comparison ncbi_egapx.xml @ 16:d167f698d5e9 draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit d5c4a9faa18df570d02ce208d301a160d8555f58

15:815d401afcfe

    ]]></command>
    <configfiles>
        <configfile name="egapx_config"><![CDATA[
#if str($cond_input_style.input_style) == "fillform"
# yaml generated by ncbi_egapx.xml
    #if str($reference_genome.genome_type_select) == "history"
        #set genome_value = $reference_genome.genome
    #elif str($reference_genome.genome_type_select) == "indexed"
        #set genome_value = $reference_genome.genome.fields.path
    #else
        #set genome_value = $reference_genome.uri
    #end if
genome: $genome_value
taxid: $taxid
    #if str($condrnaseq.rna_type_select) == "list"
        #set $reads_values = $rnaseq.split()
    #else
        #set $reads_values = $rnaseq
    #end if
reads:

                help="Use the tool form to select inputs from the history, or use a pre-prepared yaml file.">
                <option value="fillform" selected="True">Provide configuration details for conversion into a configuration yaml</option>
                <option value="history">Use a pre-prepared yaml egapx configuration</option>
            </param> 
            <when value="fillform">
                <conditional name="reference_genome">
                    <param name="genome_type_select" type="select" label="Reference genome source for mapping supplied RNA-seq reads"
                        help="Select a built in, history or remote URI for the reference genome FASTA">
                        <option value="history" selected="True">Use a genome FASTA file from the current history</option>
                        <option value="indexed">Use a Galaxy server built-in genome</option>
                        <option value="uri">Provide a remote web link URI ("https://...") pointing at the required genome reference FASTA file</option>
                    </param>

                    </when>
                    <when value="uri">
                        <param name="uri" type="text" label="URI pointing to the reference genome FASTA file"/>
                    </when>
                </conditional>
                <param name="taxid" type="integer" min="0" value="0" label="NCBI Taxon ID" help="Used to identify the HMM model files needed"/>

                <conditional name="condrnaseq">
                    <param name="rna_type_select" type="select" label="RNA sequence data source"
                        help="Select RNAseq input data from history or input a list of SRA identifiers or remote URI">
                        <option value="list" selected="True">Type in a list of SRA identifiers and/or remote RNA-seq FASTA URI</option>
                        <option value="history">Select one or more RNA-seq fastq datasets from the current history</option>
                    </param>
                    <when value="list">
                        <param name="rnaseq" type="text" area="true" label="List all required individual RNA-seq URI or SRA identifiers, separated by spaces or newlines"
                            help="Either a working URI for a RNA-seq FASTA, or a bare SRA identifier will work - can be mixed">
                            <validator type="empty_field"/>
                        </param>
                    </when>
                    <when value="history">
                        <param name="rnaseq" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Select multiple RNA-seq fastqsanger inputs from the current history"
                            help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration"/>
                    </when>
                </conditional>
                <param name="proteins" type="data" format="fasta,fasta.gz" optional="true" label="Select a protein set"/>
                <param name="xtra" type="text" area="true" label="Additional yaml to append to the egapx.yaml configuration"
                    help="Not normally needed but useful for testing additional configuration elements">

    </outputs>
    <tests>
        <test expect_test_failure="true">
            <param name="input_style" value="fillform"/>
            <param name="taxid" value="6954"/>
            <param name="genome_type_select" 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="rna_type_select" value="list"/>
            <param name="rnaseq" value="https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.2 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.2"/>
            <param name="xtra" value="hmm: https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/gnomon/hmm_parameters/6956.params&#10;tasks:&#10;  star_wnode:&#10;    star_wnode: -cpus-per-worker 4"/>
            <output name="output"><assert_contents><has_size min="1"/></assert_contents></output>
            <output_collection name="nextflow_stats" type="list">
                <element name="nf_log"><assert_contents><has_size min="1"/></assert_contents></element>

16:d167f698d5e9

    ]]></command>
    <configfiles>
        <configfile name="egapx_config"><![CDATA[
#if str($cond_input_style.input_style) == "fillform"
# yaml generated by ncbi_egapx.xml
    #if str($cond_input_style.cond_genome_style.genome_style) == "history"
        #set genome_value = $cond_input_style.cond_genome_style.genome
    #elif str($cond_input_style.cond_genome_style.genome_style) == "indexed"
        #set genome_value = $cond_input_style.cond_genome_style.genome.fields.path
    #else
        #set genome_value = $cond_input_style.cond_genome_style.uri
    #end if
genome: $genome_value
taxid: $taxid
    #if str($cond_rnaseq_style.rnaseq_style) == "list"
        #set $reads_values = $rnaseq.split()
    #else
        #set $reads_values = $rnaseq
    #end if
reads:

                help="Use the tool form to select inputs from the history, or use a pre-prepared yaml file.">
                <option value="fillform" selected="True">Provide configuration details for conversion into a configuration yaml</option>
                <option value="history">Use a pre-prepared yaml egapx configuration</option>
            </param> 
            <when value="fillform">
                <conditional name="cond_genome_style">
                    <param name="genome_style" type="select" label="Reference genome source for mapping supplied RNA-seq reads"
                        help="Select a built in, history or remote URI for the reference genome FASTA">
                        <option value="history" selected="True">Use a genome FASTA file from the current history</option>
                        <option value="indexed">Use a Galaxy server built-in genome</option>
                        <option value="uri">Provide a remote web link URI ("https://...") pointing at the required genome reference FASTA file</option>
                    </param>

                    </when>
                    <when value="uri">
                        <param name="uri" type="text" label="URI pointing to the reference genome FASTA file"/>
                    </when>
                </conditional>

                <param name="taxid" type="text" label="NCBI Taxon ID" help="Used to identify the HMM model files needed">
                    <validator type="regex" message="Numeric">^[0-9]+$</validator>
                </param>

                <conditional name="cond_rnaseq_style">
                    <param name="rnaseq_style" type="select" label="RNA sequence data source"
                        help="Select RNAseq input data from history or input a list of SRA identifiers or remote URI">
                        <option value="history" selected="True">Select one or more RNA-seq fastq datasets from the current history</option>
                        <option value="list">Type in a list of SRA identifiers and/or remote RNA-seq FASTA URI</option>
                    </param>
                    <when value="history">
                        <param name="rnaseq" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Select multiple RNA-seq fastqsanger inputs from the current history"
                            help="All selected rna-seq fastqsanger will be added to the yaml for egapx configuration"/>
                    </when>
                    <when value="list">
                        <param name="rnaseq" type="text" area="true" label="List all required individual RNA-seq URI or SRA identifiers, separated by spaces or newlines"
                            help="Either a working URI for a RNA-seq FASTA, or a bare SRA identifier will work - can be mixed">
                            <validator type="empty_field"/>
                        </param>
                    </when>
                </conditional>
                <param name="proteins" type="data" format="fasta,fasta.gz" optional="true" label="Select a protein set"/>
                <param name="xtra" type="text" area="true" label="Additional yaml to append to the egapx.yaml configuration"
                    help="Not normally needed but useful for testing additional configuration elements">

    </outputs>
    <tests>
        <test expect_test_failure="true">
            <param name="input_style" value="fillform"/>
            <param name="taxid" value="6954"/>
            <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="rnaseq_style" value="list"/>
            <param name="rnaseq" value="https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR8506572.2 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.1 https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/sample_data/Dermatophagoides_farinae_small/SRR9005248.2"/>
            <param name="xtra" value="hmm: https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/EGAP/gnomon/hmm_parameters/6956.params&#10;tasks:&#10;  star_wnode:&#10;    star_wnode: -cpus-per-worker 4"/>
            <output name="output"><assert_contents><has_size min="1"/></assert_contents></output>
            <output_collection name="nextflow_stats" type="list">
                <element name="nf_log"><assert_contents><has_size min="1"/></assert_contents></element>