annotate seurat_macros.xml @ 6:07fc9f4841b3 draft default tip

planemo upload commit 0264c359f1d638bbbbab515a3502231f679cdcf6
author ebi-gxa
date Sat, 02 Mar 2024 10:42:01 +0000
parents 3dd20b758756
children
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1 <?xml version="1.0"?>
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2 <macros>
6
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3 <token name="@VERSION@">4.0.0</token>
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4 <token name="@SEURAT_VERSION@">4.0.4</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">seurat-scripts</requirement>
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8 </requirements>
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9 </xml>
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10 <xml name="version">
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11 <version_command><![CDATA[
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12 echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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13 ]]></version_command>
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14 </xml>
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15
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16 <xml name="input_object_params" token_multiple="False" token_varname="input" token_optional="False">
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17 <conditional name="@VARNAME@" label="Input format">
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18 <param type="select" name="format" label="Choose the format of the @VARNAME@" help="Seurat RDS, Seurat H5, Single Cell Experiment RDS, Loom or AnnData">
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19 <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
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20 <option value="loom">Loom</option>
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21 <option value="h5seurat">Seurat HDF5</option>
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22 <option value="anndata">AnnData</option>
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23 <option value="rds_sce">RDS with a Single Cell Experiment object</option>
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24 </param>
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25 <when value="anndata">
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26 <param type="data" name="anndata_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="AnnData file" help="Select AnnData files for @VARNAME@" format="h5,h5ad"/>
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27 </when>
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28 <when value="loom">
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29 <param type="data" name="loom_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="Loom file" help="Select Loom file(s) for @VARNAME@" format="h5,h5loom"/>
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30 </when>
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31 <when value="rds_seurat">
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32 <param type="data" name="rds_seurat_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="RDS file" help="Select RDS file(s) with Seurat object for @VARNAME@" format="rdata"/>
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33 </when>
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34 <when value="rds_sce">
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35 <param type="data" name="rds_sce_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="RDS file" help="Select RDS file(s) with Single Cell Experiment object for @VARNAME@" format="rdata"/>
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36 </when>
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37 <when value="h5seurat">
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38 <param type="data" name="h5seurat_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="Seurat HDF5" help="Select Seurat HDF5 file(s) for @VARNAME" format="h5"/>
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39 </when>
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40 </conditional>
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41 </xml>
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42
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43 <token name="@INPUT_OBJ_PREAMBLE@">
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44 #if $input.format == 'loom'
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45 ln -s '$input.loom_file' input.loom;
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46 #else if $input.format == 'h5seurat'
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47 ln -s '$input.h5seurat_file' input.h5seurat;
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48 #else if $input.format == 'anndata'
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49 ## it complains when using links for AnnData...
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50 cp '$input.anndata_file' input.h5ad;
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51 #end if
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52 </token>
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53
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54 <token name="@INPUT_OBJECT@">
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55 #if $input.format == "anndata"
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56 --input-object-file input.h5ad --input-format anndata
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57 #else if $input.format == "loom"
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58 --input-object-file input.loom --input-format loom
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59 #else if $input.format == "rds_seurat"
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60 --input-object-file '$input.rds_seurat_file' --input-format seurat
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61 #else if $input.format == "rds_sce"
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62 --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment
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63 #else if $input.format == "h5seurat"
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64 --input-object-file input.h5seurat --input-format h5seurat
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65 #end if
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66 </token>
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67
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68 <token name="@QUERY_OBJ_PREAMBLE@">
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69 #if $query.format == 'loom'
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70 ln -s '$query.loom_file' query.loom;
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71 #else if $query.format == 'h5seurat'
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72 ln -s '$query.h5seurat_file' query.h5seurat;
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73 #else if $query.format == 'anndata'
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74 ## it complains when using links for AnnData...
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75 cp '$query.anndata_file' query.h5ad;
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76 #end if
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77 </token>
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78
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79 <token name="@QUERY_OBJECT@">
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80 #if $query.format == "anndata"
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81 --query-object-file query.h5ad --query-format anndata
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82 #else if $query.format == "loom"
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83 --query-object-file query.loom --query-format loom
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84 #else if $query.format == "rds_seurat"
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85 --query-object-file '$query.rds_seurat_file' --query-format seurat
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86 #else if $query.format == "rds_sce"
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87 --query-object-file '$query.rds_sce_file' --query-format singlecellexperiment
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88 #else if $query.format == "h5seurat"
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89 --query-object-file query.h5seurat --query-format h5seurat
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90 #end if
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91 </token>
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92
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93 <token name="@ANCHORS_OBJ_PREAMBLE@">
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94 #if $anchors.format == 'loom'
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95 ln -s '$anchors.loom_file' anchors.loom;
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96 #else if $anchors.format == 'h5seurat'
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97 ln -s '$anchors.h5seurat_file' anchors.h5seurat;
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98 #else if $anchors.format == 'anndata'
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99 ## it complains when using links for AnnData...
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100 cp '$anchors.anndata_file' anchors.h5ad;
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101 #end if
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102 </token>
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103
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104 <token name="@ANCHORS_OBJECT@">
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105 #if $anchors.format == "anndata"
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106 --anchors-object-file anchors.h5ad --anchors-format anndata
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107 #else if $anchors.format == "loom"
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108 --anchors-object-file anchors.loom --anchors-format loom
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109 #else if $anchors.format == "rds_seurat"
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110 --anchors-object-file '$anchors.rds_seurat_file' --anchors-format seurat
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111 #else if $anchors.format == "rds_sce"
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112 --anchors-object-file '$anchors.rds_sce_file' --anchors-format singlecellexperiment
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113 #else if $anchors.format == "h5seurat"
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114 --anchors-object-file anchors.h5seurat --anchors-format h5seurat
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115 #end if
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116 </token>
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117
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118 <token name="@REFERENCE_OBJ_PREAMBLE@">
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119 #if $reference.format == 'loom'
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120 ln -s '$reference.loom_file' reference.loom;
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121 #else if $reference.format == 'h5seurat'
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122 ln -s '$reference.h5seurat_file' reference.h5seurat;
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123 #else if $reference.format == 'anndata'
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124 ## it complains when using links for AnnData...
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125 cp '$reference.anndata_file' reference.h5ad;
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126 #end if
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127 </token>
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128
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129 <token name="@REFERENCE_OBJECT@">
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130 #if $reference.format == "anndata"
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131 --reference-object-file reference.h5ad --reference-format anndata
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132 #else if $reference.format == "loom"
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133 --reference-object-file reference.loom --reference-format loom
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134 #else if $reference.format == "rds_seurat"
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135 --reference-object-file '$reference.rds_seurat_file' --reference-format seurat
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136 #else if $reference.format == "rds_sce"
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137 --reference-object-file '$reference.rds_sce_file' --reference-format singlecellexperiment
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138 #else if $reference.format == "h5seurat"
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139 --reference-object-file reference.h5seurat --reference-format h5seurat
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140 #end if
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141 </token>
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142
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143 <token name="@INPUT_OBJS_PREAMBLE@">
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144 #if $input.format == 'loom'
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145 #for $i, $fh in enumerate($input.loom_file):
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146 ln -s '$fh' input.${i}.loom;
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147 #end for
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148 #else if $input.format == 'h5seurat'
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149 #for $i, $fh in enumerate($input.h5seurat_file):
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150 ln -s '$fh' input.${i}.h5seurat;
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151 #end for
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152 #else if $input.format == 'anndata'
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153 ## it complains when using links for AnnData...
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154 #for $i, $fh in enumerate($input.anndata_file):
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155 cp '$fh' input.${i}.h5ad;
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156 #end for
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157 #end if
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158 </token>
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159
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160 <token name="@INPUT_OBJECTS@">
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161 #if $input.format == "anndata"
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162 --input-object-files
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163 #set file_array = [ "input."+str($i)+".h5ad" for $i, $fh in enumerate($input.anndata_file)]
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164 #set files = ",".join($file_array)
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165 ${files}
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166 --input-format anndata
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167 #else if $input.format == "loom"
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168 --input-object-files
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169 #set file_array = [ "input."+str($i)+".loom" for $i, $fh in enumerate($input.loom_file)]
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170 #set files = ",".join($file_array)
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171 ${files}
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172 --input-format loom
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173 #else if $input.format == "rds_seurat"
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174 --input-object-files
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175 #set file_array = $input.rds_seurat_file
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176 #set files = ",".join([ str($fh) for $fh in $file_array ])
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177 ${files}
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178 --input-format seurat
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179 #else if $input.format == "rds_sce"
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180 --input-object-files
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181 #set file_array = $input.rds_sce_file
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182 #set files = ",".join([ str($fh) for $fh in $file_array ])
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183 ${files}
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184 --input-format singlecellexperiment
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185 #else if $input.format == "h5seurat"
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186 --input-object-files
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187 #set file_array = [ "input."+str($i)+".h5seurat" for $i, $fh in enumerate($input.h5seurat)]
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188 #set files = ",".join($file_array)
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189 ${files}
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190 --input-format h5seurat
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191 #end if
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192 </token>
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193
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194 <token name="@REFERENCE_OBJS_PREAMBLE@">
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195 #if $reference.format == 'loom'
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196 #for $i, $fh in enumerate($reference.loom_file):
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197 ln -s '$fh' reference.${i}.loom;
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198 #end for
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199 #else if $reference.format == 'h5seurat'
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200 #for $i, $fh in enumerate($reference.h5seurat_file):
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201 ln -s '$fh' reference.${i}.h5seurat;
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202 #end for
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203 #else if $reference.format == 'anndata'
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204 ## it complains when using links for AnnData...
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205 #for $i, $fh in enumerate($reference.anndata_file):
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206 cp '$fh' reference.${i}.h5ad;
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207 #end for
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208 #end if
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209 </token>
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210
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211 <token name="@REFERENCE_OBJECTS@">
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212 #if $reference.format == "anndata" and $reference.anndata_file:
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213 --reference-object-files
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214 #set file_array = [ "reference."+str($i)+".h5ad" for $i, $fh in enumerate($reference.anndata_file)]
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215 #set files = ",".join($file_array)
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216 ${files}
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217 --reference-format anndata
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218 #else if $reference.format == "loom" and $reference.loom_file:
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219 --reference-object-files
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220 #set file_array = [ "reference."+str($i)+".loom" for $i, $fh in enumerate($reference.loom_file)]
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221 #set files = ",".join($file_array)
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222 ${files}
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223 --reference-format loom
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224 #else if $reference.format == "rds_seurat" and $reference.rds_seurat_file:
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225 --reference-object-files
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226 #set files = ",".join([ str($fh) for $fh in $reference.rds_seurat_file ])
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227 ${files}
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228 --reference-format seurat
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229 #else if $reference.format == "rds_sce" and $reference.rds_sce_file:
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230 --reference-object-files
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231 #set files = ",".join([ str($fh) for $fh in $reference.rds_sce_file ])
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232 ${files}
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233 --reference-format singlecellexperiment
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234 #else if $reference.format == "h5seurat" and $reference.h5seurat:
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235 --reference-object-files
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236 #set file_array = [ "reference."+str($i)+".h5seurat" for $i, $fh in enumerate($reference.h5seurat)]
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237 #set files = ",".join($file_array)
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238 ${files}
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239 --reference-format h5seurat
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240 #end if
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241 </token>
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242
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243 <xml name="output_object_params">
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244 <param type="select" name="format" label="Choose the format of the output" help="Seurat, Single Cell Experiment, AnnData or Loom">
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245 <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
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246 <option value="anndata">AnnData written by Seurat</option>
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247 <option value="loom">Loom</option>
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248 <option value="rds_sce">RDS with a Single Cell Experiment object</option>
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249 </param>
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250 </xml>
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251
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252 <xml name="output_files">
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253 <data name="loom_file" from_work_dir="seurat_obj.loom" format="h5" label="${tool.name} on ${on_string}: Seurat Loom">
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254 <filter>format == 'loom'</filter>
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255 </data>
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256 <data name="rds_seurat_file" format="rdata" label="${tool.name} on ${on_string}: Seurat RDS">
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257 <filter>format == 'rds_seurat'</filter>
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258 </data>
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259 <data name="anndata_file" format="h5ad" label="${tool.name} on ${on_string}: AnnData from Seurat">
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260 <filter>format == 'anndata'</filter>
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261 </data>
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262 <data name="rds_sce_file" format="rdata" label="${tool.name} on ${on_string}: Seurat Single Cell Experiment RDS">
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263 <filter>format == 'rds_sce'</filter>
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264 </data>
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265 </xml>
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266
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267 <token name="@OUTPUT_OBJECT@">
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268 #if $format == "anndata"
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269 --output-object-file '$anndata_file' --output-format anndata
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270 #else if $format == "loom"
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271 --output-object-file seurat_obj.loom --output-format loom
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272 #else if $format == "rds_seurat"
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273 --output-object-file '$rds_seurat_file' --output-format seurat
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274 #else if $format == "rds_sce"
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275 --output-object-file '$rds_sce_file' --output-format singlecellexperiment
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276 #end if
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277 </token>
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278
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279 <xml name="plot_output_files_format" token_format="png">
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280 <data label="Seurat ${plot_type.plot_type_selector} on ${on_string}: @FORMAT@ plot" name="plot_out_@FORMAT@" format='@FORMAT@' >
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281 <filter>plot_format == '@FORMAT@'</filter>
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282 </data>
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283 </xml>
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284
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285 <token name="@OUTPUT_PLOT@">
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286 #if $plot_format == "png"
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287 --plot-out '$plot_out_png'
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288 #else if $plot_format == "pdf"
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289 --plot-out '$plot_out_pdf'
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290 #else if $plot_format == "eps"
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291 --plot-out '$plot_out_eps'
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292 #else if $plot_format == "ps"
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293 --plot-out '$plot_out_ps'
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294 #else if $plot_format == "jpg"
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295 --plot-out '$plot_out_jpg'
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296 #else if $plot_format == "tiff"
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297 --plot-out '$plot_out_tiff'
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298 #else if $plot_format == "svg"
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299 --plot-out '$plot_out_svg'
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300 #end if
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301 </token>
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302
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303 <xml name="genes-use-input">
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304 <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv,txt,tabular" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/>
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305 </xml>
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306 <xml name="dims-use-input">
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307 <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/>
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308 </xml>
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309
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310 <token name="@SEURAT_INTRO@"><![CDATA[
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311 Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
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312 It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
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313 interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
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314 types of single cell data.
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315 ]]></token>
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316
0
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317 <token name="@VERSION_HISTORY@"><![CDATA[
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318 **Version history**
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319 4.0.0: Moves to Seurat 4.0.0, introducing a number of methods for merging datasets, plus the whole suite of Seurat plots. Pablo Moreno with funding from AstraZeneca.
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320
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321 3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support.
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322
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323 3.1.2_0.0.8: Update metadata parsing
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324
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325 3.1.1_0.0.7: Exposes perplexity and enables tab input.
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326
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327 3.1.1_0.0.6+galaxy0: Moved to Seurat 3.
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328
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329 Find clusters: removed dims-use, k-param, prune-snn.
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330
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331 2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home at
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332 EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski (GitHub drosofff) and Lea Bellenger (GitHub bellenger-l).
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333
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334 0.0.1: Initial contribution. Maria Doyle (GitHub mblue9).
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335 ]]></token>
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336
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337
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338 <xml name="citations">
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339 <citations>
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340 <citation type="doi">10.1038/s41592-021-01102-w</citation>
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341 <citation type="doi">10.1038/nbt.4096</citation>
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342 <citation type="bibtex">
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343 @misc{r-seurat-scripts.git,
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344 author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team},
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345 year = {2018},
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346 title = {Seurat-scripts: command line interface for Seurat},
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347 publisher = {GitHub},
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348 journal = {GitHub repository},
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349 url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
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350 }
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351 </citation>
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352 </citations>
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353 </xml>
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354 </macros>