comparison iedb_api.xml @ 3:153d5fa7af53 draft

"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 250d6261ba8c695446f845f2f31c6cca8d87a427-dirty"

2:883cdf0ffae5

        #else:
          #for $seq in str($sequence.seq_text).strip().split():
            -s $seq.strip()
          #end for
        #end if
        -o $output
    ]]></command>
    <inputs>
        <conditional name="prediction">
            <param name="tool" type="select" label="Prediction">
                <option value="mhci">MHC-I Binding</option>

                    <option value="nn_align">nn_align</option>
                    <option value="smm_align">smm_align</option>
                    <option value="comblib">comblib</option>
                    <option value="tepitope">tepitope</option>
                </param>
                <expand macro="alleles" hla_regex="((DPA1\*0[1-3](:0[1-3])?/DPB1\*0[1-6]:0[12]|DQA1\*0[1-5]:0[12]/DQB1\*0[2-6]:0[12]|DRB[1-5]\*[01][1-9]:0[1-5]|H2-IA[bd]),(asis|[1-2][0-9]|30))*" hla_examples="DPA1*01/DPB1*04:01 HLA-DRB1*01:01 H2-IAb" hlalen_examples="DPA1*01/DPB1*04:01,11,15"/>
                <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
                    <help>Used for any alleles which don't include specified lengths</help>
                    <option value="asis">asis</option>
                    <option value="11">11</option>
                    <option value="12">12</option>

               <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/>
               <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" />
               <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/>
           </when>
           <when value="entry">
               <param name="seq_text" type="text" size="80" label="Peptide Sequence"/>
           </when>
        </conditional>

    </inputs>
    <outputs>

**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

.. 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

  - 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

3:153d5fa7af53

        #else:
          #for $seq in str($sequence.seq_text).strip().split():
            -s $seq.strip()
          #end for
        #end if
        -o '$output'
    ]]></command>
    <inputs>
        <conditional name="prediction">
            <param name="tool" type="select" label="Prediction">
                <option value="mhci">MHC-I Binding</option>

                    <option value="nn_align">nn_align</option>
                    <option value="smm_align">smm_align</option>
                    <option value="comblib">comblib</option>
                    <option value="tepitope">tepitope</option>
                </param>
                <expand macro="alleles" hla_regex="(DPA1\*0[1-3](:0[1-3])?/DPB1\*0[1-6]:0[12]|DQA1\*0[1-5]:0[12]/DQB1\*0[2-6]:0[12]|DRB[1-5]\*[01][1-9]:0[1-5]|H2-IA[bd])(,(asis|[1-2][0-9]|30))*" hla_examples="DPA1*01/DPB1*04:01 HLA-DRB1*01:01 H2-IAb" hlalen_examples="DPA1*01/DPB1*04:01,11,15"/>
                <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
                    <help>Used for any alleles which don't include specified lengths</help>
                    <option value="asis">asis</option>
                    <option value="11">11</option>
                    <option value="12">12</option>

               <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/>
               <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" />
               <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/>
           </when>
           <when value="entry">
               <param name="seq_text" type="text" label="Peptide Sequence"/>
           </when>
        </conditional>

    </inputs>
    <outputs>

**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 


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

.. 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

  - SQL Query to generate tabular output

    * SELECT c1 FROM t1 UNION SELECT c2 FROM t1


The IEDB formatting can also be performed by TextProcessing tools:

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