Mercurial > repos > iuc > anndata_import

annotate import.xml @ 7:cfc3f5a57dc6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
author iuc
date Thu, 07 Jan 2021 23:28:53 +0000
parents 32e547223c9e
children ae1e5d9d8972
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7
cfc3f5a57dc6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
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1 <tool id="anndata_import" name="Import Anndata and loom" version="@VERSION@+@GALAXY_VERSION@" profile="20.09">
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2 <description>from different format</description>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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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'?"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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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="1.4.4.post1">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
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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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 '$hd5_format.in.tenx.genes' 'mtx/genes.tsv'
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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26 && cp '$hd5_format.in.tenx.barcodes' 'mtx/barcodes.tsv'
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27 #else if $hd5_format.in.tenx.use == 'v3_10x'
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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28 && cp '$hd5_format.in.matrix' 'mtx/matrix.mtx'
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29 && gzip 'mtx/matrix.mtx'
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30 && cp '$hd5_format.in.tenx.features' 'mtx/features.tsv'
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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31 && gzip 'mtx/features.tsv'
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32 && cp '$hd5_format.in.tenx.barcodes' 'mtx/barcodes.tsv'
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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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 $hd5_format.in.adata_format == 'umi_tools'
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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37 gzip '$hd5_format.in.input'
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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
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43 #if $hd5_format.in.adata_format == 'mtx'
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44 && rm -rf mtx
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45 #end if
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46
3
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47 #else:
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48 python '$__tool_directory__/tsv_to_loompy.py'
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49 -c '${hd5_format.coldata}'
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50 -r '${hd5_format.rowdata}'
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51 -f '${hd5_format.mainmatrix}'
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52 #if $hd5_format.other_files:
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53 '${hd5_format.other_files}'
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54 #end if
0
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55 #end if
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56 ]]></command>
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57 <configfiles>
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58 <configfile name="script_file"><![CDATA[
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59 @CMD_imports@
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60 #if $hd5_format.filetype == 'anndata'
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61 #if $hd5_format.in.adata_format == 'loom'
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62 adata = ad.read_loom(
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63 '$hd5_format.in.input',
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64 sparse=$hd5_format.in.sparse,
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65 cleanup=$hd5_format.in.cleanup,
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66 X_name='$hd5_format.in.x_name',
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67 obs_names='$hd5_format.in.obs_names',
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68 var_names='$hd5_format.in.var_names')
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69
7
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70 #else if $hd5_format.in.adata_format == 'tabular'
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71 #set delimiter=$hd5_format.in.input.metadata.delimiter
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72 #if $delimiter != ','
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73 #set delimiter='\\t'
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74 #end if
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75 adata = ad.read_csv(
3
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76 '$hd5_format.in.input',
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77 delimiter='$delimiter',
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78 first_column_names=$hd5_format.in.first_column_names)
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79
7
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80 #else if $hd5_format.in.adata_format == '10x_h5'
5
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81 import scanpy as sc
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82 adata = sc.read_10x_h5('$hd5_format.in.input')
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83
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84 #else if $hd5_format.in.adata_format == 'mtx'
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85 #if $hd5_format.in.tenx.use == 'no'
3
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86 adata = ad.read_mtx(filename='$hd5_format.in.matrix')
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87 #else
0
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88 import scanpy as sc
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89 adata = sc.read_10x_mtx(
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90 'mtx',
3
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91 var_names='$hd5_format.in.tenx.var_names',
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92 make_unique=$hd5_format.in.tenx.make_unique,
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93 cache=False,
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94 gex_only=$hd5_format.in.tenx.gex_only)
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95 #end if
0
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96
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97 #else if $hd5_format.in.adata_format == 'umi_tools'
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98 adata = ad.read_umi_tools('${hd5_format.in.input}.gz')
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99 #end if
0
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100 adata.write('anndata.h5ad')
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101 #end if
0
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102 ]]></configfile>
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103 </configfiles>
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104 <inputs>
3
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105 <conditional name="hd5_format">
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106 <param name="filetype" type="select" label="hd5 format to be created">
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107 <option value="anndata" selected="true">Anndata file</option>
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108 <option value="loom">Loom file</option>
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109 </param>
3
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110 <when value="anndata">
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111 <conditional name="in">
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112 <param name="adata_format" type="select" label="Format for the annotated data matrix">
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113 <option value="loom">Loom</option>
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114 <option value="tabular">Tabular, CSV, TSV</option>
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115 <option value="10x_h5">H5 format from Cell ranger or not</option>
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116 <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option>
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117 <option value="umi_tools">UMI tools</option>
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118 </param>
3
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119 <when value="loom">
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120 <param name="input" type="data" format="loom" label="Annotated data matrix"/>
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121 <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/>
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122 <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/>
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123 <param name="x_name" type="text" value="spliced" label="X_name"/>
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124 <param name="obs_names" type="text" value="CellID" label="obs_names"/>
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125 <param name="var_names" type="text" value="Gene" label="var_names"/>
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126 </when>
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127 <when value="tabular">
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128 <param name="input" type="data" format="tabular,csv,tsv" label="Annotated data matrix"/>
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129 <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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130 </when>
5
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131 <when value="10x_h5" >
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132 <param name="input" type="data" format="h5" label="Data matrix"/>
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133 </when>
3
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134 <when value="mtx">
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135 <param name="matrix" type="data" format="mtx" label="Matrix"/>
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136 <conditional name="tenx">
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137 <param name="use" type="select" label="Use 10x Genomics formatted mtx">
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138 <option value="no">No</option>
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139 <option value="legacy_10x">Output from Cell Ranger v2 or earlier versions</option>
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140 <option value="v3_10x">Output from Cell Ranger v3 or later versions</option>
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141 </param>
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142 <when value="no"/>
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143 <when value="legacy_10x">
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144 <param name="genes" type="data" format="tabular" label="Genes"/>
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145 <expand macro="params_10x"/>
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146 </when>
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147 <when value="v3_10x">
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148 <param name="features" type="data" format="tabular" label="Features"/>
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149 <expand macro="params_10x"/>
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150 </when>
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151 </conditional>
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152 </when>
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153 <when value="umi_tools">
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154 <param name="input" type="data" format="tabular" label="condensed count matrix from UMI tools"/>
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155 </when>
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156 </conditional>
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157 </when>
3
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158 <when value="loom">
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159 <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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160 <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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161 <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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162 <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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163 </when>
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164 </conditional>
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165 </inputs>
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166 <outputs>
3
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167 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="Anndata import on ${on_string}">
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168 <filter>hd5_format['filetype'] == 'anndata'</filter>
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169 </data>
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diff changeset
170 <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
171 <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
172 </data>
0
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
173 </outputs>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
174 <tests>
3
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
175 <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
176 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
177 <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
178 <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
179 <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
180 <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
181 <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
182 <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
183 <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
184 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
185 <assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
186 <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
187 <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
188 <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
189 <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
190 <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
191 <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
192 </assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
193 <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
194 </test>
3
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
diff changeset
195 <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
196 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
197 <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
198 <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
199 <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
200 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
201 <assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
202 <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
203 <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
204 <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
205 </assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
206 <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
207 </test>
3
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
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="tabular"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
211 <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
212 <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
213 </conditional>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
214 <assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
215 <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
216 <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
217 <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
218 </assert_stdout>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
219 <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
220 </test>
7
cfc3f5a57dc6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
iuc
parents: 5
diff changeset
221 <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
222 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
223 <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
224 <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
225 <conditional name="tenx">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
226 <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
227 </conditional>
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 <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
230 </test>
7
cfc3f5a57dc6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
iuc
parents: 5
diff changeset
231 <!--<test>
0
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
232 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
233 <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
234 <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
235 <conditional name="tenx">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
236 <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
237 <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
238 <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
239 <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
240 <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
241 <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
242 </conditional>
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 <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
245 </test>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
246 <test>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
247 <conditional name="in">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
248 <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
249 <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
250 <conditional name="tenx">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff changeset
251 <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
252 <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
253 <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
254 <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
255 <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
256 <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
257 </conditional>
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 <output name="anndata" value="import.mtx.v3_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
260 </test>!-->
3
b5c7ba11401d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents: 2
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261 <test expect_num_outputs="1">
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262 <param name="filetype" value="anndata"/>
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263 <conditional name="in">
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264 <param name="adata_format" value="umi_tools"/>
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265 <param name="input" value="umi_tools.tsv"/>
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266 </conditional>
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267 <output name="anndata" value="import.umi_tools.h5ad" ftype="h5ad" compare="sim_size"/>
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268 </test>
3
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269 <test expect_num_outputs="1">
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270 <param name="filetype" value="loom"/>
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271 <param name="mainmatrix" value="firstlayer.tsv"/>
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272 <param name="other_files" value="secondlayer.tsv"/>
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273 <param name="coldata" value="cols.tsv"/>
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274 <param name="rowdata" value="rows.tsv"/>
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275 <output name="loomdata" value="converted.loom.test" ftype="loom" compare="sim_size"/>
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276 </test>
5
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277 <test expect_num_outputs="1"><!-- 10x h5 test -->
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278 <conditional name="hd5_format">
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279 <param name="filetype" value="anndata"/>
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280 <conditional name="in">
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281 <param name="adata_format" value="10x_h5"/>
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282 <param name="input" value="dropletutils_input.h5"/>
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283 </conditional>
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284 </conditional>
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285 <output name="anndata">
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286 <assert_contents>
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287 <has_text text="HDF"/>
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288 <has_text text="ENSG00000258728" />
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289 <has_text text="GCGAGAAAGTTGTAGA" />
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290 </assert_contents>
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291 </output>
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292 </test>
0
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293 </tests>
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294 <help><![CDATA[
7
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295
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296 **What it does**
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297
3
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298 This tool creates an AnnData or loom dataset from several input types:
0
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299
3
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300 - Loom (`read_loom method <https://anndata.readthedocs.io/en/latest/anndata.read_loom.html>`__)
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301 - Tabular (`read_csv method <https://anndata.readthedocs.io/en/latest/anndata.read_csv.html>`__)
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302 - Matrix Market (mtx), from Cell ranger or not (`read_mtx method <https://anndata.readthedocs.io/en/latest/anndata.read_mtx.html>`__)
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303 - UMI tools (`read_umi_tools method <https://anndata.readthedocs.io/en/latest/anndata.read_umi_tools.html>`__)
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304
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305 @HELP@
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306 ]]></help>
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307 <expand macro="citations"/>
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308 </tool>