comparison ncbi_egapx.xml @ 41:d129c3d0e920 draft default tip

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 8278322cb9db499c593669d2bb8b740024ecf5dc

40:b095c69eab5b

    ##   - nextflow conda environment
    ##   - EGPAx python virtual environment
    source /galaxy/env.bash &&
    python3 /galaxy/scripts/galaxy-resource-config.py &&
    ## run EGAPx
    python3 /galaxy/egapx/ui/egapx.py '$yamlconfig' -e galaxy -o 'egapx_out' &&
    ## hack to support 0.2-alpha
    if [ -e egapx_out/accept.gff ]; then ln -s accept.gff egapx_out/complete.genomic.gff; fi
    #if $developer.collect_star_bams
    && bash '$__tool_directory__/get-bams.bash'
    #end if
    ]]></command>
    <environment_variables>
         <environment_variable name="NXF_DEBUG">3</environment_variable>
    </environment_variables>
    <configfiles>
        <configfile name="short_reads_config"><![CDATA[#slurp
        #if $cond_input_style.input_style == "fillform" and $cond_input_style.cond_short_reads_style.short_reads_style == "history"
            #import re

                <param name="yamlin" type="data" format="yaml" label="egapx configuration yaml file to pass to Nextflow"/>
            </when>
        </conditional>
        <section name="developer" title="Developer options" expanded="false">
            <param name="collect_star_bams" type="boolean" checked="false" label="Collect BAM output from STAR"/>
        </section>
    </inputs>
    <outputs>
        <data name="complete_genomic_gff" format="gff" label="Final annotation for ${on_string}" from_work_dir="egapx_out/complete.genomic.gff"/>
        <collection name="output_files" type="list" label="EGAPx output for ${on_string}">

            <discover_datasets pattern="(?:.+/)?bam\.[0-9A-Za-z]{10}/(?P&lt;designation&gt;.+)\.bam" format="bam" directory="egapx_out" recurse="true" match_relative_path="true"/>
            <filter>developer['collect_star_bams']</filter>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="27" expect_test_failure="true">
            <conditional name="cond_input_style">
                <param name="input_style" value="fillform"/>
                <conditional name="cond_genome_style">
                    <param name="genome_style" value="uri"/>
                    <param name="uri" value="https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/809/275/GCF_020809275.1_ASM2080927v1/GCF_020809275.1_ASM2080927v1_genomic.fna.gz"/>

                    <param name="short_reads" value="https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572_1.gz https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572_2.gz https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248_1.gz https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248_2.gz"/>
                </conditional>
            </conditional>
            <section name="developer">
                <param name="collect_star_bams" value="true"/>
            </section>
            <expand macro="test_outputs"/>
        </test>
        <test expect_num_outputs="27" expect_test_failure="true">
            <conditional name="cond_input_style">
                <param name="input_style" value="history"/>
                <param name="yamlin" value="input.yaml"/>
            </conditional>
            <section name="developer">
                <param name="collect_star_bams" value="true"/>
            </section>
            <expand macro="test_outputs"/>
        </test>
    </tests>
    <help><![CDATA[

41:d129c3d0e920

    ##   - nextflow conda environment
    ##   - EGPAx python virtual environment
    source /galaxy/env.bash &&
    python3 /galaxy/scripts/galaxy-resource-config.py &&
    ## run EGAPx
    python3 /galaxy/egapx/ui/egapx.py
    #if $developer.query_limit.query_limit_selector == "false"
        --force
    #end if
    '$yamlconfig' -e galaxy -o 'egapx_out' &&
    ## hack to support 0.2-alpha
    if [ -e egapx_out/accept.gff ]; then ln -s accept.gff egapx_out/complete.genomic.gff; fi
    #if $developer.collect_star_bams
    && bash '$__tool_directory__/get-bams.bash'
    #end if
    ]]></command>
    <environment_variables>
         <environment_variable name="NXF_DEBUG">3</environment_variable>
         <environment_variable name="EGAPX_RNASEQ_QUERY_LIMIT">$getVar('developer.query_limit.rnaseq_query_limit', '20')</environment_variable>
    </environment_variables>
    <configfiles>
        <configfile name="short_reads_config"><![CDATA[#slurp
        #if $cond_input_style.input_style == "fillform" and $cond_input_style.cond_short_reads_style.short_reads_style == "history"
            #import re

                <param name="yamlin" type="data" format="yaml" label="egapx configuration yaml file to pass to Nextflow"/>
            </when>
        </conditional>
        <section name="developer" title="Developer options" expanded="false">
            <param name="collect_star_bams" type="boolean" checked="false" label="Collect BAM output from STAR"/>
            <conditional name="query_limit">
                <param name="query_limit_selector" type="select" label="Enforce SRA query limit">
                    <option value="true" selected="True">Yes</option>
                    <option value="false">No</option>
                </param>
                <when value="true">
                    <param name="rnaseq_query_limit" type="integer" min="0" value="20" label="SRA query limit"/>
                </when>
                <when value="false"/>
            </conditional>
        </section>
    </inputs>
    <outputs>
        <data name="complete_genomic_gff" format="gff" label="Final annotation for ${on_string}" from_work_dir="egapx_out/complete.genomic.gff"/>
        <collection name="output_files" type="list" label="EGAPx output for ${on_string}">

            <discover_datasets pattern="(?:.+/)?bam\.[0-9A-Za-z]{10}/(?P&lt;designation&gt;.+)\.bam" format="bam" directory="egapx_out" recurse="true" match_relative_path="true"/>
            <filter>developer['collect_star_bams']</filter>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="27" expect_test_failure="false">
            <conditional name="cond_input_style">
                <param name="input_style" value="fillform"/>
                <conditional name="cond_genome_style">
                    <param name="genome_style" value="uri"/>
                    <param name="uri" value="https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/020/809/275/GCF_020809275.1_ASM2080927v1/GCF_020809275.1_ASM2080927v1_genomic.fna.gz"/>

                    <param name="short_reads" value="https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572_1.gz https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572_2.gz https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248_1.gz https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248_2.gz"/>
                </conditional>
            </conditional>
            <section name="developer">
                <param name="collect_star_bams" value="true"/>
                <conditional name="query_limit">
                    <param name="query_limit_selector" value="true"/>
                    <param name="rnaseq_query_limit" value="20"/>
                </conditional>
            </section>
            <expand macro="test_outputs"/>
        </test>
        <test expect_num_outputs="27" expect_test_failure="false">
            <conditional name="cond_input_style">
                <param name="input_style" value="history"/>
                <param name="yamlin" value="input.yaml"/>
            </conditional>
            <section name="developer">
                <param name="collect_star_bams" value="true"/>
                <conditional name="query_limit">
                    <param name="query_limit_selector" value="true"/>
                    <param name="rnaseq_query_limit" value="20"/>
                </conditional>
            </section>
            <expand macro="test_outputs"/>
        </test>
    </tests>
    <help><![CDATA[