comparison nanocompore_db.xml @ 2:ca9e70c0fef8 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit c2985b5c91a932e175cbfaf9b54a76e23beff9e9"

1:2af554112418

<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**

2:ca9e70c0fef8

<tool id="nanocompore_db" name="NanoComporeDB" version="@TOOL_VERSION@+galaxy2">
    <description>Process SampComp results database</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
mkdir -p results plots && 
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'
--pvalue-types '$pvalue_types'
--pvalue-threshold $pvalue_threshold
--out-dir ./plots/
$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="--pvalue-types" type="text" value="GMM_logit_pvalue,KS_dwell_pvalue,KS_intensity_pvalue" label="pvalue field names" help="Comma-separated values.">
            <validator type="regex" message="No valid pvalue field name list.">^(\w+(,\w+)*)?$</validator>
        </param>
        <param argument="pvalue-threshold" type="float" value="1.0" min="0.0" label="Maximum reported p-value"/>
        <param argument="--bedgraph" type="boolean" truevalue="--bedgraph" falsevalue="" label="Write output in BedGraph format instead of BED"/>
    </inputs>
    <outputs>
        <collection name="pvalue_output" type="list">
            <discover_datasets pattern="__name_and_ext__" directory="plots" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="reference" value="reference.fa"/>
            <param name="annotation" value="annot.bed"/>
            <param name="db" value="DB.tar" ftype="tar" />
            <output_collection name="pvalue_output" type="list" count="3">
                <element name="GMM_logit_pvalue" file="GMM_logit_pvalue.bed" ftype="bed"/>
                <element name="KS_dwell_pvalue" file="KS_dwell_pvalue.bed" ftype="bed"/>
                <element name="KS_intensity_pvalue" file="KS_intensity_pvalue.bed" ftype="bed"/>
            </output_collection>
        </test>
        <test>
            <param name="reference" value="reference.fa"/>
            <param name="annotation" value="annot.bed"/>
            <param name="db" value="DB.tar" ftype="tar" />
            <param name="bedgraph" value="true"/>
            <param name="pvalue_types" value="GMM_logit_pvalue,KS_dwell_pvalue"/>
            <output_collection name="pvalue_output" type="list" count="2">
                <element name="GMM_logit_pvalue" file="GMM_logit_pvalue.bedgraph" ftype="bedgraph"/>
                <element name="KS_dwell_pvalue" file="KS_dwell_pvalue.bedgraph" ftype="bedgraph"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Produces interval bed and bedgraph outputs from NanoCompore SampComp results as input using NaonComporeDB API. 

**References**