comparison macros.xml @ 3:18ece3d5bcde draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 3febcc9ba3d3717877c36bf96742209012a13ac4-dirty

2:9a01840eac52

                <option value="cached">local cached database</option>
                <option value="history">history</option>
            </param>
            <when value="cached">
                <param name="cat_builtin" type="select" label="Use a built-in CAT database" help="If the CAT database of interest is not listed, contact your Galaxy administrator">
                    <options from_data_table="cat_databases">
                        <filter type="sort_by" column="2" />
                        <validator type="no_options" message="No CAT database is available." />
                    </options>
                </param>
            </when>

      --proteins_fasta '$previous.proteins_fasta'
      --diamond_alignment '$previous.diamond_alignment'
      #end if
      --out_prefix 'cat_output'
]]></token>

    <xml name="custom_settings">
        <param argument="--range" type="integer" value="10" min="0" max="49" label="range"/>
        <param argument="--fraction" type="float" value="0.5" min="0" max="0.99" label="fraction"/>
    </xml>
    <token name="@CUSTOM_SETTINGS@"><![CDATA[

            <when value="both">
                <expand macro="add_names_options"/>
            </when>
        </conditional>
    </xml>
    <token name="@ADD_NAMES@"><![CDATA[
    #if $names.add_names in ['classification','both']:
        && CAT add_names $names.only_official $names.exclude_scores 
            @CAT_TAXONOMY@
            #if $bcat == 'CAT'
                -i cat_output.contig2classification.tsv
            #else
                -i cat_output.bin2classification.tsv
            #end if
            -o classification_names.txt
        && @TXT2TSV@ -i classification_names.txt -o $classification_names
    #end if
    #if $names.add_names in ['orf2lca','both']:
        && CAT add_names $names.only_official $names.exclude_scores 
            @CAT_TAXONOMY@
            -i cat_output.ORF2LCA.tsv 
            -o orf2lca_names.txt
        && @TXT2TSV@ -i orf2lca_names.txt -o $orf2lca_names
    #end if
]]></token>
    <xml name="summarise">
        <param name="summarise" type="select" label="summarise">
            <option value="no">No</option>

            #if $bcat == 'CAT'
                -c $contigs_fasta
            #end if
            -i $summary_input
            -o classification_summary.txt
        && @TXT2TSV@ -i classification_summary.txt -o $classification_summary
    #end if
]]></token>
    
    <xml name="select_outputs">
        <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">

        <param name="bin_col" type="hidden" value="bin,"/>
        <expand macro="select_outputs">
            <option value="bin2classification" selected="true">bin2classification.txt</option>
        </expand>
    </xml>
    
    <token name="@TXT2TSV@"><![CDATA[
    $__tool_directory__/tabpad.py 
]]></token>
    <xml name="outputs">
        <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log">
            <filter>'log' in select_outputs or not select_outputs</filter>
        </data>
        <data name="predicted_proteins_faa" format="fasta" label="${bcat}.predicted_proteins.faa" from_work_dir="cat_output.predicted_proteins.faa">

]]></token>
    <xml name="citations">
        <citations>
            <citation type="doi">https://doi.org/10.1101/072868</citation>
            <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation>
            <yield />
        </citations>
    </xml>
</macros>

3:18ece3d5bcde

                <option value="cached">local cached database</option>
                <option value="history">history</option>
            </param>
            <when value="cached">
                <param name="cat_builtin" type="select" label="Use a built-in CAT database" help="If the CAT database of interest is not listed, contact your Galaxy administrator">
                    <options from_data_table="cat_database">
                        <filter type="sort_by" column="2" />
                        <validator type="no_options" message="No CAT database is available." />
                    </options>
                </param>
            </when>

      --proteins_fasta '$previous.proteins_fasta'
      --diamond_alignment '$previous.diamond_alignment'
      #end if
      --out_prefix 'cat_output'
]]></token>
    <xml name="custom_settings">
        <param argument="--range" type="integer" value="10" min="0" max="49" label="range"/>
        <param argument="--fraction" type="float" value="0.5" min="0" max="0.99" label="fraction"/>
    </xml>
    <token name="@CUSTOM_SETTINGS@"><![CDATA[

            <when value="both">
                <expand macro="add_names_options"/>
            </when>
        </conditional>
    </xml>
    <token name="@TXT2TSV@">${__tool_directory__}/tabpad.py</token>
    <token name="@ADD_NAMES@"><![CDATA[
    #if $names.add_names in ['classification','both']:
        && CAT add_names $names.only_official $names.exclude_scores 
            @CAT_TAXONOMY@
            #if $bcat == 'CAT'
                -i cat_output.contig2classification.tsv
            #else
                -i cat_output.bin2classification.tsv
            #end if
            -o classification_names.txt
        && ${__tool_directory__}/tabpad.py -i classification_names.txt -o $classification_names
    #end if
    #if $names.add_names in ['orf2lca','both']:
        && CAT add_names $names.only_official $names.exclude_scores 
            @CAT_TAXONOMY@
            -i cat_output.ORF2LCA.tsv 
            -o orf2lca_names.txt
        && ${__tool_directory__}/tabpad.py -i orf2lca_names.txt -o $orf2lca_names
    #end if
]]></token>
    <xml name="summarise">
        <param name="summarise" type="select" label="summarise">
            <option value="no">No</option>

            #if $bcat == 'CAT'
                -c $contigs_fasta
            #end if
            -i $summary_input
            -o classification_summary.txt
        && ${__tool_directory__}/tabpad.py -i classification_summary.txt -o $classification_summary
    #end if
]]></token>
    
    <xml name="select_outputs">
        <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">

        <param name="bin_col" type="hidden" value="bin,"/>
        <expand macro="select_outputs">
            <option value="bin2classification" selected="true">bin2classification.txt</option>
        </expand>
    </xml>
    <xml name="outputs">
        <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log">
            <filter>'log' in select_outputs or not select_outputs</filter>
        </data>
        <data name="predicted_proteins_faa" format="fasta" label="${bcat}.predicted_proteins.faa" from_work_dir="cat_output.predicted_proteins.faa">

]]></token>
    <xml name="citations">
        <citations>
            <citation type="doi">https://doi.org/10.1101/072868</citation>
            <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation>
            <citation type="doi">https://doi.org/10.1038/nmeth.3176</citation>
            <citation type="doi">https://doi.org/10.1186/1471-2105-11-119</citation>
            <yield />
        </citations>
    </xml>
</macros>