annotate raven.xml @ 5:5c55448d0f33 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven commit 7bd5e845f7f0a531d619f66193470127a2a7a7ea

<tool id="raven" name="Raven" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>De novo assembly of Oxford Nanopore Technologies data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <!--TODO in future version : enable CUDA support for racon polishing-->
    <command detect_errors="exit_code"><![CDATA[
#if $input_reads.is_of_type("fasta")
    ln -s '$input_reads' ./input.fa &&
    #set input = "input.fa"
#elif $input_reads.is_of_type("fasta.gz")
    ln -s '$input_reads' ./input.fa.gz &&
    #set input = "input.fa.gz"
#elif $input_reads.is_of_type("fastq")
    ln -s '$input_reads' ./input.fq &&
    #set input = "input.fq"
#elif $input_reads.is_of_type("fastq.gz")
    ln -s '$input_reads' ./input.fq.gz &&
    #set input = "input.fq.gz"
#end if
raven
--kmer-len '$kmer_len'
--window-len '$window_len'
--frequency '$frequency'
--polishing-rounds '$polishing_rounds'
--match '$match'
--mismatch '$mismatch'
--gap '$gap'
--kMaxNumOverlaps '$kMaxNumOverlaps'
--identity $identity
--min-unitig-size $min_unitig_size
--use-micromizers $use_micromizers
$graphical_fragment_assembly
--disable-checkpoints
-t \${GALAXY_SLOTS:-4}
'$input'
> '$out_fasta'
    ]]></command>
    <inputs>
        <param name="input_reads" type="data" format="fasta,fastq,fasta.gz,fastq.gz"/>
        <param argument="--kmer-len" type="integer" value="15" label="Length of minimizers used to find overlaps"/>
        <param argument="--window-len" type="integer" value="5" label="Length of sliding window from which minimizers are sampled"/>
        <param argument="--frequency" type="float" value="0.001" label="Threshold for ignoring most frequent minimizers"/>
        <param argument="--identity" type="float" value="0" label="Threshold for overlap between two reads in order to construct an edge between them" help="If set to zero, this functionality is disabled"/>
        <param argument="--kMaxNumOverlaps" type="integer" value="32" label="Maximum number of overlaps that will be taken during FindOverlapsAndCreatePiles stage"/>
        <param argument="--min-unitig-size" type="integer" value="9999" label="Minimal unitig size"/>

        <param argument="--polishing-rounds" type="integer" value="2" min="0" label="Number of times racon polishing is invoked"/>
        <param argument="--match" type="integer" value="3"/>
        <param argument="--mismatch" type="integer" value="-5"/>
        <param argument="--gap" type="integer" value="-4" max="-1"/>
        <param argument="--graphical-fragment-assembly" type="boolean" truevalue="--graphical-fragment-assembly out.gfa" falsevalue="" label="output graphical fragment assembly file?" checked="true"/>
        <param argument="--use-micromizers" type="boolean" truevalue="--use-micromizers" falsevalue="" label="Use micromizers instead of mimizers in graph construction" help="Performance will increase slightly and memory consumption will decrease but results could be slightly worse"/>
    </inputs>
    <outputs>
        <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)" from_work_dir="out.gfa">
            <filter>graphical_fragment_assembly</filter>
        </data>
        <data name="out_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)"/>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/>
            <output name="out_gfa">
                <assert_contents>
                    <has_n_lines n="2"/>
                    <has_text_matching expression="^S\tUtg52\t[ATCG]{30000,40000}\tLN:i:36[0-9]{3}\tRC:i:22\tdp:f:8\nS\tCtg54\t[ATCG]{9000,10000}\tLN:i:9361\tRC:i:4"/>
                </assert_contents>
            </output>
            <output name="out_fasta">
                <assert_contents>
                    <has_n_lines n="2"/>
                    <has_text_matching expression="^&gt;Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/>
                </assert_contents>
            </output>
        </test>
        <!-- <test expect_num_outputs="1">
            <param name="input_reads" ftype="fastq.gz" value="ERA476754.fastq.gz"/>
            <param name="graphical_fragment_assembly" value="false"/>
            <output name="out_fasta">
                <assert_contents>
                    <has_n_lines n="2"/>
                    <has_text_matching expression="^>Utg52 LN:i:36[0-9]{3} RC:i:22 XO:i:0\n[ATCG]{30000,40000}$"/>
                </assert_contents>
            </output>
        </test> -->
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

@WID@

**Input**
- fasta / fastq / fasta.gz / fastq.gz data

**Output**

- Assembled genome (FASTA)
- Graphical fragment assembly (optional) (.txt)

**References**

@REFERENCES@
    ]]></help>
    <expand macro="citations"/>
</tool>