comparison iedb_api.xml @ 2:883cdf0ffae5 draft

"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"

1:4a89ba6cfc63

**OUTPUTS**
  
  A tabular file containing the results returned from the IEDB web service

    ]]></help>
    <citations>
       <citation type="doi">10.1093/nar/gku938</citation>
    </citations>
</tool>

2:883cdf0ffae5

**OUTPUTS**
  
  A tabular file containing the results returned from the IEDB web service

**Typical Workflow for Human MHC I Binding Prediction** 

The RNAseq data for the subject would be used for:

  - HLA prediction by seq2HLA_
  - Novel Antigen Prediction by a variety of workflows to generate a Antigen peptide fasta 

.. _seq2HLA: https://toolshed.g2.bx.psu.edu/view/iuc/seq2hla/52bba1cd3823

.. image:: $PATH_TO_IMAGES/IEDB_Workflow_QueryTabular.png
   :width: 584
   :height: 430

.. note:: The seq2HLA ClassI.HLAgenotype4digits output needs to be converted for IEDB alleles.

The seq2HLA ClassI.HLAgenotype4digits output:

.. image:: $PATH_TO_IMAGES/seq2HLA_ClassI.HLAgenotype4digits.png
   :width: 285
   :height: 77

Needs to be converted into IEDB formatted alleles:

.. image:: $PATH_TO_IMAGES/IEDB_formatted_alleles.png
   :width: 74
   :height: 81

In the workflow above QueryTabular_ tool converts the alleles:

  - Filter Dataset Input

    * skip leading lines - *skip lines:* 1
    * select columns - *columns:* 2,4
    * regex replace value in column - *column:* 1  *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$  *replacement expression:* HLA-\\1
    * regex replace value in column - *column:* 2  *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$  *replacement expression:* HLA-\\1

  - SQL Query to generate tabular output

    * SELECT c1 FROM t1 UNION SELECT c2 FROM t1

.. _QueryTabular: https://toolshed.g2.bx.psu.edu/view/iuc/query_tabular/0c95a3f1654f


The IEDB formatting can also be performed by TextProcessing_ tools:

.. _TextProcessing: https://toolshed.g2.bx.psu.edu/view/bgruening/text_processing/0a8c6b61f0f4

.. image:: $PATH_TO_IMAGES/TextProcessingConversion.png
   :width: 608
   :height: 87

The TextProcessing steps to convert the alleles:

  - Remove beginning -  removes the header line
  - Replace Text - picks Allele 1 and Allele 2 from each line and reformats each on a separate line 

    * *Find pattern:* ^.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*$
    * *Replace with:* HLA-\\1\\nHLA-\\2

  - Unique - remove duplicates


    ]]></help>
    <citations>
       <citation type="doi">10.1093/nar/gku938</citation>
    </citations>
</tool>