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Added missing step-by-step part for all sample analysis step #4281

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Jul 13, 2023
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Added missing step-by-step part for all sample analysis step #4281

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63 changes: 51 additions & 12 deletions ...agenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md
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Expand Up @@ -1083,37 +1083,76 @@ We use **Heatmap w ggplot** tool along with other tabular manipulating tools to

> <hands-on-title> Heatmap </hands-on-title>
>
> 1. {% tool [Multi-Join](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1) %} with the following parameters:
> - {% icon param-file %} *"File to join"*: `VFs accessions` collection output of **cut** {% icon tool %} from the **Gene based Pathogentic Identification** section
> 1. {% tool [Collapse Collection](toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0) %} with the following parameters:
> - {% icon param-collection %} *"Collection of files to collapse into single dataset"*: `VFs accessions` collection output of **cut** {% icon tool %} from the **Gene based Pathogentic Identification** section
> - *"Prepend File name"*: `No`
> 2. {% tool [Add line to file](toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file/0.1.0) %} with the following parameters:
> - {% icon param-file %} *"input file"*: `VFs accessions` output from **Collapse Collection** {% icon tool %}
> - *"text to add"*: `All_VFs`
> 3. {% tool [Multi-Join](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1) %} with the following parameters:
> - {% icon param-file %} *"File to join"*: `VFs accessions` output from **Add line to file** {% icon tool %}
> - {% icon param-file %} *"add additional file"*: `VFs accessions with SampleID` collection output of **Add line to file** {% icon tool %} from the **Gene based Pathogentic Identification** section
> - *"Common key column"*: `1`
> - *"Column with values to preserve"*: `Column: 1`
> - *"Add header line to the output file"*: `Yes`
> - *"Input files contain a header line (as first line)"*: `Yes`
> - *"Ignore duplicated keys"*: `Yes`
>
> 2. {% tool [Replace](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4) %} with the following parameters:
> 4. {% tool [Replace](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4) %} with the following parameters:
> - {% icon param-file %} *"File to process"*: output of **Multi-Join** {% icon tool %}
> - In *"Find and Replace"*:
> - {% icon param-repeat %} *"Insert Find and Replace"*
> - *"Find pattern"*: `^[^0]\w+`
> - *"Replace with"*: `1`
> - *"Find pattern"*: `dataset_(.*?)_`
> - *"Replace with"*: `Sample_`
> - *"Find-Pattern is a regular expression"*: `Yes`
> - *"Replace all occurences of the pattern"*: `Yes`
> - *"Ignore first line"*: `No`
> - *"Find and Replace text in"*: `entire line`
> - {% icon param-repeat %} *"Insert Find and Replace"*
> - *"Find pattern"*: `(\S+)`
> - *"Replace with"*: `Acc_$1`
> - *"Find-Pattern is a regular expression"*: `Yes`
> - *"Case-Insensitive search"*: `Yes`
> - *"Replace all occurences of the pattern"*: `Yes`
> - *"Ignore first line"*: `Yes`
> - *"Find and Replace text in"*: `specific column`
> - *"in column*": `Column: 2`
> 3. {% tool [Replace](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4) %} with the following parameters:
> - *"Find and Replace text in"*: `entire line`
> 5. {% tool [Replace](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4) %} with the following parameters:
> - {% icon param-file %} *"File to process"*: output of **Replace** {% icon tool %}
> - In *"Find and Replace"*:
> - {% icon param-repeat %} *"Insert Find and Replace"*
> - *"Find pattern"*: `^[^0]\w+`
> - *"Find pattern"*: `Acc_0`
> - *"Replace with"*: `0`
> - *"Find-Pattern is a regular expression"*: `No`
> - *"Case-Insensitive search"*: `Yes`
> - *"Replace all occurences of the pattern"*: `Yes`
> - *"Ignore first line"*: `Yes`
> - *"Find and Replace text in"*: `entire line`
> 6. {% tool [Replace](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4) %} with the following parameters:
> - {% icon param-file %} *"File to process"*: output of **Replace** {% icon tool %}
> - In *"Find and Replace"*:
> - {% icon param-repeat %} *"Insert Find and Replace"*
> - *"Find pattern"*: `Acc_\S*`
> - *"Replace with"*: `1`
> - *"Find-Pattern is a regular expression"*: `Yes`
> - *"Replace all occurences of the pattern"*: `Yes`
> - *"Ignore first line"*: `Yes`
> - *"Find and Replace text in"*: `specific column`
> - *"in column*": `Column: 3`
> - *"Case-Insensitive search"*: `No`
> - *"Find and Replace text in"*: `entire line`
> 7. {% tool [Advanced Cut](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0) %} with the following parameters:
> - {% icon param-file %} *"File to cut"*: output of **Multi-Join** {% icon tool %}
> - *"Operation"*:`Keep`
> - *"Delimited by"*:`Tab`
> - *"Cut by"*:`fields`
> - *"List of Fields"*:`1`
> 8. {% tool [Advanced Cut](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0) %} with the following parameters:
> - {% icon param-file %} *"File to cut"*: output of the last **Replace** {% icon tool %}
> - *"Operation"*:`Discard`
> - *"Delimited by"*:`Tab`
> - *"Cut by"*:`fields`
> - *"List of Fields"*:`1,2`
> 9. {% tool [Paste](Paste1) %} with the following parameters:
> - {% icon param-file %} *"Paste"*: output of **Advanced Cut** (Tool N. 7) {% icon tool %}
> - {% icon param-file %} *"and"*: output of **Advanced Cut** (Tool N. 8) {% icon tool %}
> - *"Delimit by"*:`Tab`
{: .hands_on}

2. Draw heatmap
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