view fastg2protlib-peptides.xml @ 0:6b226c5907a1 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"

<tool id="fastg2protlib-peptides" name="FASTG2Protlib-Peptides" version="@VERSION@">
    <macros>
        <import>macros.xml</import>
    </macros>
    <description>Generate FASTA from FASTG</description>
    <expand macro="pkg_requirement" />
    <command detect_errors="exit_code">
        <![CDATA[
        python '$__tool_directory__/application.py' 
        -m $min_peptide_length
        -p $min_protein_length  
        -c $cleavage 
        -d 'results.db' 
        -l $show_plots
        '$fastg_file'
        ]]>
    </command>
    <inputs>
        <param name="fastg_file" type="data" format="fastg" label="FASTG file" />
        <param name="cleavage" type="select" label="Peptide Cleavage">
            <option value="trypsin" selected="true">Trypsin</option>
            <expand macro="cleavages" />
        </param>
        <param name="min_protein_length" type="integer" value="55" label="Minimum Protein Length in Amino Acids" />
        <param name="min_peptide_length" type="integer" value="8" label="Minimum Peptide Length in Amino Acids" />
        <param name="show_plots" type="boolean" checked="true" label="Create Diagnostic Plots" />
    </inputs>
    <outputs>
        <data name="peptide_fasta" format="txt" from_work_dir="peptide.fasta" label="${on_string} Peptides from FASTG" />
        <data name="results_db" format="sqlite" from_work_dir="results.db" label="${on_string} Results DB" />
        <data name="aa_count_plot" format="png" from_work_dir="aa_count_chart.png" label="${on_string} AA Count Plot">
            <filter>show_plots == True</filter>
        </data>
        <data name="fastg_length_plot" format="png" from_work_dir="fastg_seq_lengths.png" label="${on_string} FASTG Sequence Length Plot">
            <filter>show_plots == True</filter>
        </data>
        <data name="protein_length_plot" format="png" from_work_dir="protein_seq_lengths.png" label="${on_string} Protein Sequence Length Plot">
            <filter>show_plots == True</filter>
        </data>
        <data name="gc_pct_plot" format="png" from_work_dir="gc_pct.png" label="${on_string} GC Percent Plot">
            <filter>show_plots == True</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="fastg_file" value="two.fastg" />
            <param name="cleavage" value="trypsin" />
            <param name="min_protein_length" value="20" />
            <param name="min_peptide_length" value="8" />
            <param name="show_plots" value="false" />
            <output name="peptide_fasta">
                <assert_contents>
                    <has_text text="IFLPFSTHSR" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <expand macro="help-text" />
</tool>