Mercurial > repos > iuc > crosscontamination_barcode_filter
annotate crosscontamination_barcode_filter.xml @ 0:582b7bd4ae4c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
| author | iuc |
|---|---|
| date | Thu, 24 Jan 2019 09:52:58 -0500 |
| parents | |
| children | 253c9448f524 |
| rev | line source |
|---|---|
|
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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changeset
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1 <tool id="crosscontamination_barcode_filter" name="Cross-contamination Barcode Filter" version="@VERSION@"> |
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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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2 <description>for use in plate-based barcoded analyses</description> |
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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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3 <macros> |
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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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4 <token name="@VERSION@">0.1</token> |
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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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5 <macro name="assert_conts" > |
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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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6 <assert_contents> |
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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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7 <has_text text="/CreationDate" /> |
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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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8 <has_text text="/Producer" /> |
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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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9 <has_line line="startxref" /> |
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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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10 <has_line line="%%EOF" /> |
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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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11 </assert_contents> |
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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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12 </macro> |
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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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13 <macro name="sanitize_batch"> |
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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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14 <sanitizer invalid_char=""> |
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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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15 <valid initial="string.digits"> |
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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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16 <add value=","/> |
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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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17 </valid> |
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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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18 </sanitizer> |
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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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19 </macro> |
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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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20 <macro name="sanitize_regex"> |
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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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changeset
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21 <sanitizer invalid_char=""> |
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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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22 <valid initial="string.letters,string.digits"> |
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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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23 <add value="!"/> |
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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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24 <add value="="/> |
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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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25 <add value="-"/> |
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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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26 <add value="."/> |
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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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27 <add value="*"/> |
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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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28 <add value="?"/> |
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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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29 <add value="+"/> |
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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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30 <add value="\\"/> |
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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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31 <add value="_"/> |
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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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32 <add value="["/> <!-- left square bracket, e.g subselecting from vec[1] --> |
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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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33 <add value="]"/> <!-- right square bracket --> |
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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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34 <add value="("/> <!-- left parenthesis --> |
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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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35 <add value=")"/> <!-- right parenthesis --> |
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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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36 </valid> |
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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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37 </sanitizer> |
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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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38 </macro> |
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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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39 </macros> |
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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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40 <requirements> |
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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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41 <requirement type="package" version="2.2.1" >r-ggplot2</requirement> |
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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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42 </requirements> |
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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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43 <version_command><![CDATA[ |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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44 Rscript '$__tool_directory__/scripts/crosscontamination_filter.R' | head -1 | cut -d' ' -f 2 |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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45 ]]></version_command> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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46 <command detect_errors="exit_code"><![CDATA[ |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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47 Rscript '$__tool_directory__/scripts/crosscontamination_filter.R' '$crossconf' |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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48 ]]></command> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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49 <configfiles> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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50 <configfile name="crossconf"><![CDATA[ |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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51 script.dir = '$__tool_directory__/scripts' |
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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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52 input_matrix <- read.table( |
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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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53 '$input_table', |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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54 stringsAsFactors = F, |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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55 na.strings=c("NA", "-", "?", "."), |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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56 header=TRUE, |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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57 row.names=1 |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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58 ) |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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59 input_matrix[is.na(input_matrix)] <- 0 |
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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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60 #if str($inbuilt_spec.select_use) == "mpi_sagar": |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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61 spec = list( |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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62 barcodes = '$input_barcodes', |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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63 format = list( |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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64 "1-96" = c(1,3,5,7), |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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65 "97-192" = c(2,4,6,8) |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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66 ), |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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67 plates = list( |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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68 "1" = c(1,2,3,4), |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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69 "2" = c(5,6,7,8) |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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70 ) |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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71 ) |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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72 #elif str($inbuilt_spec.select_use) == "custom": |
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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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73 spec = list( |
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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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74 barcodes = '$input_barcodes', |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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75 format = list( |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
76 #for $i, $s in enumerate($inbuilt_spec.barcode_format) |
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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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changeset
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77 "${s.range_start}-${s.range_end}" = c( ${s.batches} ) |
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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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78 #if $i < len(list($inbuilt_spec.barcode_format)) - 1 |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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parents:
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79 , |
|
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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80 #end if |
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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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81 #end for |
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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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changeset
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82 ), |
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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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changeset
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83 plates = list( |
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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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changeset
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84 #for $i, $s in enumerate($inbuilt_spec.plate_format) |
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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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85 "${s.plate}" = c( ${s.batches} ) |
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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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86 #if $i < len(list($inbuilt_spec.plate_format)) - 1 |
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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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87 , |
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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 #end if |
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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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89 #end for |
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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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90 ) |
|
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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91 ) |
|
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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92 #end if |
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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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93 regex.extract = '$advanced.regex_extract' |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
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94 regex.display = '$advanced.regex_display' |
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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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95 out.pdf = '$out_plots' |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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96 out.table = '$out_table' |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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97 ]]> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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98 </configfile> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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99 </configfiles> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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100 <inputs> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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101 <param name="input_table" type="data" format="tsv,tabular" label="Input Matrix" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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102 <param name="input_barcodes" type="data" format="tsv,tabular,txt" label="Complete Barcodes" /> |
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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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103 <conditional name="inbuilt_spec" > |
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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="select_use" type="select" label="Plate Protocol" > |
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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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105 <option value="mpi_sagar">CelSeq2 Plate Protocol (Sagar)</option> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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106 <option value="custom">Custom</option> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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107 </param> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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108 <when value="mpi_sagar" /> |
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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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109 <when value="custom"> |
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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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110 <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
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111 <param name="range_start" type="integer" min="1" value="1" label="Barcode Range: Start" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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112 <param name="range_end" type="integer" min="2" value="100" label="Barcode Range: End" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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113 <param name="batches" type="text" value="1,4" label="Batches utilizing this Range" > |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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114 <expand macro="sanitize_batch" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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115 </param> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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116 </repeat> |
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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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117 <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
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118 <param name="plate" type="integer" min="1" value="1" label="Plate Number" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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119 <param name="batches" type="text" value="1,2,3,4" label="Batches within this Plate Number" > |
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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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120 <expand macro="sanitize_batch" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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121 </param> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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122 </repeat> |
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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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123 </when> |
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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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124 </conditional> |
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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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125 <section name="advanced" expanded="false" title="RegEx Parameters" > |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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126 <param name="regex_extract" type="text" value=".*P(\\d)_(\\d)_([ACTG]+)" label="RegEx to extract Plate, Batch, and Barcodes from headers" > |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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127 <expand macro="sanitize_regex" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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128 </param> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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129 <param name="regex_display" type="text" value="P\\1_B\\2_\\3" label="RegEx to replace Plate, Batch, and Barcodes from headers" > |
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582b7bd4ae4c
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130 <expand macro="sanitize_regex" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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131 </param> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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132 </section> |
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133 </inputs> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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134 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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135 <data name="out_plots" format="pdf" label="${tool.name} on ${on_string}: Plots" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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136 <data name="out_table" format="tabular" label="${tool.name} on ${on_string}: Filtered Table" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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137 </outputs> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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138 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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139 <test><!-- Inbuilt MPI --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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140 <param name="input_table" value="out3.subtable" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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141 <param name="input_barcodes" value="celseq_barcodes.192.raw" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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142 <conditional name="inbuilt_spec" > |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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143 <param name="select_use" value="mpi_sagar" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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144 </conditional> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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145 <output name="out_plots" > |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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146 <expand macro="assert_conts" /> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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147 </output> |
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582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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148 <output name="out_table" value="test.table" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
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149 </test> |
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150 <test><!-- Plate and Lane test --> |
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151 <param name="input_table" value="out3.subtable" /> |
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152 <param name="input_barcodes" value="celseq_barcodes.192.raw" /> |
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153 <conditional name="inbuilt_spec" > |
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154 <param name="select_use" value="custom" /> |
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155 <repeat name="barcode_format" > |
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156 <param name="range_start" value="1"/> |
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157 <param name="range_end" value="96" /> |
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158 <param name="batches" value="1,3,5,7" /> |
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159 </repeat> |
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160 <repeat name="barcode_format" > |
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161 <param name="range_start" value="97"/> |
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162 <param name="range_end" value="192" /> |
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163 <param name="batches" value="2,4,6,8" /> |
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164 </repeat> |
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165 <repeat name="plate_format" > |
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166 <param name="plate" value="1" /> |
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167 <param name="batches" value="1,2,3,4" /> |
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168 </repeat> |
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169 <repeat name="plate_format" > |
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170 <param name="plate" value="2" /> |
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171 <param name="batches" value="5,6,7,8" /> |
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172 </repeat> |
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173 </conditional> |
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174 <output name="out_plots" > |
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175 <expand macro="assert_conts" /> |
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176 </output> |
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177 <output name="out_table" value="test.table" /> |
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178 </test> |
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179 </tests> |
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180 <help><![CDATA[ |
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181 Cross-contamination Filter Plot |
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182 ################################### |
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183 |
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184 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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185 |
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186 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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187 |
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188 .. image:: $PATH_TO_IMAGES/crosscontam_pretopost.png |
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189 :scale: 50 % |
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190 |
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191 |
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192 Example |
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193 ~~~~~~~~ |
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194 |
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195 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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196 |
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197 :: |
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198 |
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199 Barcodes |
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200 |
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201 1 - 10 | AAA AAC AAT AAG ACA AGA ATA CAC GAG TAT |
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202 11 - 20 | CCC CCA CCT CCG CTC CGC TCT GCG TCT CGT |
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203 . |
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204 . |
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205 91 -100 | TTT TAT TCT TGT TTA TTC TTG TCC TGG TAA |
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206 |
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207 |
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208 |
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209 Plate 1 +-------+-------+-------+-------+ |
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210 | B1 | B2 | B3 | B4 | |
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211 +-------+-------+-------+-------+ |
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212 1-50 51-100 51-100 1-50 |
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213 |
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214 Plate 2 +-------+-------+-------+-------+ |
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215 | B5 | B6 | B7 | B8 | |
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216 +-------+-------+-------+-------+ |
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217 1-40 41-80 1-40 41-80 |
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218 |
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219 Plate 3 +-------+-------+-------+-------+ |
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220 | B9 | B10 | B11 | B12 | |
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221 +-------+-------+-------+-------+ |
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222 1-40 41-80 1-40 41-80 |
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223 |
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224 |
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225 **** |
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226 |
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227 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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228 |
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229 :: |
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230 |
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231 *Barcodes → Batches* |
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232 1- 50: B1, B4 |
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233 51-100: B2, B3 |
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234 1- 40: B5, B7, B9 , B11 |
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235 41- 80: B6, B8, B10, B12 |
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236 |
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237 *Plates → Batches* |
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238 1: B1, B2 , B3 , B4 |
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239 2: B5, B6 , B7 , B8 |
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240 3: B9, B10, B11, B12 |
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241 |
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242 ]]></help> |
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243 <citations> |
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244 <citation type="doi">10.1007/978-1-4939-7768-0_15</citation> |
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245 </citations> |
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246 </tool> |
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247 |