comparison iedb_api.xml @ 5:1911ec100221 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api commit 6007a6fe7005df2f7fd1de85ce63156511534b6e

4:7ed6dda64a81

<tool id="iedb_api" name="IEDB" version="2.15.2">
    <description>MHC Binding prediction</description>
    <macros>
        <xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples=""> 
            <conditional name="alleles">
               <param name="allelesrc" type="select" label="Alleles">
                   <option value="history">From history</option>
                   <option value="entry">Entered</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]|(HLA-)?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>

            <conditional name="prediction">
                <param name="tool" value="mhcii"/>
                <param name="method" value="recommended"/>
                <conditional name="alleles">
                    <param name="allelesrc" value="entry"/>
                    <param name="allele_text" value="DPA1*01/DPB1*04:01"/>
                </conditional>
                <param name="lengths" value="asis"/>
            </conditional>
            <conditional name="sequence">
                <param name="seqsrc" value="entry"/>
                <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_text text="LYNTVATLY" />
                </assert_contents>
            </output>
        </test>
        <!-- test5 -->
        <test>

    </tests>
    <help><![CDATA[
The IEDB is a free resource, funded by a contract from the National Institute of Allergy and Infectious Diseases. It offers easy searching of experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species. 

This tool retrieves epitope binding information about input peptide sequences by using the RESTful web services provided by IEDB.  
The webservices are described at:  http://tools.immuneepitope.org/main/tools-api/
That page also describes how to retrieve the available HLA alleles for class of epitope binding.

**INPUTS**

  peptide sequences from a fasta file or a column in a tabular file

5:1911ec100221

<tool id="iedb_api" name="IEDB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>MHC Binding prediction</description>
    <macros>
        <token name="@TOOL_VERSION@">2.15.3</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">24.2</token>
        <xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples=""> 
            <conditional name="alleles">
               <param name="allelesrc" type="select" label="Alleles">
                   <option value="history">From history</option>
                   <option value="entry">Entered</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]|(HLA-)?DRB[1-5]\*[01][1-9]:0[1-5]|H2-IA[bd])(,(asis|[1-2][0-9]|30))*" hla_examples="DPA1*01:03/DPB1*04:01 HLA-DRB1*01:01 H2-IAb" hlalen_examples="DPA1*01:03/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>

            <conditional name="prediction">
                <param name="tool" value="mhcii"/>
                <param name="method" value="recommended"/>
                <conditional name="alleles">
                    <param name="allelesrc" value="entry"/>
                    <param name="allele_text" value="DPA1*01:03/DPB1*04:01"/>
                </conditional>
                <param name="lengths" value="asis"/>
            </conditional>
            <conditional name="sequence">
                <param name="seqsrc" value="entry"/>
                <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_text text="VATLYCVHQ" />
                </assert_contents>
            </output>
        </test>
        <!-- test5 -->
        <test>

    </tests>
    <help><![CDATA[
The IEDB is a free resource, funded by a contract from the National Institute of Allergy and Infectious Diseases. It offers easy searching of experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species. 

This tool retrieves epitope binding information about input peptide sequences by using the RESTful web services provided by IEDB.  
The webservices are described at:  https://tools.iedb.org/main/tools-api/
That page also describes how to retrieve the available HLA alleles for class of epitope binding.

**INPUTS**

  peptide sequences from a fasta file or a column in a tabular file