
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146 <when value="no"/>
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147 <when value="legacy_10x">
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148 <param name="genes" type="data" format="tabular" label="2-column genes file with gene id and gene name"/>
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149 <expand macro="params_10x"/>
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150 </when>
12
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151 <when value="v3_10x">
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152 <param name="features" type="data" format="tabular" label="3-column features file with feature id, feature name and feature type" help="For scRNA-seq, features are genes. The 3rd column typically contains the word 'Gene Expression'"/>
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153 <expand macro="params_10x"/>
0
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154 </when>
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155 </conditional>
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156 </when>
12
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157 <when value="umi_tools">
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158 <param name="input" type="data" format="tabular" label="condensed count matrix from UMI tools"/>
0
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159 </when>
15
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160 <when value="custom">
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161 <param name="mtx" type="data" format="mtx" label="Matrix in Matrix Market format"/>
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162 <param name="obs" type="data" format="tabular,tabular.gz" label="Annotated cells (first column will be obs_index)"/>
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163 <param name="var" type="data" format="tabular,tabular.gz" label="Annotated genes (first column will be var_index)"/>
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164 </when>
0
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165 </conditional>
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166 </inputs>
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167 <outputs>
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168 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="Anndata import on ${on_string}"/>
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169 </outputs>
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170 <tests>
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171 <test expect_num_outputs="1">
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172 <conditional name="in">
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173 <param name="adata_format" value="loom"/>
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174 <param name="input" ftype="loom" value="krumsiek11.loom" />
0
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175 <param name="sparse" value="True"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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176 <param name="cleanup" value="False"/>
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177 <param name="x_name" value="spliced"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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178 <param name="obs_names" value="CellID" />
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179 <param name="var_names" value="Gene"/>
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180 </conditional>
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181 <assert_stdout>
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182 <has_text_matching expression="ad.read_loom"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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183 <has_text_matching expression="sparse=True"/>
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184 <has_text_matching expression="cleanup=False"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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185 <has_text_matching expression="X_name='spliced'"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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186 <has_text_matching expression="obs_names='CellID'"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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187 <has_text_matching expression="var_names='Gene'"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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188 </assert_stdout>
12
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189 <output name="anndata" ftype="h5ad">
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190 <assert_contents>
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191 <has_h5_keys keys="obs/cell_type"/>
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192 <has_h5_keys keys="obs/obs_names"/>
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193 <has_h5_keys keys="var/var_names"/>
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194 </assert_contents>
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195 </output>
0
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196 </test>
3
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197 <test expect_num_outputs="1">
0
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198 <conditional name="in">
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199 <param name="adata_format" value="tabular"/>
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200 <param name="input" value="adata.csv"/>
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201 <param name="first_column_names" value="true"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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202 </conditional>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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203 <assert_stdout>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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204 <has_text_matching expression="ad.read_csv"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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205 <has_text_matching expression="delimiter=','"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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206 <has_text_matching expression="first_column_names=True"/>
12
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207 <has_text_matching expression="3 × 2"/>
0
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208 </assert_stdout>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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209 </test>
3
b68022a5c83f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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210 <test expect_num_outputs="1">
0
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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211 <conditional name="in">
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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212 <param name="adata_format" value="tabular"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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213 <param name="input" value="adata.tsv"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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214 <param name="first_column_names" value="true"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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215 </conditional>
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216 <assert_stdout>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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217 <has_text_matching expression="ad.read_csv"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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218 <has_text_matching expression="delimiter='\\t'"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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219 <has_text_matching expression="first_column_names=True"/>
12
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220 <has_text_matching expression="3 × 2"/>
0
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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221 </assert_stdout>
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222 </test>
7
546e3c9d261c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
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223 <test expect_num_outputs="1">
0
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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224 <conditional name="in">
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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225 <param name="adata_format" value="mtx"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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226 <param name="matrix" value="matrix_10x_v1.2.0.mtx"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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227 <conditional name="tenx">
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228 <param name="use" value="no"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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229 </conditional>
12
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230 </conditional>
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diff changeset
231 <assert_stdout>
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232 <has_text_matching expression="343 × 12"/>
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233 </assert_stdout>
0
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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234 </test>
12
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235 <test expect_num_outputs="1">
0
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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236 <conditional name="in">
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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237 <param name="adata_format" value="mtx"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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238 <param name="matrix" value="matrix_10x_v1.2.0.mtx"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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239 <conditional name="tenx">
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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240 <param name="use" value="legacy_10x"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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241 <param name="genes" value="genes_10x_v1.2.0.tsv"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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242 <param name="barcodes" value="barcodes_10x_v1.2.0.tsv"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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243 <param name="var_names" value="gene_symbols"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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244 <param name="make_unique" value="true"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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245 <param name="gex_only" value="true"/>
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246 </conditional>
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247 </conditional>
12
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248 <assert_stdout>
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249 <has_text_matching expression="12 × 343"/>
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250 </assert_stdout>
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251 <output name="anndata" ftype="h5ad">
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252 <assert_contents>
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253 <has_h5_keys keys="var/gene_ids"/>
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254 </assert_contents>
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255 </output>
0
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256 </test>
12
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257 <test expect_num_outputs="1">
0
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258 <conditional name="in">
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259 <param name="adata_format" value="mtx"/>
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260 <param name="matrix" value="matrix_10x_v3.0.0.mtx"/>
c6a4df4d3d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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261 <conditional name="tenx">
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262 <param name="use" value="v3_10x"/>
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263 <param name="features" value="features_10x_v3.0.0.tsv"/>
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264 <param name="barcodes" value="barcodes_10x_v3.0.0.tsv"/>
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265 <param name="var_names" value="gene_symbols"/>
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266 <param name="make_unique" value="true"/>
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267 <param name="gex_only" value="true"/>
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268 </conditional>
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269 </conditional>
12
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270 <assert_stdout>
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271 <has_text_matching expression="1107 × 507"/>
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272 </assert_stdout>
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273 <output name="anndata" ftype="h5ad">
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274 <assert_contents>
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275 <has_h5_keys keys="var/gene_ids"/>
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276 <has_h5_keys keys="var/feature_types"/>
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277 </assert_contents>
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278 </output>
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279 </test>
3
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280 <test expect_num_outputs="1">
0
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281 <conditional name="in">
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282 <param name="adata_format" value="umi_tools"/>
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283 <param name="input" value="umi_tools.tsv"/>
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284 </conditional>
12
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285 <assert_stdout>
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286 <has_text_matching expression="2 × 13"/>
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287 </assert_stdout>
3
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288 </test>
5
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289 <test expect_num_outputs="1"><!-- 10x h5 test -->
12
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290 <conditional name="in">
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291 <param name="adata_format" value="10x_h5"/>
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292 <param name="input" value="dropletutils_input.h5"/>
5
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293 </conditional>
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294 <output name="anndata">
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295 <assert_contents>
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296 <has_text text="HDF"/>
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297 <has_text text="ENSG00000258728" />
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298 <has_text text="GCGAGAAAGTTGTAGA" />
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299 </assert_contents>
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300 </output>
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301 </test>
15
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302 <test expect_num_outputs="1">
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303 <conditional name="in">
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304 <param name="adata_format" value="custom"/>
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305 <param name="mtx" value="trimmed_matrix.mtx"/>
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306 <param name="obs" value="trimmed_barcode.tabular"/>
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307 <param name="var" value="trimmed_gene.tabular"/>
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308 </conditional>
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309 <assert_stdout>
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310 <has_text_matching expression="1000 × 500"/>
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311 </assert_stdout>
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312 <output name="anndata" ftype="h5ad">
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313 <assert_contents>
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314 <has_h5_keys keys="var/symbol,var/mito"/>
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315 </assert_contents>
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316 </output>
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317 </test>
0
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318 </tests>
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319 <help><![CDATA[
7
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320
0
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321 **What it does**
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322
12
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323 This tool creates an AnnData from several input types:
0
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324
13
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325 - Loom (`read_loom method <https://anndata.readthedocs.io/en/latest/generated/anndata.io.read_loom.html>`__)
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326 - Tabular (`read_csv method <https://anndata.readthedocs.io/en/latest/generated/anndata.io.read_csv.html>`__)
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327 - Matrix Market (mtx), from Cell ranger or not (`read_mtx method <https://anndata.readthedocs.io/en/latest/generated/anndata.io.read_mtx.html>`__)
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328 - UMI tools (`read_umi_tools method <https://anndata.readthedocs.io/en/latest/generated/anndata.io.read_umi_tools.html>`__)
0
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329
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330 @HELP@
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331 ]]></help>
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332 <expand macro="citations"/>
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333 </tool>