comparison generate_cannot_links.xml @ 6:fd17362def4f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6

5:a490494875c7

    <command detect_errors="exit_code"><![CDATA[
#import re
@FASTA_FILES@
SemiBin2
    generate_cannot_links
    --input-fasta 'contigs.fasta'
    --output 'output'
    --cannot-name 'cannot'
#if $mode.ref.select == "cached"
    --reference-db-data-dir '$mode.ref.cached_db.fields.path'
#end if

    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="mode">
                <param name="select" value="single"/>
                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
                <conditional name="ref">
                    <param name="select" value="taxonomy"/>
                    <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
                </conditional>
            </conditional>

            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="mode">
                <param name="select" value="single"/>
                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
                <conditional name="ref">
                    <param name="select" value="taxonomy"/>
                    <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
                </conditional>
            </conditional>

6:fd17362def4f

    <command detect_errors="exit_code"><![CDATA[
#import re
@FASTA_FILES@
SemiBin2
    generate_cannot_links
#if $mode.select == 'single' or $mode.select == 'co'
    --input-fasta 'contigs.$input_fasta.ext'
#else
    --input_fasta 'contigs.fasta'
#end if
    --output 'output'
    --cannot-name 'cannot'
#if $mode.ref.select == "cached"
    --reference-db-data-dir '$mode.ref.cached_db.fields.path'
#end if

    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="mode">
                <param name="select" value="single"/>
                <param name="input_fasta" ftype="fasta.gz" value="input_single.fasta.gz"/>
                <conditional name="ref">
                    <param name="select" value="taxonomy"/>
                    <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
                </conditional>
            </conditional>

            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="mode">
                <param name="select" value="single"/>
                <param name="input_fasta" ftype="fasta.bz2" value="input_single.fasta.bz2"/>
                <conditional name="ref">
                    <param name="select" value="taxonomy"/>
                    <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
                </conditional>
            </conditional>