comparison bio_hansel.xml @ 7:af59ac462926 draft

planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4fee4519135f7677cf50f721cf1ad7a7335ad66d-dirty

6:5a42e475436e

<tool id="bio_hansel" name="Bio Hansel" version="1.2.1">
    <description>SNV Subtyping with genome assemblies or reads</description>
    <requirements>
        <requirement type="package" version="1.2.0">bio_hansel</requirement>
        <requirement type="package" version="17.2.0">attrs</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ## Preparing file input.
        #if $data_type.type == "paired":

            <param name="type" value="single"/>
            <param name="type_of_scheme" value="heidelberg"/>
            <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/>
            <output name="results.tab">
                <assert_contents>
                    <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+qc_status\s+qc_message"/>
                </assert_contents>
            </output>
            <output name="match_results.tab">
                <assert_contents>
                    <has_text_matching expression="tilename\s+seq\s+is_revcomp\s+contig_id\s+match_index\s+refposition\s+subtype\s+is_pos_tile\s+sample\s+file_path\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/>

            <param name="type_of_scheme" value="heidelberg"/>
            <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/>
            <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/>
            <output name="results.tab">
                <assert_contents>
                    <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path"/>
                </assert_contents>
            </output>
            <output name="match_results.tab">
                <assert_contents>
                    <has_text_matching expression="tilename\s+seq\s+freq\s+refposition\s+subtype\s+is_pos_tile\s+is_kmer_freq_okay\s+sample\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/>

    ]]></help>
    <citations>
        <citation type="bibtex">@ARTICLE{a1,
            title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.},
            author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Chad R. Laing, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Marisa Rankin, Joanne MacKinnon, Roger Johnson, John H.E. Nash.},
            url = {https://github.com/phac-nml/bio_hansel}
            }
        }</citation>
    </citations>
</tool>

7:af59ac462926

<tool id="bio_hansel" name="Bio Hansel" version="1.3.0">
    <description>SNV Subtyping with genome assemblies or reads</description>
    <requirements>
        <requirement type="package" version="1.3.0">bio_hansel</requirement>
        <requirement type="package" version="17.2.0">attrs</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ## Preparing file input.
        #if $data_type.type == "paired":

            <param name="type" value="single"/>
            <param name="type_of_scheme" value="heidelberg"/>
            <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/>
            <output name="results.tab">
                <assert_contents>
                    <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+qc_status\s+qc_message"/>
                </assert_contents>
            </output>
            <output name="match_results.tab">
                <assert_contents>
                    <has_text_matching expression="tilename\s+seq\s+is_revcomp\s+contig_id\s+match_index\s+refposition\s+subtype\s+is_pos_tile\s+sample\s+file_path\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/>

            <param name="type_of_scheme" value="heidelberg"/>
            <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/>
            <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/>
            <output name="results.tab">
                <assert_contents>
                    <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+avg_tile_coverage\s+qc_status\s+qc_message"/>
                </assert_contents>
            </output>
            <output name="match_results.tab">
                <assert_contents>
                    <has_text_matching expression="tilename\s+seq\s+freq\s+refposition\s+subtype\s+is_pos_tile\s+is_kmer_freq_okay\s+sample\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/>

    ]]></help>
    <citations>
        <citation type="bibtex">@ARTICLE{a1,
            title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.},
            author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Marisa Rankin, Joanne MacKinnon, Roger Johnson, John H.E. Nash.},
            url = {https://github.com/phac-nml/bio_hansel}
            }
        }</citation>
    </citations>
</tool>