Mercurial > repos > iuc > modify_loom

annotate modify_loom.xml @ 9:6e7355ea9228 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit c1d84c1850c53deccc384de3960d2cec37bb2869
author iuc
date Fri, 08 Nov 2024 21:56:47 +0000
parents e4847e917c2b
children
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e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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1 <tool id="modify_loom" name="Loom operations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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2 <description>Manipulate, export and import loom data</description>
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3 <macros>
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4 <import>macros.xml</import>
540a34575492 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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5 </macros>
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6e7355ea9228 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit c1d84c1850c53deccc384de3960d2cec37bb2869
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6 <expand macro="bio_tools"/>
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e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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7 <expand macro="requirements">
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8 <requirement type="package" version="1.26.4">numpy</requirement><!-- loompy seems to adapt to numpy 2.x. Remove this in the next update -->
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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9 </expand>
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10 <expand macro="version_command"/>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #if $operation.to_perform == 'manipulate'
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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13 cp '${operation.loom}' converted.loom &&
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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14 python '$__tool_directory__/modify_loom.py' -f 'converted.loom'
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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15 #if $operation.which_add.add_type == "cols":
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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16 -a cols -c '${operation.which_add.cols}'
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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17 #else if $operation.which_add.add_type == "rows":
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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18 -a rows -r '${operation.which_add.rows}'
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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19 #else if $operation.which_add.add_type == "layers":
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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20 -a layers -l '${operation.which_add.layers}'
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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21 #end if
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23 #else if $operation.to_perform == 'export'
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24 mkdir ./output &&
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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25 mkdir ./attributes &&
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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26 python '$__tool_directory__/loompy_to_tsv.py' -f '$operation.loom'
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27
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28 #else if $operation.to_perform == 'import'
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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29 #if $operation.from.file_type == 'ad'
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30 @CMD@
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31 #else if $operation.from.file_type == 'tab'
e4847e917c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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32 python '$__tool_directory__/tsv_to_loompy.py'
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33 -c '${operation.coldata}'
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34 -r '${operation.rowdata}'
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35 -f '${operation.mainmatrix}'
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36 #if $operation.other_files
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37 '${operation.other_files}'
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38 #end if
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39 #end if
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40 #end if
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41 ]]></command>
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42 <configfiles>
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43 <configfile name="script_file"><![CDATA[
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44 @CMD_imports@
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45 #if $operation.to_perform == 'import'
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46 #if $operation.from.file_type == 'ad'
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47 adata = ad.read_h5ad('$operation.anndata')
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48 adata.write_loom('converted.loom')
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49 #end if
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50 #end if
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51 ]]></configfile>
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52 </configfiles>
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53 <inputs>
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54 <conditional name="operation">
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55 <param name="to_perform" type="select" label="Operation to perform on loom data">
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56 <option value="manipulate">Manipulate loom data</option>
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57 <option value="export">Export loom layers and attributes</option>
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58 <option value="import">Import loom from an anndata or tabular files</option>
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59 </param>
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60 <when value="manipulate">
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61 <param name="loom" type="data" format="loom" label="Loom file"/>
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62 <conditional name="which_add">
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63 <param name="add_type" type="select" label="Select data attribute to add to loom">
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64 <option value="cols">Columns</option>
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65 <option value="rows">Rows</option>
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66 <option value="layers">Layers</option>
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67 </param>
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68 <when value="cols">
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69 <param name="cols" type="data" format="tabular" label="Column file of same dimensions as existing file"/>
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70 </when>
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71 <when value="rows">
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72 <param name="rows" type="data" format="tabular" label="Row file of same dimensions as existing file"/>
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73 </when>
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74 <when value="layers">
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75 <param name="layers" type="data" multiple="true" format="tabular" label="Layer file(s) of same dimensions as existing file"/>
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76 </when>
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77 </conditional>
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78 </when>
8
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79 <when value="export">
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80 <param name="loom" type="data" format="loom" label="Loom file"/>
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81 </when>
8
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82 <when value="import">
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83 <conditional name="from">
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84 <param name="file_type" type="select" label="Create loom file from">
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85 <option value="ad">an anndata object</option>
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86 <option value="tab">from tabular files of matrix and row and column attributes</option>
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87 </param>
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88 <when value="ad">
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89 <param name="anndata" type="data" format="h5ad" label="Anndata file"/>
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90 </when>
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91 <when value="tab">
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92 <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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93 <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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94 <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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95 <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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96 </when>
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97 </conditional>
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98
0
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99 </when>
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100 </conditional>
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101 </inputs>
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102 <outputs>
8
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103 <data name="loomout" format="loom" from_work_dir='converted.loom' label="${tool.name} (${operation.to_perform}) on ${on_string} Loom file">
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104 <filter>operation['to_perform'] == 'manipulate' or operation['to_perform'] == 'import'</filter>
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105 </data>
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106 <collection name="layer_tsvs" type="list" label="Layer matrices" >
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107 <filter>operation['to_perform'] == 'export'</filter>
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108 <discover_datasets pattern="__designation__" format="tabular" directory="output" visible="false" />
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109 </collection>
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110 <collection name="attribute_tsvs" type="list" label="Attribute matrices" >
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111 <filter>operation['to_perform'] == 'export'</filter>
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112 <discover_datasets pattern="__designation__" format="tabular" directory="attributes" visible="false" />
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113 </collection>
0
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114 </outputs>
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115 <tests>
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116 <test expect_num_outputs="1">
8
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117 <conditional name="operation">
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118 <param name="to_perform" value="manipulate"/>
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119 <param name="loom" value="addtest.loom"/>
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120 <conditional name="which_add">
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121 <param name="add_type" value="cols"/>
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122 <param name="cols" value="cols.tsv"/>
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123 </conditional>
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124 </conditional>
0
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125 <output name="loomout" value="addloomout1.loom" ftype="loom" compare="sim_size"/>
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126 </test>
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127 <test expect_num_outputs="1">
8
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128 <conditional name="operation">
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129 <param name="to_perform" value="manipulate"/>
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130 <param name="loom" value="addtest.loom"/>
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131 <conditional name="which_add">
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132 <param name="add_type" value="rows"/>
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133 <param name="rows" value="rows.tsv"/>
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134 </conditional>
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135 </conditional>
0
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136 <output name="loomout" value="addloomout2.loom" ftype="loom" compare="sim_size"/>
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137 </test>
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138 <test expect_num_outputs="1">
8
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139 <conditional name="operation">
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140 <param name="to_perform" value="manipulate"/>
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141 <param name="loom" value="addtest.loom"/>
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142 <conditional name="which_add">
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143 <param name="add_type" value="layers"/>
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144 <param name="layers" value="addlayer1.tsv"/>
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145 </conditional>
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146 </conditional>
0
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147 <output name="loomout" value="addloomout3.loom" ftype="loom" compare="sim_size"/>
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148 </test>
8
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149 <test expect_num_outputs="2">
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150 <conditional name="operation">
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151 <param name="to_perform" value="export"/>
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152 <param name="loom" value="loomtest.loom"/>
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153 </conditional>
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154 <output_collection name="layer_tsvs" type="list">
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155 <element name="extralayer.tsv" value="secondlayer.tsv" ftype="tabular"/>
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156 <element name="mainmatrix.tsv" value="firstlayer.tsv" ftype="tabular"/>
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157 <element name="thirdlayer.tsv" value="finallayer.tsv" ftype="tabular"/>
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158 </output_collection>
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159 <output_collection name="attribute_tsvs" type="list">
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160 <element name="col_attr.tsv" value="cols.tsv" ftype="tabular"/>
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161 <element name="row_attr.tsv" value="rows.tsv" ftype="tabular"/>
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162 </output_collection>
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163 </test>
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164 <test expect_num_outputs="1">
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165 <conditional name="operation">
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166 <param name="to_perform" value="import"/>
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167 <conditional name="from">
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168 <param name="file_type" value="ad"/>
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169 <param name="anndata" value="krumsiek11.h5ad"/>
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170 </conditional>
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171 </conditional>
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172 <assert_stdout>
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173 <has_text_matching expression="adata.write_loom"/>
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174 </assert_stdout>
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175 <output name="loomout" value="export.krumsiek11.loom" ftype="loom" compare="sim_size"/>
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176 </test>
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177 <test expect_num_outputs="1">
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178 <conditional name="operation">
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179 <param name="to_perform" value="import"/>
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180 <conditional name="from">
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181 <param name="file_type" value="tab"/>
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182 <param name="mainmatrix" value="firstlayer.tsv"/>
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183 <param name="other_files" value="secondlayer.tsv"/>
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184 <param name="coldata" value="cols.tsv"/>
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185 <param name="rowdata" value="rows.tsv"/>
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186 </conditional>
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187 </conditional>
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188 <output name="loomout" value="converted.loom.test" ftype="loom" compare="sim_size"/>
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189 </test>
0
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190 </tests>
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191 <help><![CDATA[
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192 This tool allows the user to modify an existing loom data file by adding column attributes, row attributes or additional layers via tsv files.
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193 ]]></help>
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194 <citations>
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195 <citation type="bibtex">@UNPUBLISHED{Linnarsson2016,
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196 author = "Linnarsson lab"
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197 title = "Loompy"
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198 year = "2013"
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199 note = "https://github.com/linnarsson-lab/loompy"}
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200 </citation>
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201 </citations>
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202 </tool>