Mercurial > repos > iuc > anndata_import

annotate import.xml @ 12:93dd15e13e6a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
author iuc
date Sun, 12 Nov 2023 16:42:57 +0000
parents fb9e030ffae4
children d330b3082107
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1 <tool id="anndata_import" name="Import Anndata and loom" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
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2 <description>from different format</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"/>
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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="1.9.6">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 $hd5_format.filetype == 'anndata'
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21 #if $hd5_format.in.adata_format == 'mtx'
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22 mkdir mtx
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23 #if $hd5_format.in.tenx.use == 'legacy_10x'
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24 && cp '$hd5_format.in.matrix' 'mtx/matrix.mtx'
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25 && cp '$hd5_format.in.tenx.genes' 'mtx/genes.tsv'
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26 && cp '$hd5_format.in.tenx.barcodes' 'mtx/barcodes.tsv'
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27 #else if $hd5_format.in.tenx.use == 'v3_10x'
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28 && cp '$hd5_format.in.matrix' 'mtx/matrix.mtx'
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29 && gzip 'mtx/matrix.mtx'
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30 && cp '$hd5_format.in.tenx.features' 'mtx/features.tsv'
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31 && gzip 'mtx/features.tsv'
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32 && cp '$hd5_format.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 $hd5_format.in.adata_format == 'umi_tools'
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37 ## avoid gzipping in the inputdir
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38 gzip -c '$hd5_format.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
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44 #if $hd5_format.in.adata_format == 'mtx'
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45 && rm -rf mtx
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46 #end if
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47
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48 #else:
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49 python '$__tool_directory__/tsv_to_loompy.py'
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50 -c '${hd5_format.coldata}'
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51 -r '${hd5_format.rowdata}'
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52 -f '${hd5_format.mainmatrix}'
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53 #if $hd5_format.other_files:
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54 '${hd5_format.other_files}'
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55 #end if
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56 #end if
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57 ]]></command>
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58 <configfiles>
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59 <configfile name="script_file"><![CDATA[
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60 @CMD_imports@
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61 #if $hd5_format.filetype == 'anndata'
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62 #if $hd5_format.in.adata_format == 'loom'
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63 adata = ad.read_loom(
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64 '$hd5_format.in.input',
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65 sparse=$hd5_format.in.sparse,
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66 cleanup=$hd5_format.in.cleanup,
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67 X_name='$hd5_format.in.x_name',
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68 obs_names='$hd5_format.in.obs_names',
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69 var_names='$hd5_format.in.var_names')
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70
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71 #else if $hd5_format.in.adata_format == 'tabular'
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72 #set delimiter=$hd5_format.in.input.metadata.delimiter
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73 #if $delimiter != ','
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74 #set delimiter='\\t'
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75 #end if
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76 adata = ad.read_csv(
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77 '$hd5_format.in.input',
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78 delimiter='$delimiter',
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79 first_column_names=$hd5_format.in.first_column_names)
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80
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81 #else if $hd5_format.in.adata_format == '10x_h5'
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82 import scanpy as sc
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83 adata = sc.read_10x_h5('$hd5_format.in.input')
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84
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85 #else if $hd5_format.in.adata_format == 'mtx'
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86 #if $hd5_format.in.tenx.use == 'no'
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87 adata = ad.read_mtx(filename='$hd5_format.in.matrix')
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88 #else
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89 import scanpy as sc
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90 adata = sc.read_10x_mtx(
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91 'mtx',
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92 var_names='$hd5_format.in.tenx.var_names',
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93 make_unique=$hd5_format.in.tenx.make_unique,
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94 cache=False,
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95 gex_only=$hd5_format.in.tenx.gex_only)
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96 #end if
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97
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98 #else if $hd5_format.in.adata_format == 'umi_tools'
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99 adata = ad.read_umi_tools('umi_tools_input.gz')
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100 #end if
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101 adata.write('anndata.h5ad')
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102 #end if
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103 ]]></configfile>
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104 </configfiles>
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105 <inputs>
3
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106 <conditional name="hd5_format">
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107 <param name="filetype" type="select" label="hd5 format to be created">
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108 <option value="anndata" selected="true">Anndata file</option>
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109 <option value="loom">Loom file</option>
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110 </param>
3
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111 <when value="anndata">
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112 <conditional name="in">
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113 <param name="adata_format" type="select" label="Format for the annotated data matrix">
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114 <option value="loom">Loom</option>
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115 <option value="tabular">Tabular, CSV, TSV</option>
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116 <option value="10x_h5">H5 format from Cell ranger or not</option>
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117 <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option>
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118 <option value="umi_tools">UMI tools</option>
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119 </param>
3
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120 <when value="loom">
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121 <param name="input" type="data" format="loom" label="Annotated data matrix"/>
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122 <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/>
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123 <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/>
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124 <param name="x_name" type="text" value="spliced" label="X_name"/>
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125 <param name="obs_names" type="text" value="CellID" label="obs_names"/>
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126 <param name="var_names" type="text" value="Gene" label="var_names"/>
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127 </when>
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128 <when value="tabular">
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129 <param name="input" type="data" format="tabular,csv,tsv" label="Annotated data matrix"/>
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130 <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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131 </when>
5
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132 <when value="10x_h5" >
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133 <param name="input" type="data" format="h5" label="Data matrix"/>
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134 </when>
3
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135 <when value="mtx">
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136 <param name="matrix" type="data" format="mtx" label="Matrix"/>
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137 <conditional name="tenx">
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138 <param name="use" type="select" label="Use 10x Genomics formatted mtx">
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139 <option value="no">No</option>
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140 <option value="legacy_10x">Output from Cell Ranger v2 or earlier versions</option>
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141 <option value="v3_10x">Output from Cell Ranger v3 or later versions</option>
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142 </param>
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143 <when value="no"/>
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144 <when value="legacy_10x">
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145 <param name="genes" type="data" format="tabular" label="Genes"/>
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146 <expand macro="params_10x"/>
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147 </when>
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148 <when value="v3_10x">
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149 <param name="features" type="data" format="tabular" label="Features"/>
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150 <expand macro="params_10x"/>
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151 </when>
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152 </conditional>
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153 </when>
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154 <when value="umi_tools">
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155 <param name="input" type="data" format="tabular" label="condensed count matrix from UMI tools"/>
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156 </when>
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157 </conditional>
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158 </when>
3
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159 <when value="loom">
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160 <param name="mainmatrix" type="data" format="tabular" label="File for main layer of loom file." help="All subsequent tsv must be the same dimensions as this file. When converted back to tsv using hd5 export, this will be labeled as 'mainmatrix.tsv'"/>
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161 <param name="other_files" type="data" format="tabular" multiple="true" optional="true" label="Add layers" help="Adds layers of same dimension to the loom file. When converted to tsv using hd5 export, these layers will retain their names."/>
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162 <param name="coldata" type="data" format="tabular" label="Tsv of column data." help="First row is column attributes, subsequent are values."/>
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163 <param name="rowdata" type="data" format="tabular" label="Tsv of row data." help="First row is row attributes, subsequent are values."/>
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164 </when>
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165 </conditional>
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166 </inputs>
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167 <outputs>
3
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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 <filter>hd5_format['filetype'] == 'anndata'</filter>
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
170 </data>
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
171 <data name="loomdata" format="loom" from_work_dir="converted.loom" label="Loom import on ${on_string}">
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
172 <filter>hd5_format['filetype'] == 'loom'</filter>
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
173 </data>
0
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
174 </outputs>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
175 <tests>
3
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
176 <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
177 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
178 <param name="adata_format" value="loom"/>
7
cfc3f5a57dc6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
iuc
parents: 5
diff changeset
179 <param name="input" ftype="loom" value="krumsiek11.loom" />
0
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
180 <param name="sparse" value="True"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
181 <param name="cleanup" value="False"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
182 <param name="x_name" value="spliced"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
183 <param name="obs_names" value="CellID" />
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
184 <param name="var_names" value="Gene"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
185 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
186 <assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
187 <has_text_matching expression="ad.read_loom"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
188 <has_text_matching expression="sparse=True"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
189 <has_text_matching expression="cleanup=False"/>
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="X_name='spliced'"/>
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="obs_names='CellID'"/>
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="var_names='Gene'"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
193 </assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
194 <output name="anndata" value="import.loom.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
195 </test>
3
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
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="tabular"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
199 <param name="input" value="adata.csv"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
200 <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
201 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
202 <assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
203 <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
204 <has_text_matching expression="delimiter=','"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
205 <has_text_matching expression="first_column_names=True"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
206 </assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
207 <output name="anndata" value="import.csv.h5ad" ftype="h5ad" compare="sim_size"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
208 </test>
3
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
209 <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
210 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
211 <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
212 <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
213 <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
214 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
215 <assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
216 <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
217 <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
218 <has_text_matching expression="first_column_names=True"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
219 </assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
220 <output name="anndata" value="import.tsv.h5ad" ftype="h5ad" compare="sim_size"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
221 </test>
7
cfc3f5a57dc6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
iuc
parents: 5
diff changeset
222 <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
223 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
224 <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
225 <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
226 <conditional name="tenx">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
227 <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
228 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
229 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
230 <output name="anndata" value="import.mtx.no_10x.h5ad" ftype="h5ad" compare="sim_size"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
231 </test>
12
93dd15e13e6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
iuc
parents: 11
diff changeset
232 <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
233 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
234 <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
235 <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
236 <conditional name="tenx">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
237 <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
238 <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
239 <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
240 <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
241 <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
242 <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
243 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
244 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
245 <output name="anndata" value="import.mtx.legacy_10x.h5ad" ftype="h5ad" compare="sim_size"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
246 </test>
12
93dd15e13e6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
iuc
parents: 11
diff changeset
247 <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
248 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
249 <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
250 <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
251 <conditional name="tenx">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
252 <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
253 <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
254 <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
255 <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
256 <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
257 <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
258 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
259 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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260 <output name="anndata" value="import.mtx.v3_10x.h5ad" ftype="h5ad" compare="sim_size"/>
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261 </test>
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262 <test expect_num_outputs="1">
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263 <param name="filetype" value="anndata"/>
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264 <conditional name="in">
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265 <param name="adata_format" value="umi_tools"/>
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266 <param name="input" value="umi_tools.tsv"/>
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267 </conditional>
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268 <output name="anndata" value="import.umi_tools.h5ad" ftype="h5ad" compare="sim_size"/>
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269 </test>
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270 <test expect_num_outputs="1">
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271 <param name="filetype" value="loom"/>
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272 <param name="mainmatrix" value="firstlayer.tsv"/>
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273 <param name="other_files" value="secondlayer.tsv"/>
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274 <param name="coldata" value="cols.tsv"/>
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275 <param name="rowdata" value="rows.tsv"/>
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276 <output name="loomdata" value="converted.loom.test" ftype="loom" compare="sim_size"/>
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277 </test>
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278 <test expect_num_outputs="1"><!-- 10x h5 test -->
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279 <conditional name="hd5_format">
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280 <param name="filetype" value="anndata"/>
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281 <conditional name="in">
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282 <param name="adata_format" value="10x_h5"/>
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283 <param name="input" value="dropletutils_input.h5"/>
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284 </conditional>
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285 </conditional>
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286 <output name="anndata">
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287 <assert_contents>
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288 <has_text text="HDF"/>
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289 <has_text text="ENSG00000258728" />
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290 <has_text text="GCGAGAAAGTTGTAGA" />
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291 </assert_contents>
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292 </output>
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293 </test>
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294 </tests>
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295 <help><![CDATA[
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296
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297 **What it does**
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298
3
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299 This tool creates an AnnData or loom dataset from several input types:
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300
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301 - Loom (`read_loom method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_loom.html>`__)
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302 - Tabular (`read_csv method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_csv.html>`__)
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303 - 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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304 - UMI tools (`read_umi_tools method <https://anndata.readthedocs.io/en/latest/generated/anndata.read_umi_tools.html>`__)
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305
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306 @HELP@
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307 ]]></help>
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308 <expand macro="citations"/>
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309 </tool>