comparison iedb_api.xml @ 3:e95d3221b7f0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 863578373c7dadc5880633115b0c348f73dac782"

2:a09849898387

<tool id="iedb_api" name="IEDB" version="2.15.0">
    <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">

            #if $prediction.alleles.allelesrc == 'history':
              -A '$prediction.alleles.allele_file'
            #else:
              -A '$entered_alleles'
            #end if
        #end if

        #if $sequence.seqsrc == 'fasta':
          -i '$sequence.seq_fasta'
        #else if $sequence.seqsrc == 'tabular':

            <when value="mhci">
                <param name="method" type="select" label="prediction method">
                    <option value="recommended" selected="true">recommended</option>
                    <option value="consensus">consensus</option>
                    <option value="netmhcpan">netmhcpan</option>
                    <option value="ann">ann</option>
                    <option value="smmpmbec">smmpmbec</option>
                    <option value="smm">smm</option>
                    <option value="comblib_sidney2008">comblib_sidney2008</option>
                    <option value="netmhccons">netmhccons</option>

            <conditional name="prediction">
                <param name="tool" value="mhci"/>
                <param name="method" value="recommended"/>
                <conditional name="alleles">
                    <param name="allelesrc" value="history"/>
                    <param name="allele_file" ftype="tabular" value="alleles.tsv"/>
                </conditional>
            </conditional>
            <conditional name="sequence">
                <param name="seqsrc" value="fasta"/>
                <param name="seq_fasta" ftype="fasta" value="seqs.fa"/>

                <param name="method" value="recommended"/>
                <conditional name="alleles">
                    <param name="allelesrc" value="history"/>
                    <param name="allele_file" ftype="tabular" value="alleles.tsv"/>
                </conditional>
            </conditional>
            <conditional name="sequence">
                <param name="seqsrc" value="tabular"/>
                <param name="seq_tsv" ftype="tabular" value="seqs.tsv"/>
                <param name="pep_col" value="3"/>

3:e95d3221b7f0

<tool id="iedb_api" name="IEDB" version="2.15.1">
    <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">

            #if $prediction.alleles.allelesrc == 'history':
              -A '$prediction.alleles.allele_file'
            #else:
              -A '$entered_alleles'
            #end if
            -l '$prediction.lengths'
        #end if

        #if $sequence.seqsrc == 'fasta':
          -i '$sequence.seq_fasta'
        #else if $sequence.seqsrc == 'tabular':

            <when value="mhci">
                <param name="method" type="select" label="prediction method">
                    <option value="recommended" selected="true">recommended</option>
                    <option value="consensus">consensus</option>
                    <option value="netmhcpan">netmhcpan</option>
                    <option value="netmhcpan_ba">netmhcpan_ba</option>
                    <option value="netmhcpan_el">netmhcpan_el</option>
                    <option value="ann">ann</option>
                    <option value="smmpmbec">smmpmbec</option>
                    <option value="smm">smm</option>
                    <option value="comblib_sidney2008">comblib_sidney2008</option>
                    <option value="netmhccons">netmhccons</option>

            <conditional name="prediction">
                <param name="tool" value="mhci"/>
                <param name="method" value="recommended"/>
                <conditional name="alleles">
                    <param name="allelesrc" value="history"/>
                    <param name="allele_file" ftype="tabular" value="alleles_len.tsv"/>
                </conditional>
            </conditional>
            <conditional name="sequence">
                <param name="seqsrc" value="fasta"/>
                <param name="seq_fasta" ftype="fasta" value="seqs.fa"/>

                <param name="method" value="recommended"/>
                <conditional name="alleles">
                    <param name="allelesrc" value="history"/>
                    <param name="allele_file" ftype="tabular" value="alleles.tsv"/>
                </conditional>
                <param name="lengths" value="8,9"/>
            </conditional>
            <conditional name="sequence">
                <param name="seqsrc" value="tabular"/>
                <param name="seq_tsv" ftype="tabular" value="seqs.tsv"/>
                <param name="pep_col" value="3"/>