view nanocompore_db.xml @ 1:2af554112418 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit a57b5b935a80db12a0ed867b4219453a2854dd32"

<tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+galaxy1">
    <description>Process SampComp results database</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
mkdir results && 
tar -xf $db --strip-components 1 -C results/ && 
python '$__tool_directory__/NanocomporeDB_process.py'
--db-path 'results/out_SampComp.db'
--ref-fasta '$reference'
--annotation-bed '$annotation'
$bedgraph
    ]]></command>
    <inputs>
        <param name="reference" type="data" format="fasta" label="The reference genome used for read alignment."/>
        <param name="annotation" format="bed" type="data" label="BED file containing the annotation of the transcriptome used as reference when mapping"/>
        <param name="db" type="data" format="tar" label="SampComp Database" />
        <param argument="--bedgraph" type="boolean" truevalue="--bedgraph" falsevalue="" label="Write output in BEDGRAPH format instead of BED"/>
    </inputs>
    <outputs>
        <data name="GMM_logit" format="bed" from_work_dir="GMM_logit_pvalue.bedgraph" label="${tool.name} on ${on_string}: GMM_logit">
            <change_format>
                <when input="bedgraph" value="true" format="bedgraph"/>
            </change_format>
        </data>

        <data name="KS_dwell" format="bed" from_work_dir="KS_dwell_pvalue.bedgraph" label="${tool.name} on ${on_string}: KS_dwell">
            <change_format>
                <when input="bedgraph" value="true" format="bedgraph"/>
            </change_format>
        </data>

        <data name="KS_intensity" format="bed" from_work_dir="KS_intensity_pvalue.bedgraph" label="${tool.name} on ${on_string}: KS_intensity">
            <change_format>
                <when input="bedgraph" value="true" format="bedgraph"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="reference" value="reference.fa"/>
            <param name="annotation" value="annot.bed"/>
            <param name="db" value="DB.tar"/>
            <output name="GMM_logit" file="GMM_logit_pvalue.bed"/>
            <output name="KS_dwell" file="KS_dwell_pvalue.bed"/>
            <output name="KS_intensity" file="KS_intensity_pvalue.bed"/>
        </test>
        <test>
            <param name="reference" value="reference.fa"/>
            <param name="annotation" value="annot.bed"/>
            <param name="db" value="DB.tar"/>
            <param name="bedgraph" value="true"/>   
            <output name="GMM_logit" file="GMM_logit_pvalue.bedgraph"/>
            <output name="KS_dwell" file="KS_dwell_pvalue.bedgraph"/>
            <output name="KS_intensity" file="KS_intensity_pvalue.bedgraph"/>
        </test>        
    </tests>
    <help><![CDATA[
Produces interval bed and bedgraph outputs from NanoCompore SampComp results as input using NaonComporeDB API. 

**References**

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