comparison ncbi_egapx.xml @ 9:28ab345ebab3 draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 92ff2adad69b7a8a49d067e525a97f3ec25a275a

8:908c494fa84e

        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
    #if str($cond_input_style.input_style) == "history":
      #set yamlconfig = $yamlin
    #else:
      #set yamlconfig = "egapx.yaml"
      rm -rf '$yamlconfig' &&
      touch '$yamlconfig' &&
      echo '# yaml generated by ncbi_egapx.xml' >> '$yamlconfig' &&
      echo 'taxid:  $taxid' >> '$yamlconfig' &&
      #if str($reference_genome.genome_type_select) == "indexed":
        echo 'genome:  $reference_genome.genome.fields.path' >> '$yamlconfig' &&
      #elif str($reference_genome.genome_type_select) == "history"
        echo 'genome:  $reference_genome.genome'  >> '$yamlconfig' &&
      #else:
        echo 'genome:  $reference_genome.uri'  >> '$yamlconfig' &&
      #end if
      echo 'reads:' >> '$yamlconfig' &&
      #if str($condrnaseq.rna_type_select) == "history":
        #for $r in $rnaseq:
          echo '  - $r'  >> '$yamlconfig' &&
        #end for
      #else:
        #set rs = $rnaseq.split()
        #set rsplit = [x.strip() for x in $rs]
        #for $r in $rsplit:
          echo '  - $r'  >> '$yamlconfig' &&
        #end for
      #end if
      #if len($xtra.strip()) > 0:
        #set lxtra = $xtra.split("\n")
        #for row in $lxtra:
            echo '$row' >> '$yamlconfig' &&
        #end for
      #end if
      echo '' >> '$yamlconfig' &&
      echo "Calculated contents of egapx yaml" &&
      cat '$yamlconfig' &&
    #end if
    source /galaxy/env.bash &&
    echo \${PATH} &&
    ln -s /galaxy/egapx/egapx_config &&
    python3 /galaxy/egapx/ui/egapx.py '$yamlconfig' -e galaxy -o 'egapx_out'
    ]]></command>
    <inputs>
    <conditional name="cond_input_style">
      <param name="input_style" type="select" label="Fill in a tool form or use an existing yaml configuration from the current history?"
        help="Use a pre-prepared yaml if available. Use the tool form if history files are needed as rna-seq or reference genome inputs for this job">
        <option selected="True" value="history">Use a pre-prepared yaml egapx configuration</option>
        <option value="fillform">Provide configuration details for conversion into a configuration yaml</option>
      </param>
      <when value="history">
        <param name="yamlin" type="data" optional="false" label="egapx configuration yaml file to pass to Nextflow" help="" format="yaml,txt"/>
      </when>
      <when value="fillform">
          <param name="taxid" type="text" optional="false" label="NCBI Taxon ID" help="Used to identify the HMM model files needed"/>
          <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="indexed">Use a Galaxy server built-in genome</option>
                <option value="history" selected="True">Use a genome fasta file from the current history</option>
                <option value="uri">Provide a remote web link URI ("https://...") pointing at the required genome reference fasta file</option>
            </param>
            <when value="indexed">
                <param name="genome" type="select" optional="true" label="Select a built in reference genome or custom genome"
                  help="If not listed, add a custom genome or use a reference genome from the history">
                    <options from_data_table="all_fasta">
                        <validator message="No genomes are available " type="no_options"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="genome" type="data" optional="true" format="fasta" label="Select the reference genome fasta from the current history"/>
            </when>
            <when value="uri">
                <param name="uri" type="text" optional="false" label="URI pointing to the reference genome fasta file" help=""/>
            </when>
          </conditional>
          <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 selected="True" value="list">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="history">
              <param name="rnaseq" type="data" format="fastqsanger, fastqsanger.gz" optional="false" 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" optional="false" 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="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">
            <sanitizer invalid_char="">
                  <valid initial="string.printable">
                </valid>
            </sanitizer>
          </param>
      </when>
    </conditional>
    </inputs>
    <outputs>
      <data name="output" format="gff" label="EGAPx annotation for ${on_string}" from_work_dir="egapx_out/accept.gff"/>
      <collection name="nextflow_stats" label="EGAPx nextflow stats for ${on_string}" type="list">
        <data name="nf_log" format="txt" label="Nextflow execution log" from_work_dir="egapx_out/nextflow.log"/>
        <data name="nf_report" format="html" label="Nextflow execution report" from_work_dir="egapx_out/run.report.html"/>
        <data name="nf_trace" format="tabular" label="Nextflow trace file" from_work_dir="egapx_out/run.trace.txt"/>
        <data name="nf_timeline" format="html" label="Nextflow execution timeline" from_work_dir="egapx_out/run.timeline.html"/>
        <data name="nf_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/run_params.yaml"/>
      </collection>
    </outputs>
    <tests>
      <test expect_test_failure="true">
        <param name="input_style" value="history"/>
        <param name="yamlin" value="input.yaml"/>
        <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>
          <element name="nf_report"><assert_contents><has_size min="1"/></assert_contents></element>
          <element name="nf_trace"><assert_contents><has_size min="1"/></assert_contents></element>
          <element name="nf_timeline"><assert_contents><has_size min="1"/></assert_contents></element>
          <element name="nf_params"><assert_contents><has_size min="1"/></assert_contents></element>
        </output_collection>
      </test>
      <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="proteins: []&#10;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>
          <element name="nf_report"><assert_contents><has_size min="1"/></assert_contents></element>
          <element name="nf_trace"><assert_contents><has_size min="1"/></assert_contents></element>
          <element name="nf_timeline"><assert_contents><has_size min="1"/></assert_contents></element>
          <element name="nf_params"><assert_contents><has_size min="1"/></assert_contents></element>
        </output_collection>
      </test>
    </tests>
  <help><![CDATA[
Galaxy tool wrapping the Eukaryotic Genome Annotation Pipeline (EGAPx)
=================================================================================================

.. class:: warningmark

 2024-03-27 11:19:18        129 .command.sh
 2024-03-27 11:20:24        276 .command.trace
 2024-03-27 11:20:25          1 .exitcode
 $ aws s3 ls s3://temp_datapath/D_farinae/96/621c4ba4e6e87a4d869c696fe50034/output/
 2024-03-27 11:20:24   17127134 aligns.paf


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

9:28ab345ebab3

        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
    #if str($cond_input_style.input_style) == "fillform":
        #set yamlconfig = "egapx.yaml"
        echo '# yaml generated by ncbi_egapx.xml' > '$yamlconfig' &&
        #if str($reference_genome.genome_type_select) == "history"
            echo 'genome: $reference_genome.genome' >> '$yamlconfig' &&
        #elif str($reference_genome.genome_type_select) == "indexed":
            echo 'genome: $reference_genome.genome.fields.path' >> '$yamlconfig' &&
        #else:
            echo 'genome: $reference_genome.uri' >> '$yamlconfig' &&
        #end if
        echo 'taxid: $taxid' >> '$yamlconfig' &&
        echo 'reads:' >> '$yamlconfig' &&
        #if str($condrnaseq.rna_type_select) == "list":
            #set rs = $rnaseq.split()
            #set rsplit = [x.strip() for x in $rs]
            #for $r in $rsplit:
                echo '  - $r'  >> '$yamlconfig' &&
            #end for
        #else:
            #for $r in $rnaseq:
                echo '  - $r'  >> '$yamlconfig' &&
            #end for
        #end if
        #if $proteins:
            echo 'proteins: $proteins' >> '$yamlconfig' &&
        #end if
        #if len($xtra.strip()) > 0:
            #set lxtra = $xtra.split("\n")
            #for row in $lxtra:
                echo '$row' >> '$yamlconfig' &&
            #end for
        #end if
        echo '' >> '$yamlconfig' &&
        echo "Calculated contents of egapx yaml" &&
        cat '$yamlconfig' &&
    #else:
        #set yamlconfig = $yamlin
    #end if
    source /galaxy/env.bash &&
    echo \${PATH} &&
    ln -s /galaxy/egapx/egapx_config &&
    python3 /galaxy/egapx/ui/egapx.py '$yamlconfig' -e galaxy -o 'egapx_out'
    ]]></command>
    <inputs>
        <conditional name="cond_input_style">
            <param name="input_style" type="select" label="Fill in a tool form or use an existing yaml configuration from the current history?"
                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 value="history">
                        <param name="genome" type="data" format="fasta" label="Select the reference genome fasta from the current history"/>
                    </when>
                    <when value="indexed">
                        <param name="genome" type="select" label="Select a built in reference genome or custom genome"
                            help="If not listed, add a custom genome or use a reference genome from the history">
                            <options from_data_table="all_fasta">
                                <validator message="No genomes are available " type="no_options"/>
                            </options>
                        </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"/>
                <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,tasta.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">
                    <sanitizer invalid_char="">
                        <valid initial="string.printable"/>
                    </sanitizer>
                </param>
            </when>
            <when value="history">
                <param name="yamlin" type="data" format="yaml,txt" label="egapx configuration yaml file to pass to Nextflow"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="gff" label="EGAPx annotation for ${on_string}" from_work_dir="egapx_out/accept.gff"/>
        <collection name="nextflow_stats" type="list" label="EGAPx nextflow stats for ${on_string}">
            <data name="nf_log" format="txt" label="Nextflow execution log" from_work_dir="egapx_out/nextflow.log"/>
            <data name="nf_report" format="html" label="Nextflow execution report" from_work_dir="egapx_out/run.report.html"/>
            <data name="nf_trace" format="tabular" label="Nextflow trace file" from_work_dir="egapx_out/run.trace.txt"/>
            <data name="nf_timeline" format="html" label="Nextflow execution timeline" from_work_dir="egapx_out/run.timeline.html"/>
            <data name="nf_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/run_params.yaml"/>
        </collection>
    </outputs>
    <tests>
        <test expect_test_failure="true">
            <param name="input_style" value="history"/>
            <param name="yamlin" value="input.yaml"/>
            <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>
                <element name="nf_report"><assert_contents><has_size min="1"/></assert_contents></element>
                <element name="nf_trace"><assert_contents><has_size min="1"/></assert_contents></element>
                <element name="nf_timeline"><assert_contents><has_size min="1"/></assert_contents></element>
                <element name="nf_params"><assert_contents><has_size min="1"/></assert_contents></element>
            </output_collection>
        </test>
        <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="proteins: []&#10;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>
                <element name="nf_report"><assert_contents><has_size min="1"/></assert_contents></element>
                <element name="nf_trace"><assert_contents><has_size min="1"/></assert_contents></element>
                <element name="nf_timeline"><assert_contents><has_size min="1"/></assert_contents></element>
                <element name="nf_params"><assert_contents><has_size min="1"/></assert_contents></element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Galaxy tool wrapping the Eukaryotic Genome Annotation Pipeline (EGAPx)
=================================================================================================

.. class:: warningmark

 2024-03-27 11:19:18        129 .command.sh
 2024-03-27 11:20:24        276 .command.trace
 2024-03-27 11:20:25          1 .exitcode
 $ aws s3 ls s3://temp_datapath/D_farinae/96/621c4ba4e6e87a4d869c696fe50034/output/
 2024-03-27 11:20:24   17127134 aligns.paf
    ]]></help>
    <expand macro="citations"/>
</tool>