Mercurial > repos > iuc > anndata_import

annotate import.xml @ 1:a61350ab6563 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
author iuc
date Wed, 16 Oct 2019 06:27:31 -0400
parents 69e2275406fd
children e175d4067b00
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69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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1 <tool id="anndata_import" name="Import AnnData" version="@VERSION@+@GALAXY_VERSION@">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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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>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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4 <import>macros.xml</import>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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5 <xml name="params_10x">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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6 <param name="barcodes" type="data" format="tabular,txt" label="Barcodes"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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7 <param name="var_names" type="select" label="Variables index">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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8 <option value="gene_symbols">gene_symbols</option>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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9 <option value="gene_ids">gene_ids</option>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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10 </param>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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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?"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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13 </xml>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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14 </macros>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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15 <expand macro="requirements">
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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16
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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17 </expand>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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18 <expand macro="version_command"/>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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19 <command detect_errors="exit_code"><![CDATA[
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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20 #if $in.adata_format == 'mtx'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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21 mkdir mtx
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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22 #if $in.tenx.use == 'legacy_10x'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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23 && cp '$in.matrix' 'mtx/matrix.mtx'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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24 && cp '$in.tenx.genes' 'mtx/genes.tsv'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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25 && cp '$in.tenx.barcodes' 'mtx/barcodes.tsv'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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26 #else if $in.tenx.use == 'v3_10x'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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27 && cp '$in.matrix' 'mtx/matrix.mtx'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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28 && gzip 'mtx/matrix.mtx'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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29 && cp '$in.tenx.features' 'mtx/features.tsv'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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30 && gzip 'mtx/features.tsv'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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31 && cp '$in.tenx.barcodes' 'mtx/barcodes.tsv'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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32 && gzip 'mtx/barcodes.tsv'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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33 #end if
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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34 &&
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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35 #else if $in.adata_format == 'umi_tools'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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36 gzip '$in.input'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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37 &&
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38 #end if
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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39
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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40 @CMD@
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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41
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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42 #if $in.adata_format == 'mtx'
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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43 && rm -rf mtx
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44 #end if
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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45 ]]></command>
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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46 <configfiles>
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47 <configfile name="script_file"><![CDATA[
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48 @CMD_imports@
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49 #if $in.adata_format == 'loom'
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50 adata = ad.read_loom(
69e2275406fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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51 '$in.input',
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52 sparse=$in.sparse,
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53 cleanup=$in.cleanup,
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54 X_name='$in.x_name',
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55 obs_names='$in.obs_names',
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56 var_names='$in.var_names')
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57
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58 #else if $in.adata_format == 'tabular'
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59 #set delimiter=$in.input.metadata.delimiter
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60 #if $delimiter != ','
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61 #set delimiter='\\t'
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62 #end if
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63 adata = ad.read_csv(
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64 '$in.input',
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65 delimiter='$delimiter',
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66 first_column_names=$in.first_column_names)
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67
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68 #else if $in.adata_format == 'mtx'
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69 #if $in.tenx.use == 'no'
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70 adata = ad.read_mtx(filename='$in.matrix')
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71 #else
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72 import scanpy as sc
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73 adata = sc.read_10x_mtx(
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74 'mtx',
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75 var_names='$in.tenx.var_names',
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76 make_unique=$in.tenx.make_unique,
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77 cache=False,
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78 gex_only=$in.tenx.gex_only)
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79 #end if
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80
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81 #else if $in.adata_format == 'umi_tools'
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82 adata = ad.read_umi_tools('${in.input}.gz')
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83
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84 #end if
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85
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86 adata.write('anndata.h5ad')
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87 ]]></configfile>
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88 </configfiles>
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89 <inputs>
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90 <conditional name="in">
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91 <param name="adata_format" type="select" label="Format for the annotated data matrix">
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92 <option value="loom">Loom</option>
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93 <option value="tabular">Tabular, CSV, TSV</option>
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94 <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option>
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95 <option value="umi_tools">UMI tools</option>
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96 </param>
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97 <when value="loom">
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98 <param name="input" type="data" format="loom" label="Annotated data matrix"/>
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99 <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/>
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100 <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/>
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101 <param name="x_name" type="text" value="spliced" label="X_name"/>
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102 <param name="obs_names" type="text" value="CellID" label="obs_names"/>
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103 <param name="var_names" type="text" value="Gene" label="var_names"/>
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104 </when>
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105 <when value="tabular">
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106 <param name="input" type="data" format="tabular,csv,tsv" label="Annotated data matrix"/>
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107 <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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108 </when>
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109 <when value="mtx">
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110 <param name="matrix" type="data" format="mtx" label="Matrix"/>
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111 <conditional name="tenx">
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112 <param name="use" type="select" label="Use 10x Genomics formatted mtx">
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113 <option value="no">No</option>
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114 <option value="legacy_10x">Output from Cell Ranger v2 or earlier versions</option>
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115 <option value="v3_10x">Output from Cell Ranger v3 or later versions</option>
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116 </param>
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117 <when value="no"/>
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118 <when value="legacy_10x">
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119 <param name="genes" type="data" format="tabular" label="Genes"/>
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120 <expand macro="params_10x"/>
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121 </when>
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122 <when value="v3_10x">
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123 <param name="features" type="data" format="tabular" label="Features"/>
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124 <expand macro="params_10x"/>
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125 </when>
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126 </conditional>
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127 </when>
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128 <when value="umi_tools">
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129 <param name="input" type="data" format="tabular" label="condensed count matrix from UMI tools"/>
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130 </when>
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131 </conditional>
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132 </inputs>
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133 <outputs>
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134 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}"/>
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135 </outputs>
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136 <tests>
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137 <test>
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138 <conditional name="in">
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139 <param name="adata_format" value="loom"/>
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140 <param name="input" value="krumsiek11.loom" />
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141 <param name="sparse" value="True"/>
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142 <param name="cleanup" value="False"/>
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143 <param name="x_name" value="spliced"/>
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144 <param name="obs_names" value="CellID" />
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145 <param name="var_names" value="Gene"/>
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146 </conditional>
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147 <assert_stdout>
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148 <has_text_matching expression="ad.read_loom"/>
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149 <has_text_matching expression="sparse=True"/>
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150 <has_text_matching expression="cleanup=False"/>
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151 <has_text_matching expression="X_name='spliced'"/>
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152 <has_text_matching expression="obs_names='CellID'"/>
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153 <has_text_matching expression="var_names='Gene'"/>
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154 </assert_stdout>
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155 <output name="anndata" value="import.loom.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
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156 </test>
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157 <test>
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158 <conditional name="in">
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159 <param name="adata_format" value="tabular"/>
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160 <param name="input" value="adata.csv"/>
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161 <param name="first_column_names" value="true"/>
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162 </conditional>
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163 <assert_stdout>
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164 <has_text_matching expression="ad.read_csv"/>
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165 <has_text_matching expression="delimiter=','"/>
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166 <has_text_matching expression="first_column_names=True"/>
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167 </assert_stdout>
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168 <output name="anndata" value="import.csv.h5ad" ftype="h5ad" compare="sim_size"/>
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169 </test>
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170 <test>
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171 <conditional name="in">
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172 <param name="adata_format" value="tabular"/>
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173 <param name="input" value="adata.tsv"/>
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174 <param name="first_column_names" value="true"/>
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175 </conditional>
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176 <assert_stdout>
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177 <has_text_matching expression="ad.read_csv"/>
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178 <has_text_matching expression="delimiter='\\t'"/>
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179 <has_text_matching expression="first_column_names=True"/>
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180 </assert_stdout>
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181 <output name="anndata" value="import.tsv.h5ad" ftype="h5ad" compare="sim_size"/>
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182 </test>
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183 <!--<test>
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184 <conditional name="in">
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185 <param name="adata_format" value="mtx"/>
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186 <param name="matrix" value="matrix_10x_v1.2.0.mtx"/>
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187 <conditional name="tenx">
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188 <param name="use" value="no"/>
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189 </conditional>
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190 </conditional>
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191 <output name="anndata" value="import.mtx.no_10x.h5ad" ftype="h5ad" compare="sim_size"/>
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192 </test>
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193 <test>
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194 <conditional name="in">
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195 <param name="adata_format" value="mtx"/>
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196 <param name="matrix" value="matrix_10x_v1.2.0.mtx"/>
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197 <conditional name="tenx">
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198 <param name="use" value="legacy_10x"/>
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199 <param name="genes" value="genes_10x_v1.2.0.tsv"/>
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200 <param name="barcodes" value="barcodes_10x_v1.2.0.tsv"/>
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201 <param name="var_names" value="gene_symbols"/>
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202 <param name="make_unique" value="true"/>
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203 <param name="gex_only" value="true"/>
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204 </conditional>
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205 </conditional>
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206 <output name="anndata" value="import.mtx.legacy_10x.h5ad" ftype="h5ad" compare="sim_size"/>
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207 </test>
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208 <test>
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209 <conditional name="in">
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210 <param name="adata_format" value="mtx"/>
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211 <param name="matrix" value="matrix_10x_v3.0.0.mtx"/>
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212 <conditional name="tenx">
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213 <param name="use" value="v3_10x"/>
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214 <param name="features" value="features_10x_v3.0.0.tsv"/>
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215 <param name="barcodes" value="barcodes_10x_v3.0.0.tsv"/>
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216 <param name="var_names" value="gene_symbols"/>
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217 <param name="make_unique" value="true"/>
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218 <param name="gex_only" value="true"/>
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219 </conditional>
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220 </conditional>
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221 <output name="anndata" value="import.mtx.v3_10x.h5ad" ftype="h5ad" compare="sim_size"/>
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222 </test>!-->
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223 <test>
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224 <conditional name="in">
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225 <param name="adata_format" value="umi_tools"/>
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226 <param name="input" value="umi_tools.tsv"/>
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227 </conditional>
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228 <output name="anndata" value="import.umi_tools.h5ad" ftype="h5ad" compare="sim_size"/>
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229 </test>
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230 </tests>
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231 <help><![CDATA[
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232 **What it does**
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233
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234 This tool creates an AnnData dataset from several input types:
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235
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236 - Loom (`read_loom method <https://anndata.readthedocs.io/en/latest/anndata.read_loom.html>`__)
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237 - Tabular (`read_csv method <https://anndata.readthedocs.io/en/latest/anndata.read_csv.html>`__)
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238 - 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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239 - UMI tools (`read_umi_tools method <https://anndata.readthedocs.io/en/latest/anndata.read_umi_tools.html>`__)
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240
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241 @HELP@
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242 ]]></help>
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243 <expand macro="citations"/>
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244 </tool>