Mercurial > repos > iuc > dropletutils

annotate dropletutils.xml @ 5:cdf4443d5625 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7"
author iuc
date Wed, 29 Jan 2020 15:07:38 -0500
parents 1797cbe967d1
children 8855361fcfc5
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4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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1 <?xml version="1.0" encoding="utf-8"?>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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2 <tool id="dropletutils" name="DropletUtils" version="@PACKAGE_VERSION@+@GALAXY_VERSION@" >
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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3 <description>Utilities for handling droplet-based single-cell RNA-seq data</description>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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4 <macros>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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5 <token name="@PACKAGE_VERSION@" >1.2.1</token>
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cdf4443d5625 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7"
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6 <token name="@GALAXY_VERSION@" >galaxy6</token>
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4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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7 <token name="@TXIN@">tenx.input</token>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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8 <token name="@TXOUT@">tenx.output</token>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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9 <xml name="test_dirin" >
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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10 <conditional name="tenx_format">
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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11 <param name="use" value="directory" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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12 <param name="input" value="in_matrix.mtx" />
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13 <param name="input_barcodes" value="in_barcodes.tsv" />
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4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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14 <param name="input_genes" value="in_genes.tsv" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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15 </conditional>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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16 </xml>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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17 </macros>
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18 <requirements>
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19 <requirement type="package" version="@PACKAGE_VERSION@">bioconductor-dropletutils</requirement>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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20 <requirement type="package" version="1.2_17" >r-matrix</requirement>
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21 <requirement type="package" version="1.10.1" >bioconductor-scater</requirement>
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22 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
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4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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23 </requirements>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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24 <version_command><![CDATA[
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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25 Rscript -e 'packageVersion("DropletUtils")' | grep -oP '\d\.\d\.\d'
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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26 ]]>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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27 </version_command>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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28 <command detect_errors='exit_code'><![CDATA[
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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29 #if str($tenx_format.use) == 'directory':
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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30 mkdir '@TXIN@' &&
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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31 ln -s '$tenx_format.input' '@TXIN@/matrix.mtx' &&
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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32 ln -s '$tenx_format.input_genes' '@TXIN@/genes.tsv' &&
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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33 ln -s '$tenx_format.input_barcodes' '@TXIN@/barcodes.tsv' &&
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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34 #end if
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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35
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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36 #if str($operation.use) == 'filter':
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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37 #if str($operation.outformat) == 'directory':
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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38 mkdir '@TXOUT@' &&
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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39 #end if
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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40 #end if
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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41
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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42 Rscript '$__tool_directory__/scripts/dropletutils.Rscript' '$droplet_conf'
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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43 ]]>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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44 </command>
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45 <configfiles>
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46 <configfile name="droplet_conf" >
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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47 ## defaults
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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48 empty.fdr_threshold = 0.01
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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49 eparams=formals(emptyDrops)
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50 dparams=formals(defaultDrops)
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51 bparams=formals(barcodeRanks)
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52
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53 ## File params
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54 in.type='$tenx_format.use'
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55 out.type=NULL
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56
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57 files=list()
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58 files\$table='$table'
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59 files\$plot='$plot'
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60 files\$out=NULL
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61
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62 #if str($tenx_format.use) == 'directory':
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63 files\$infile='@TXIN@'
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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64 #else
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65 files\$infile='$input'
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66 #end if
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67
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68 #if str($operation.use) == 'filter':
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69 #if str($operation.method.use) == 'defaultdrops':
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70 do.method="defaultDrops"
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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71 dparams\$expected=as.integer('$operation.method.expected')
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72 dparams\$upper.quant=as.numeric('$operation.method.upperquant')
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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73 dparams\$lower.prop=as.numeric('$operation.method.lowerprop')
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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74 #else if str($operation.method.use) == 'emptydrops':
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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75 do.method="emptyDrops"
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76 eparams\$lower=as.integer('$operation.method.lower')
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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77 empty.fdr_threshold=as.numeric('$operation.method.fdr_thresh')
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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78 #end if
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79
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80 out.type='$operation.outformat'
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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81 #if str($operation.outformat) == 'directory':
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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82 files\$out='@TXOUT@'
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83 #else if str($operation.outformat) == 'h5':
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84 files\$out='$fileout_h5'
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85 #else if str($operation.outformat) == 'tsv':
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86 files\$out='$fileout_tsv'
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87 #end if
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88
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89 #else if str($operation.use) == 'barcode_rank':
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90 do.method="barcodeRankings"
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91 bparams\$lower=as.integer('$operation.lower')
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92 #end if
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93
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94 seed.val=as.integer('$seed')
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95
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96 </configfile>
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97 </configfiles>
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98 <inputs>
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99 <conditional name="tenx_format">
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100 <param name="use" type="select" label="Format for the input matrix">
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101 <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option>
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102 <option value="h5" selected="true" >H5</option>
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103 <option value="tsv">Tabular</option>
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104 </param>
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105 <when value="directory">
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106 <param name="input" type="data" format="mtx,txt" label="Count Data"/>
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107 <param name="input_genes" type="data" format="tabular,tsv,txt" label="Genes List"/>
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108 <param name="input_barcodes" type="data" format="tabular,tsv,txt" label="Barcodes List"/>
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109 </when>
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110 <when value="h5">
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111 <param name="input" type="data" format="h5" label="Count Data"/>
0
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112 </when>
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113 <when value="tsv">
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114 <param name="input" type="data" format="tabular,tsv" label="Count Data" help="The first column must contain gene names, and the first row must contain barcode identifiers." />
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115 </when>
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116 </conditional>
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117 <conditional name="operation" >
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118 <param name="use" type="select" label="Operation" help="The filtering uses intelligent methods to generate output 10X matrices as would be otherwise generated by CellRanger. The ranking option serves to illustrate the number of detected barcodes in the sample.">
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119 <option value="filter" selected="true">Filter for Barcodes</option>
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120 <option value="barcode_rank">Rank Barcodes</option>
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121 </param>
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122 <when value="filter">
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123 <conditional name="method">
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124 <param name="use" type="select" label="Method" help="The DefaultDrops method calls cells according to the number of UMIs associated with each barcode as implemented by CellRanger. The EmptyDrops method identifies empty droplets using a smart ambient background model." >
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125 <option value="defaultdrops" selected="true">DefaultDrops</option>
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126 <option value="emptydrops">EmptyDrops</option>
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127 </param>
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128 <when value="defaultdrops">
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129 <param name="expected" type="integer" min="1" value="3000" label="Expected Number of Cells" help="The expected number of cells in the sample." />
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130 <param name="upperquant" type="float" min="0" max="1.0" value="0.99" label="Upper Quantile" help="The quantile of the top expected barcodes to consider." />
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131 <param name="lowerprop" type="float" min="0" max="1.0" value="0.1" label="Lower Proportion" help="The fraction of molecules of the upper quantile that must be exceeded for a cell barcode to be detected." />
0
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132 </when>
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133 <when value="emptydrops">
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134 <param name="lower" type="integer" min="1" value="100" label="Lower-bound Threshold" help="The lower-bound threshold of the total UMI count at which barcodes beneath this are assumed to be empty droplets." />
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135 <param name="fdr_thresh" type="float" min="0" max="1" value="0.01" label="FDR Threshold" help="False Discovery Rate threshold at which droplets with significant deviations from the ambient profile are detected at this threshold. If set to 0, the threshold is ignored." />
0
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136 </when>
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137 </conditional>
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138 <param name="outformat" type="select" label="Format for output matrices">
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139 <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option>
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140 <option value="h5" selected="true" >H5</option>
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141 <option value="tsv">Tabular</option>
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142 </param>
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143 </when>
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144 <when value="barcode_rank">
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145 <param name="lower" type="integer" min="1" value="100" label="Lower Bound" help="Lower bound on the total UMI count, at or below which all barcodes are assumed to correspond to empty droplets."/>
0
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146 </when>
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147 </conditional>
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148 <param name="seed" type="integer" value="100" label="Random Seed" />
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149 </inputs>
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150 <outputs>
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151 <data name="fileout_tsv" format="tsv" label="${tool.name} Count Matrix on ${on_string}">
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152 <filter>operation['use']=='filter' and operation['outformat'] == 'tsv' </filter>
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153 </data>
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154 <data name="fileout_h5" format="h5" label="${tool.name} H5 Matrix on ${on_string}">
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155 <filter>operation['use']=='filter' and operation['outformat'] == 'h5'</filter>
0
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156 </data>
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157 <data name="barcodes_out" format="tsv" from_work_dir="@TXOUT@/barcodes.tsv" label="${tool.name} 10X Barcodes on ${on_string}" >
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158 <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter>
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159 </data>
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160 <data name="genes_out" format="tsv" from_work_dir="@TXOUT@/genes.tsv" label="${tool.name} 10X Genes on ${on_string}" >
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161 <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter>
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162 </data>
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163 <data name="matrix_out" format="mtx" from_work_dir="@TXOUT@/matrix.mtx" label="${tool.name} 10X Matrices on ${on_string}" >
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164 <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter>
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165 </data>
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166 <data name="plot" format="png" label="${tool.name} Plot on ${on_string}">
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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167 <filter>(operation['use']=='filter' and operation['method']['use']=="emptydrops") or operation['use']=='barcode_rank'</filter>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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168 </data>
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169 <data name="table" format="tsv" label="${tool.name} Table on ${on_string}">
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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170 <filter>operation['use']=='filter' and operation['method']['use']=="emptydrops"</filter>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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171 </data>
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172 </outputs>
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173 <tests>
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174 <!-- Directory input tests -->
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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175 <!-- ::: Default Drops -->
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176 <test expect_num_outputs="1">
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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177 <expand macro="test_dirin" />
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178 <conditional name="operation">
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179 <param name="use" value="filter" />
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180 <param name="outformat" value="h5" /><!-- H5 -->
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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181 </conditional>
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182 <output name="fileout_h5" value="defs_defaultdrops.h5" compare="sim_size" delta="10" />
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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183 </test>
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184 <test expect_num_outputs="1">
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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185 <expand macro="test_dirin" />
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186 <conditional name="operation">
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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187 <param name="use" value="filter" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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188 <param name="outformat" value="tsv" /><!-- TSV -->
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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189 </conditional>
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190 <output name="fileout_tsv" >
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191 <assert_contents>
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192 <has_n_columns n="1026" />
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193 <has_text_matching expression="^\sTCGCCAAGAA\sGGACTTAGAA\sTGCGCCTGAA\sACGGACACAA\sGCGGACACAA" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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194 <has_text_matching expression="GENE50\s4\s0\s0\s0\s0\s5\s11\s8\s5" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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195 <has_text_matching expression="GENE100\s6\s3\s5\s0\s0\s16\s31\s15\s26" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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196 </assert_contents>
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197 </output>
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198 </test>
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199 <!-- :: Barcode Ranks -->
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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200 <test expect_num_outputs="1">
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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201 <expand macro="test_dirin" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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202 <conditional name="operation">
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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203 <param name="use" value="barcode_rank" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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204 <param name="lower" value="120" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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205 </conditional>
4
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206 <output name="plot" value="defs_barcoderankings.png" compare="sim_size" delta="400"/>
0
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207 </test>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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208 <!-- ::: Empty Drops -->
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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209 <test expect_num_outputs="3">
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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210 <expand macro="test_dirin" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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211 <conditional name="operation">
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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212 <param name="use" value="filter" />
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213 <param name="outformat" value="h5" />
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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214 <conditional name="method">
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215 <param name="use" value="emptydrops" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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216 <param name="lower" value="150" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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217 <param name="fdr_thresh" value="0.02" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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218 </conditional>
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219 </conditional>
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220 <output name="fileout_h5" value="defs_emptydrops_150_0002.h5" compare="sim_size" delta="10" />
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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221 <output name="table" >
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222 <assert_contents>
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223 <has_n_columns n="9" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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224 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
2
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225 <has_line_matching expression="^994\sGGCATTACAA\s338\s-246.922772388055\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" />
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226 <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166.644236503983\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" />
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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227 </assert_contents>
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228 </output>
4
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229 <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="400" />
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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230 </test>
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231 <!-- Other format input tests -->
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232 <!-- ::: Empty Drops, same as above but input is h5 -->
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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233 <test expect_num_outputs="3">
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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234 <conditional name="tenx_format" >
5
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235 <param name="use" value="h5" />
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diff changeset
236 <param name="input" value="in_matrix.h5" />
0
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237 </conditional>
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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238 <conditional name="operation">
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239 <param name="use" value="filter" />
5
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parents: 4
diff changeset
240 <param name="outformat" value="h5" />
0
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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diff changeset
241 <conditional name="method">
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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242 <param name="use" value="emptydrops" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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243 <param name="lower" value="150" />
4cd9f0008d9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit e66ab3d4fc0c1a72523e8f93447cc07cdd6816b7
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diff changeset
244 <param name="fdr_thresh" value="0.02" />
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245 </conditional>
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246 </conditional>
5
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247 <output name="fileout_h5" value="defs_emptydrops_150_0002a.h5" compare="sim_size" delta="400" />
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248 <output name="table" >
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249 <assert_contents>
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250 <has_n_columns n="9" />
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251 <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
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252 <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198.117943099773\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" />
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253 <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196.181449214729\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" />
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254 </assert_contents>
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255 </output>
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256 <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="400" />
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257 </test>
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258 <!-- Output a directory -->
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259 <test expect_num_outputs="3">
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260 <conditional name="tenx_format" >
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261 <param name="use" value="tsv" />
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262 <param name="input" value="in_matrix.tsv" />
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263 </conditional>
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264 <conditional name="operation">
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265 <param name="use" value="filter" />
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266 <param name="outformat" value="directory" />
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267 <conditional name="method">
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268 <param name="use" value="defaultdrops" />
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269 <param name="expected" value="2000" />
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270 <param name="upperquant" value="0.85" />
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271 <param name="lowerpopr" value="0.2" />
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272 </conditional>
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273 </conditional>
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274 <output name="genes_out" file="in_genes.tsv" ftype="tsv" /><!-- same as the input in this case -->
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275 <output name="barcodes_out" ftype="tsv" >
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276 <assert_contents>
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277 <has_n_columns n="1" />
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278 <has_line line="GGAAGAAGAA" />
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279 <has_line line="TCGAATGGAA" />
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280 </assert_contents>
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281 </output>
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282 <output name="matrix_out" ftype="mtx" >
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283 <assert_contents>
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284 <has_line_matching expression="^100\s2650\s64072$" />
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285 <has_line_matching expression="^19\s1\s1$" />
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286 <has_line_matching expression="^100\s2650\s1$" />
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287 </assert_contents>
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288 </output>
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289 </test>
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290 </tests>
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291 <help><![CDATA[
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292 Utilities to process 10X data in a variety of formats. Methods include:
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293
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294 *Filter data:*
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295
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296 * **DefaultDrops** emulates the native 10X method to produce a filtered count matrix
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297 * **EmptyDrops** is a more informative quantile-based approach to produce a filtered count matrix.
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298
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299 *Metrics:*
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300
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301 * **RankBarcodes** produces a gap statistic plot to estimate the number of barcodes detected in the sample matrix.
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302
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303 *Background*
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304
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305 Droplet-based single-cell RNA sequencing (scRNA-seq) technologies allow researchers to obtain transcriptome-wide expression profiles for thousands of cells at once. Briefly, each cell is encapsulated in a droplet in a oil-water emulsion, along with a bead containing reverse transcription primers with a unique barcode sequence. After reverse transcription inside the droplet, each cell’s cDNA is labelled with that barcode (referred to a “cell barcode”). Bursting of the droplets yields a pool of cDNA for library preparation and sequencing. Debarcoding of the sequences can then be performed to obtain the expression profile for each cell.
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306
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307 This tool implements some general utilities for handling these data after quantification of expression. In particular, we focus on the 10X Genomics platform, providing functions to load in the matrix of unique molecule identifier (UMI) counts as well as the raw molecule information. Functions are also available for downsampling the UMI count matrix or the raw reads; for distinguishing cells from empty droplets, based on the UMI counts; and to eliminate the effects of barcode swapping on Illumina 4000 sequencing machine.
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308 ]]></help>
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309 <citations>
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310 <citation type="doi">10.1186/s13059-019-1662-y</citation>
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311 </citations>
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312 </tool>