Mercurial > repos > iuc > crosscontamination_barcode_filter

annotate crosscontamination_barcode_filter.xml @ 1:253c9448f524 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
author iuc
date Mon, 03 Jun 2019 14:55:24 -0400
parents 582b7bd4ae4c
children 5ade5cf200da
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582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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1 <tool id="crosscontamination_barcode_filter" name="Cross-contamination Barcode Filter" version="@VERSION@">
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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2 <description>for use in plate-based barcoded analyses</description>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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3 <macros>
1
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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4 <token name="@VERSION@">0.2</token>
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5 <macro name="sanitize_batch">
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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6 <sanitizer invalid_char="">
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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7 <valid initial="string.digits">
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8 <add value=","/>
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9 </valid>
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10 </sanitizer>
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11 </macro>
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12 <macro name="sanitize_regex">
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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13 <sanitizer invalid_char="">
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14 <valid initial="string.letters,string.digits">
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15 <add value="!"/>
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16 <add value="="/>
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17 <add value="-"/>
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18 <add value="."/>
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19 <add value="*"/>
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20 <add value="?"/>
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21 <add value="+"/>
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22 <add value="\\"/>
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23 <add value="_"/>
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24 <add value="&#91;"/> <!-- left square bracket, e.g subselecting from vec[1] -->
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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25 <add value="&#93;"/> <!-- right square bracket -->
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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26 <add value="&#40;"/> <!-- left parenthesis -->
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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27 <add value="&#41;"/> <!-- right parenthesis -->
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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28 </valid>
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29 </sanitizer>
1
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30 </macro>
0
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31 </macros>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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32 <requirements>
1
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33 <requirement type="package" version="3.1.1">r-ggplot2</requirement>
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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34 <requirement type="package" version="1.12.2">r-data.table </requirement>
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35 </requirements>
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36 <version_command><![CDATA[
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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37 Rscript '$__tool_directory__/scripts/crosscontamination_filter.R' | head -1 | cut -d' ' -f 2
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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38 ]]></version_command>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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39 <command detect_errors="exit_code"><![CDATA[
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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40 Rscript '$__tool_directory__/scripts/crosscontamination_filter.R' '$crossconf'
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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41 ]]></command>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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42 <configfiles>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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43 <configfile name="crossconf"><![CDATA[
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44 script.dir = '$__tool_directory__/scripts'
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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45 input_matrix <- read.table(
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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46 '$input_table',
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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47 stringsAsFactors = F,
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48 na.strings=c("NA", "-", "?", "."),
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49 header=TRUE,
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50 row.names=1
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51 )
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52 input_matrix[is.na(input_matrix)] <- 0
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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53 #if str($inbuilt_spec.select_use) == "mpi_sagar":
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54 spec = list(
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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55 barcodes = '$input_barcodes',
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56 format = list(
1
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57 "1-96" = c(1,3),
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58 "97-192" = c(2,4)
0
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59 ),
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60 plates = list(
1
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61 "1" = c(1,2),
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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62 "2" = c(3,4)
0
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63 )
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64 )
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65 #elif str($inbuilt_spec.select_use) == "custom":
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66 spec = list(
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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67 barcodes = '$input_barcodes',
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68 format = list(
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69 #for $i, $s in enumerate($inbuilt_spec.barcode_format)
1
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70 "${s.range_start}-${s.range_end}" = c( ${s.batches} )
0
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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71 #if $i < len(list($inbuilt_spec.barcode_format)) - 1
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72 ,
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73 #end if
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74 #end for
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75 ),
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76 plates = list(
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77 #for $i, $s in enumerate($inbuilt_spec.plate_format)
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78 "${s.plate}" = c( ${s.batches} )
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79 #if $i < len(list($inbuilt_spec.plate_format)) - 1
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80 ,
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81 #end if
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82 #end for
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83 )
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
84 )
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
85 #end if
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
86 regex.extract = '$advanced.regex_extract'
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
87 regex.display = '$advanced.regex_display'
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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88 out.pdf = '$out_plots'
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
89 out.table = '$out_table'
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
90 ]]>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
91 </configfile>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
92 </configfiles>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
93 <inputs>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
94 <param name="input_table" type="data" format="tsv,tabular" label="Input Matrix" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
95 <param name="input_barcodes" type="data" format="tsv,tabular,txt" label="Complete Barcodes" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
96 <conditional name="inbuilt_spec" >
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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97 <param name="select_use" type="select" label="Plate Protocol" >
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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98 <option value="mpi_sagar">CelSeq2 Plate Protocol (Sagar)</option>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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99 <option value="custom">Custom</option>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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100 </param>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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101 <when value="mpi_sagar" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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102 <when value="custom">
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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103 <repeat name="barcode_format" title="Barcode Format" help="e.g. Batches 1 and 4 use barcodes 1-100 in the Barcodes file, and Batches 2 and 3 use barcodes 101-200 in the Barcodes file; specify '1' and '100' as Range values, and '1,4' as Batch values, and in the next format specify '101' and '200' as Range values and '2,3' as Batch values" >
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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104 <param name="range_start" type="integer" min="1" value="1" label="Barcode Range: Start" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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105 <param name="range_end" type="integer" min="2" value="100" label="Barcode Range: End" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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106 <param name="batches" type="text" value="1,4" label="Batches utilizing this Range" >
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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107 <expand macro="sanitize_batch" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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108 </param>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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109 </repeat>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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110 <repeat name="plate_format" title="Plate Format" help="e.g. Plate 1 encompasses Batches 1-4, and Plate 2 encompasses Batches 5-8; specify '1' as a Plate value, and '1,2,3,4' as Batch values, and in the next format specify '2' as a Plate value and '5,6,7,8' as Batch values">
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
111 <param name="plate" type="integer" min="1" value="1" label="Plate Number" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
112 <param name="batches" type="text" value="1,2,3,4" label="Batches within this Plate Number" >
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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113 <expand macro="sanitize_batch" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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diff changeset
114 </param>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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diff changeset
115 </repeat>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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116 </when>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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117 </conditional>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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118 <section name="advanced" expanded="false" title="RegEx Parameters" >
1
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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119 <param name="regex_extract" type="text" value=".*P(\\d)_B(\\d)_([ACTG]+)" label="RegEx to extract Plate, Batch, and Barcodes from headers" >
0
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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120 <expand macro="sanitize_regex" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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121 </param>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
122 <param name="regex_display" type="text" value="P\\1_B\\2_\\3" label="RegEx to replace Plate, Batch, and Barcodes from headers" >
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
123 <expand macro="sanitize_regex" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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124 </param>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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125 </section>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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126 </inputs>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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127 <outputs>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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128 <data name="out_plots" format="pdf" label="${tool.name} on ${on_string}: Plots" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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129 <data name="out_table" format="tabular" label="${tool.name} on ${on_string}: Filtered Table" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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130 </outputs>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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131 <tests>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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132 <test><!-- Inbuilt MPI -->
1
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
iuc
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diff changeset
133 <param name="input_table" value="test.matrix" />
0
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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134 <param name="input_barcodes" value="celseq_barcodes.192.raw" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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135 <conditional name="inbuilt_spec" >
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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136 <param name="select_use" value="mpi_sagar" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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137 </conditional>
1
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
iuc
parents: 0
diff changeset
138 <output name="out_plots" value="out.pdf" compare="sim_size" />
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
iuc
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diff changeset
139 <output name="out_table" value="out.table" />
0
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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140 </test>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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141 <test><!-- Plate and Lane test -->
1
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
iuc
parents: 0
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142 <param name="input_table" value="test.matrix" />
0
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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143 <param name="input_barcodes" value="celseq_barcodes.192.raw" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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144 <conditional name="inbuilt_spec" >
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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145 <param name="select_use" value="custom" />
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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146 <repeat name="barcode_format" >
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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147 <param name="range_start" value="1"/>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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148 <param name="range_end" value="96" />
1
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
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diff changeset
149 <param name="batches" value="1,3" />
0
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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150 </repeat>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
151 <repeat name="barcode_format" >
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
152 <param name="range_start" value="97"/>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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153 <param name="range_end" value="192" />
1
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
iuc
parents: 0
diff changeset
154 <param name="batches" value="2,4" />
0
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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diff changeset
155 </repeat>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
156 <repeat name="plate_format" >
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
157 <param name="plate" value="1" />
1
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
iuc
parents: 0
diff changeset
158 <param name="batches" value="1,2" />
0
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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159 </repeat>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
160 <repeat name="plate_format" >
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff changeset
161 <param name="plate" value="2" />
1
253c9448f524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit f967afe562781e5c8ed4e24e9d1e0bc3ebb29401
iuc
parents: 0
diff changeset
162 <param name="batches" value="3,4" />
0
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
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163 </repeat>
582b7bd4ae4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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164 </conditional>
1
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165 <output name="out_plots" value="out.pdf" compare="sim_size" />
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166 <output name="out_table" value="out.table" />
0
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167 </test>
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168 </tests>
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169 <help><![CDATA[
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170 Cross-contamination Filter Plot
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171 ###################################
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172
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173 For a set of barcodes and an experimental setup that uses a subset of these barcodes for each batch, this tool compares each batch against the full range of barcodes in order to determine whether any cross-contamination between batches has occured.
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174
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175 If a significant number of transcripts are shown in a batch for cell barcodes that were not designed for that batch, then this tool will show that. In the below plot, we can see that there is no significant cross-contamination taking place (pre-filter), and so we can filter out the false barcodes (post-filter).
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176
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177 .. image:: $PATH_TO_IMAGES/crosscontam_pretopost.png
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178 :scale: 50 %
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179
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180
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181 Example
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182 ~~~~~~~~
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183
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184 Consider the following experimental setup, with a list of 100 possible barcodes, used over 3 sequencing plates, with each plate containing 4 unique batches, and each plate using a specific subset of the 100 barcodes.
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185
1
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186 ::
0
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187
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188 Barcodes
1
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189
0
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190 1 - 10 | AAA AAC AAT AAG ACA AGA ATA CAC GAG TAT
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191 11 - 20 | CCC CCA CCT CCG CTC CGC TCT GCG TCT CGT
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192 .
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193 .
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194 91 -100 | TTT TAT TCT TGT TTA TTC TTG TCC TGG TAA
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195
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196
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197
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198 Plate 1 +-------+-------+-------+-------+
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199 | B1 | B2 | B3 | B4 |
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200 +-------+-------+-------+-------+
1
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201 1-50 51-100 51-100 1-50
0
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202
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203 Plate 2 +-------+-------+-------+-------+
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204 | B5 | B6 | B7 | B8 |
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205 +-------+-------+-------+-------+
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206 1-40 41-80 1-40 41-80
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207
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208 Plate 3 +-------+-------+-------+-------+
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209 | B9 | B10 | B11 | B12 |
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210 +-------+-------+-------+-------+
1
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211 1-40 41-80 1-40 41-80
0
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212
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213
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214 ****
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215
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216 The above plate and barcoding setup can be more textually represented by specifying barcode ranges and plate numbers, with each denoting which batch numbers they describe as outlined below:
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217
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218 ::
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219
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220 *Barcodes → Batches*
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221 1- 50: B1, B4
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222 51-100: B2, B3
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223 1- 40: B5, B7, B9 , B11
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224 41- 80: B6, B8, B10, B12
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225
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226 *Plates → Batches*
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227 1: B1, B2 , B3 , B4
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228 2: B5, B6 , B7 , B8
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229 3: B9, B10, B11, B12
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230
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231 ]]></help>
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232 <citations>
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233 <citation type="doi">10.1007/978-1-4939-7768-0_15</citation>
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234 </citations>
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235 </tool>