comparison immuneml_train_recept.xml @ 3:ed3932e6d616 draft

"planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"

2:9bf78cb6b91d

      && mv ${html_outfile.files_path}/immuneML_output.zip $archive
      && mv ${html_outfile.files_path}/exported_models/*.zip ${optimal_model}
      ]]>
</command>
    <inputs>
        <param name="iml_input" type="data" format="iml_dataset" label="Input dataset (immune receptors)" help="This field accepts receptor datasets in the ImmuneML dataset format, as created by the Create Dataset tool."/>
        <param type="text" name="labels" optional="false" label="Which property (“label”) of the receptors would you like to predict?" help="A receptor property to predict could for example be the epitope it binds to. Such properties must be present as receptor sequence metadata. For example, when using data in VDJdb format, the default fields are named ‘epitope’, ‘epitope_gene’ and ‘epitope_species’. One of these labels must be chosen here."/>

        <conditional name="gap_cond">
            <param type="select" name="gap_type" label="The immune receptors will be classified based on subsequences found in the CDR3 region. I assume that the signal that determines the receptor label is:" display="radio">
                <option value="ungapped">A contiguous subsequence of amino acids</option>

3:ed3932e6d616

      && mv ${html_outfile.files_path}/immuneML_output.zip $archive
      && mv ${html_outfile.files_path}/exported_models/*.zip ${optimal_model}
      ]]>
</command>
    <inputs>
        <param name="iml_input" type="data" format="immuneml_receptors" label="Input dataset (immune receptors)" help="This field accepts receptor datasets in the ImmuneML dataset format, as created by the Create Dataset tool."/>
        <param type="text" name="labels" optional="false" label="Which property (“label”) of the receptors would you like to predict?" help="A receptor property to predict could for example be the epitope it binds to. Such properties must be present as receptor sequence metadata. For example, when using data in VDJdb format, the default fields are named ‘epitope’, ‘epitope_gene’ and ‘epitope_species’. One of these labels must be chosen here."/>

        <conditional name="gap_cond">
            <param type="select" name="gap_type" label="The immune receptors will be classified based on subsequences found in the CDR3 region. I assume that the signal that determines the receptor label is:" display="radio">
                <option value="ungapped">A contiguous subsequence of amino acids</option>