comparison idba_ud.xml @ 3:1542a2fffe0c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a

2:694b0f55b744

<tool id="idba_ud" name="IDBA-UD" version="@IDBA_VERSION@+galaxy1">
    <description>
        Iterative de Bruijn Graph Assembler for data with highly uneven depth
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[

                <not_has_text text="--no_local" />
                <not_has_text text="--no_coverage" />
                <not_has_text text="--no_correct" />
                <not_has_text text="--pre_correction" />
            </assert_command>
            <output name="output" file="out/scaffold.fa" ftype="fasta"/>
        </test>
        <!-- read levels test -->
        <test>
            <param name="read" value="merged.fa" ftype="fasta"/>
            <param name="read_level_2" ftype="fasta" value="merged.fa"/>

                <has_text text="--read_level_2" />
                <has_text text="--read_level_3" />
                <has_text text="--read_level_4" />
                <has_text text="--read_level_5" />
            </assert_command>
            <output name="output" file="out/scaffold.fa" ftype="fasta" lines_diff="2"/>
        </test>
        <!-- k-mer options -->
        <test>
            <param name="read" value="merged.fa" ftype="fasta"/>
            <param name="mink" value="19"/>

                <has_text text="--prefix 2" />
                <has_text text="--min_count 1" />
                <has_text text="--min_support 2" />
                <has_text text="--seed_kmer 29" />
            </assert_command>
            <output name="output" file="out/scaffold.fa" lines_diff="2"/>
        </test>
        <!-- filter options -->
        <test>
            <param name="read" value="merged.fa" ftype="fasta"/>
            <param name="min_contig" value="199"/>

            <assert_command>
                <has_text text="--min_contig 199" />
                <has_text text="--similar 0.96" />
                <has_text text="--max_mismatch 2" />
            </assert_command>
            <output name="output" file="out/scaffold.fa" lines_diff="2"/>
        </test>
        <!-- min-pairs and other options -->
        <test>
            <param name="read" value="merged.fa" ftype="fasta"/>
            <param name="min_pairs" value="2"/>

                <has_text text="--no_local" />
                <has_text text="--no_coverage" />
                <has_text text="--no_correct" />
                <has_text text="--pre_correction" />
            </assert_command>
            <output name="output" file="out/scaffold.fa" lines_diff="2"/>
        </test>
    </tests>
    <expand macro="help" more_help="IDBA-UD is an extension of IDBA algorithm for Short Reads Sequencing data with Highly Uneven Sequencing Depth. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions."/>
    <expand macro="citations">
        <citation type="doi">10.1093/bioinformatics/bts174</citation>

3:1542a2fffe0c

<tool id="idba_ud" name="IDBA-UD" version="@IDBA_VERSION@+galaxy1">
    <description>
        Iterative de Bruijn Graph Assembler for data with highly uneven depth
    </description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[

                <not_has_text text="--no_local" />
                <not_has_text text="--no_coverage" />
                <not_has_text text="--no_correct" />
                <not_has_text text="--pre_correction" />
            </assert_command>
            <output name="output" file="out/scaffold.fa" ftype="fasta" compare="re_match"/>
        </test>
        <!-- read levels test -->
        <test>
            <param name="read" value="merged.fa" ftype="fasta"/>
            <param name="read_level_2" ftype="fasta" value="merged.fa"/>

                <has_text text="--read_level_2" />
                <has_text text="--read_level_3" />
                <has_text text="--read_level_4" />
                <has_text text="--read_level_5" />
            </assert_command>
            <output name="output" file="out/scaffold.fa" ftype="fasta" compare="re_match"/>
        </test>
        <!-- k-mer options -->
        <test>
            <param name="read" value="merged.fa" ftype="fasta"/>
            <param name="mink" value="19"/>

                <has_text text="--prefix 2" />
                <has_text text="--min_count 1" />
                <has_text text="--min_support 2" />
                <has_text text="--seed_kmer 29" />
            </assert_command>
            <output name="output" file="out/scaffold.fa" compare="re_match"/>
        </test>
        <!-- filter options -->
        <test>
            <param name="read" value="merged.fa" ftype="fasta"/>
            <param name="min_contig" value="199"/>

            <assert_command>
                <has_text text="--min_contig 199" />
                <has_text text="--similar 0.96" />
                <has_text text="--max_mismatch 2" />
            </assert_command>
            <output name="output" file="out/scaffold.fa" compare="re_match"/>
        </test>
        <!-- min-pairs and other options -->
        <test>
            <param name="read" value="merged.fa" ftype="fasta"/>
            <param name="min_pairs" value="2"/>

                <has_text text="--no_local" />
                <has_text text="--no_coverage" />
                <has_text text="--no_correct" />
                <has_text text="--pre_correction" />
            </assert_command>
            <output name="output" file="out/scaffold.fa" compare="re_match"/>
        </test>
    </tests>
    <expand macro="help" more_help="IDBA-UD is an extension of IDBA algorithm for Short Reads Sequencing data with Highly Uneven Sequencing Depth. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions."/>
    <expand macro="citations">
        <citation type="doi">10.1093/bioinformatics/bts174</citation>