Mercurial > repos > iuc > anndata_import

annotate import.xml @ 13:d330b3082107 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
author iuc
date Sat, 14 Sep 2024 19:58:24 +0000
parents 93dd15e13e6a
children 6f143dfe902a
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13
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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1 <tool id="anndata_import" name="Import Anndata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" 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="requirements">
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16 <requirement type="package" version="1.10.2">scanpy</requirement>
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17 </expand>
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18 <expand macro="version_command"/>
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19 <command detect_errors="exit_code"><![CDATA[
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20 #if $in.adata_format == 'mtx'
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21 mkdir mtx
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22 #if $in.tenx.use == 'legacy_10x'
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23 && cp '$in.matrix' 'mtx/matrix.mtx'
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24 && cp '$in.tenx.genes' 'mtx/genes.tsv'
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25 && cp '$in.tenx.barcodes' 'mtx/barcodes.tsv'
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26 #else if $in.tenx.use == 'v3_10x'
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27 && cp '$in.matrix' 'mtx/matrix.mtx'
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28 && gzip 'mtx/matrix.mtx'
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29 && cp '$in.tenx.features' 'mtx/features.tsv'
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30 && gzip 'mtx/features.tsv'
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31 && cp '$in.tenx.barcodes' 'mtx/barcodes.tsv'
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32 && gzip 'mtx/barcodes.tsv'
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33 #end if
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34 &&
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35 #else if $in.adata_format == 'umi_tools'
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36 ## avoid gzipping in the inputdir
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37 gzip -c '$in.input' > umi_tools_input.gz
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38 &&
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39 #end if
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40
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41 @CMD@
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42 ]]></command>
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43 <configfiles>
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44 <configfile name="script_file"><![CDATA[
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45 @CMD_imports@
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46 #if $in.adata_format == 'loom'
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47 adata = ad.read_loom(
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48 '$in.input',
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49 sparse=$in.sparse,
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50 cleanup=$in.cleanup,
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51 X_name='$in.x_name',
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52 obs_names='$in.obs_names',
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53 var_names='$in.var_names')
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54
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55 #else if $in.adata_format == 'tabular'
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56 #set delimiter=$in.input.metadata.delimiter
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57 #if $delimiter != ','
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58 #set delimiter='\\t'
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59 #end if
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60 adata = ad.read_csv(
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61 '$in.input',
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62 delimiter='$delimiter',
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63 first_column_names=$in.first_column_names)
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64 ## convert into sparse matrix. Dense matrix needs large disk space and higher access times
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65 from scipy.sparse import csr_matrix
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66 adata.X = csr_matrix(adata.X)
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67
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68 #else if $in.adata_format == '10x_h5'
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69 import scanpy as sc
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70 adata = sc.read_10x_h5('$in.input')
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71
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72 #else if $in.adata_format == 'mtx'
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73 #if $in.tenx.use == 'no'
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74 adata = ad.read_mtx(filename='$in.matrix')
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75 #else
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76 import scanpy as sc
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77 adata = sc.read_10x_mtx(
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78 'mtx',
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79 var_names='$in.tenx.var_names',
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80 make_unique=$in.tenx.make_unique,
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81 cache=False,
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82 gex_only=$in.tenx.gex_only)
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83 #end if
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84
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85 #else if $in.adata_format == 'umi_tools'
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86 adata = ad.read_umi_tools('umi_tools_input.gz')
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87 #end if
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88 adata.write('anndata.h5ad', compression='gzip')
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89 print(adata)
0
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90 ]]></configfile>
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91 </configfiles>
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92 <inputs>
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93 <conditional name="in">
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94 <param name="adata_format" type="select" label="Create annadata from">
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95 <option value="loom">Loom data</option>
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96 <option value="tabular">Tabular, CSV, TSV</option>
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97 <option value="10x_h5">H5 format from Cell ranger or not</option>
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98 <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option>
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99 <option value="umi_tools">UMI tools count matrix</option>
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100 </param>
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101 <when value="loom">
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102 <param name="input" type="data" format="loom" label="Annotated data matrix"/>
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103 <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/>
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104 <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/>
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105 <param name="x_name" type="text" value="spliced" label="X_name"/>
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106 <param name="obs_names" type="text" value="CellID" label="obs_names"/>
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107 <param name="var_names" type="text" value="Gene" label="var_names"/>
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108 </when>
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109 <when value="tabular">
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110 <param name="input" type="data" format="tabular,csv,tsv" label="Annotated data matrix"/>
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111 <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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112 </when>
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113 <when value="10x_h5" >
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114 <param name="input" type="data" format="h5" label="Data matrix"/>
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115 </when>
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116 <when value="mtx">
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117 <param name="matrix" type="data" format="mtx" label="Matrix in Matrix Market format"/>
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118 <conditional name="tenx">
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119 <param name="use" type="select" label="Use 10x Genomics formatted mtx">
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120 <option value="no">No</option>
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121 <option value="legacy_10x">Output from Cell Ranger v2 or earlier versions</option>
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122 <option value="v3_10x">Output from Cell Ranger v3 or later versions</option>
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123 </param>
13
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124 <when value="no"/>
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125 <when value="legacy_10x">
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126 <param name="genes" type="data" format="tabular" label="2-column genes file with gene id and gene name"/>
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127 <expand macro="params_10x"/>
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128 </when>
13
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129 <when value="v3_10x">
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130 <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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131 <expand macro="params_10x"/>
0
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132 </when>
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133 </conditional>
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134 </when>
13
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135 <when value="umi_tools">
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136 <param name="input" type="data" format="tabular" label="condensed count matrix from UMI tools"/>
0
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137 </when>
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138 </conditional>
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139 </inputs>
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140 <outputs>
13
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141 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="Anndata import on ${on_string}"/>
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142 </outputs>
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143 <tests>
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144 <test expect_num_outputs="1">
0
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145 <conditional name="in">
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146 <param name="adata_format" value="loom"/>
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147 <param name="input" ftype="loom" value="krumsiek11.loom" />
0
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148 <param name="sparse" value="True"/>
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149 <param name="cleanup" value="False"/>
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150 <param name="x_name" value="spliced"/>
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151 <param name="obs_names" value="CellID" />
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152 <param name="var_names" value="Gene"/>
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153 </conditional>
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154 <assert_stdout>
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155 <has_text_matching expression="ad.read_loom"/>
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156 <has_text_matching expression="sparse=True"/>
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157 <has_text_matching expression="cleanup=False"/>
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158 <has_text_matching expression="X_name='spliced'"/>
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159 <has_text_matching expression="obs_names='CellID'"/>
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160 <has_text_matching expression="var_names='Gene'"/>
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161 </assert_stdout>
13
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162 <output name="anndata" ftype="h5ad">
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163 <assert_contents>
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164 <has_h5_keys keys="obs/cell_type"/>
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165 <has_h5_keys keys="obs/obs_names"/>
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166 <has_h5_keys keys="var/var_names"/>
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167 </assert_contents>
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168 </output>
0
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169 </test>
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170 <test expect_num_outputs="1">
0
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171 <conditional name="in">
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172 <param name="adata_format" value="tabular"/>
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173 <param name="input" value="adata.csv"/>
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174 <param name="first_column_names" value="true"/>
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175 </conditional>
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176 <assert_stdout>
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177 <has_text_matching expression="ad.read_csv"/>
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178 <has_text_matching expression="delimiter=','"/>
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179 <has_text_matching expression="first_column_names=True"/>
13
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
180 <has_text_matching expression="3 × 2"/>
0
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
181 </assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
182 </test>
3
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
183 <test expect_num_outputs="1">
0
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
184 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
185 <param name="adata_format" value="tabular"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
186 <param name="input" value="adata.tsv"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
187 <param name="first_column_names" value="true"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
188 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
189 <assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
190 <has_text_matching expression="ad.read_csv"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
191 <has_text_matching expression="delimiter='\\t'"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
192 <has_text_matching expression="first_column_names=True"/>
13
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
193 <has_text_matching expression="3 × 2"/>
0
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
194 </assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
195 </test>
7
cfc3f5a57dc6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
iuc
parents: 5
diff changeset
196 <test expect_num_outputs="1">
0
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
197 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
198 <param name="adata_format" value="mtx"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
199 <param name="matrix" value="matrix_10x_v1.2.0.mtx"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
200 <conditional name="tenx">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
201 <param name="use" value="no"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
202 </conditional>
13
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
203 </conditional>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
204 <assert_stdout>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
205 <has_text_matching expression="343 × 12"/>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
206 </assert_stdout>
0
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
207 </test>
12
93dd15e13e6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
iuc
parents: 11
diff changeset
208 <test expect_num_outputs="1">
0
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
209 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
210 <param name="adata_format" value="mtx"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
211 <param name="matrix" value="matrix_10x_v1.2.0.mtx"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
212 <conditional name="tenx">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
213 <param name="use" value="legacy_10x"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
214 <param name="genes" value="genes_10x_v1.2.0.tsv"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
215 <param name="barcodes" value="barcodes_10x_v1.2.0.tsv"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
216 <param name="var_names" value="gene_symbols"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
217 <param name="make_unique" value="true"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
218 <param name="gex_only" value="true"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
219 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
220 </conditional>
13
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
221 <assert_stdout>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
222 <has_text_matching expression="12 × 343"/>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
223 </assert_stdout>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
224 <output name="anndata" ftype="h5ad">
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
225 <assert_contents>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
226 <has_h5_keys keys="var/gene_ids"/>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
227 </assert_contents>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
228 </output>
0
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
229 </test>
12
93dd15e13e6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
iuc
parents: 11
diff changeset
230 <test expect_num_outputs="1">
0
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
231 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
232 <param name="adata_format" value="mtx"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
233 <param name="matrix" value="matrix_10x_v3.0.0.mtx"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
234 <conditional name="tenx">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
235 <param name="use" value="v3_10x"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
236 <param name="features" value="features_10x_v3.0.0.tsv"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
237 <param name="barcodes" value="barcodes_10x_v3.0.0.tsv"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
238 <param name="var_names" value="gene_symbols"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
239 <param name="make_unique" value="true"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
240 <param name="gex_only" value="true"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
241 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
242 </conditional>
13
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
243 <assert_stdout>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
244 <has_text_matching expression="1107 × 507"/>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
245 </assert_stdout>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
246 <output name="anndata" ftype="h5ad">
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
247 <assert_contents>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
248 <has_h5_keys keys="var/gene_ids"/>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
249 <has_h5_keys keys="var/feature_types"/>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
250 </assert_contents>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
251 </output>
12
93dd15e13e6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
iuc
parents: 11
diff changeset
252 </test>
3
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
253 <test expect_num_outputs="1">
0
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
254 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
255 <param name="adata_format" value="umi_tools"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
256 <param name="input" value="umi_tools.tsv"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
257 </conditional>
13
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
258 <assert_stdout>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
259 <has_text_matching expression="2 × 13"/>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
260 </assert_stdout>
3
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
261 </test>
5
32e547223c9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
iuc
parents: 3
diff changeset
262 <test expect_num_outputs="1"><!-- 10x h5 test -->
13
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
263 <conditional name="in">
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
264 <param name="adata_format" value="10x_h5"/>
d330b3082107 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 12
diff changeset
265 <param name="input" value="dropletutils_input.h5"/>
5
32e547223c9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
iuc
parents: 3
diff changeset
266 </conditional>
32e547223c9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
iuc
parents: 3
diff changeset
267 <output name="anndata">
32e547223c9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
iuc
parents: 3
diff changeset
268 <assert_contents>
32e547223c9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
iuc
parents: 3
diff changeset
269 <has_text text="HDF"/>
32e547223c9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
iuc
parents: 3
diff changeset
270 <has_text text="ENSG00000258728" />
32e547223c9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
iuc
parents: 3
diff changeset
271 <has_text text="GCGAGAAAGTTGTAGA" />
32e547223c9e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
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272 </assert_contents>
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273 </output>
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274 </test>
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275 </tests>
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276 <help><![CDATA[
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277
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278 **What it does**
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279
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280 This tool creates an AnnData from several input types:
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281
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282 - Loom (`read_loom method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_loom.html>`__)
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283 - Tabular (`read_csv method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_csv.html>`__)
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284 - Matrix Market (mtx), from Cell ranger or not (`read_mtx method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_mtx.html>`__)
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285 - UMI tools (`read_umi_tools method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_umi_tools.html>`__)
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286
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287 @HELP@
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288 ]]></help>
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289 <expand macro="citations"/>
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290 </tool>