comparison cat_contigs.xml @ 3:f41dbb0b9ff8 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 47be73f0ca2b3a3bcb79a1fa7cf15a63c7facd19

2:7aebc0137f20

<tool id="cat_contigs" name="CAT contigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>annotate with taxonomic classification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
    CAT contigs 
    -c '$contigs_fasta'

    </inputs>
    <outputs>
        <expand macro="outputs" />
    </outputs>
    <tests>
        <test>
            <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
            <expand macro="test_catdb"/>
            <param name="select_outputs" value="contig2classification"/>
            <output name="contig2classification">
                <assert_contents>
                    <has_text text="contig_38063" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
            <expand macro="test_catdb"/>
            <param name="select_outputs" value="predicted_proteins_faa"/>
            <conditional name="names">
                <param name="add_names" value="both"/>

3:f41dbb0b9ff8

<tool id="cat_contigs" name="CAT contigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>annotate with taxonomic classification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
    CAT contigs 
    -c '$contigs_fasta'

    </inputs>
    <outputs>
        <expand macro="outputs" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
            <expand macro="test_catdb"/>
            <param name="select_outputs" value="contig2classification"/>
            <output name="contig2classification">
                <assert_contents>
                    <has_text text="contig_38063" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="4">
            <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
            <expand macro="test_catdb"/>
            <param name="select_outputs" value="predicted_proteins_faa"/>
            <conditional name="names">
                <param name="add_names" value="both"/>