comparison CreateSchema.xml @ 2:6a8df4d75f3a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 501c1cb91f4b91ec93e6df6e555323bbe8e2b703

1:220e2f7ff8bb

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        mkdir 'input' &&
        #for $file in $input_file
        ln -sf '$file' 'input/${file.element_identifier}' &&
        #end for
        chewBBACA.py CreateSchema 
            #if $training_file:
                --ptf '$training_file'
            #end if

                    <has_archive_member path="schema_seed/\.schema_config"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
            <param name="training_file" value="Streptococcus_agalactiae.trn"/>
            <output name="schema">
                <assert_contents>
                    <has_archive_member path="schema_seed/.*\.fasta" n="198"/>

        <test expect_num_outputs="1">
            <param name="input_file" value="CDS_Str_agalactiae.fasta"/>
            <param name="cds_input" value="true"/>
            <output name="schema">
                <assert_contents>
                    <has_archive_member path="schema_seed/CDS-Str-agalactiae-protein1.fasta"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

2:6a8df4d75f3a

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #import re
        mkdir 'input' &&
        #for $file in $input_file
        #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($file.element_identifier))
        ln -sf '$file' 'input/${escaped_element_identifier}.${file.ext}' &&
        #end for
        chewBBACA.py CreateSchema 
            #if $training_file:
                --ptf '$training_file'
            #end if

                    <has_archive_member path="schema_seed/\.schema_config"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic"/>
            <output name="schema">
                <assert_contents>
                    <has_archive_member path="schema_seed/.*\.fasta" n="204"/>
                    <has_archive_member path="schema_seed/short/.*\.fasta" n="102"/>
                    <has_archive_member path="schema_seed/\.schema_config"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/>
            <param name="training_file" value="Streptococcus_agalactiae.trn"/>
            <output name="schema">
                <assert_contents>
                    <has_archive_member path="schema_seed/.*\.fasta" n="198"/>

        <test expect_num_outputs="1">
            <param name="input_file" value="CDS_Str_agalactiae.fasta"/>
            <param name="cds_input" value="true"/>
            <output name="schema">
                <assert_contents>
                    <has_archive_member path="schema_seed/CDS-Str-agalactiae-fasta-protein1.fasta"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>