comparison make_EAR.xml @ 2:a34826ae0a73 draft

planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176

1:b61022e1b807

#if $pre_curation_assembly_data.hap2_precuration_data.hap2_exists_precuration == "yes"
# ASSEMBLY DATA
ASSEMBLIES:
    Pre-curation:
        pipeline: [Hifiasm_v0.19.4|HiC|l0, Purge_Dups_v1.2.6|, Bionano_vGalaxy_3.7.0, YaHS_v1.1]
        '${pre_curation_assembly_data.haplotype_selection}': 
            gfastats--nstar-report_txt: '${pre_curation_assembly_data.gfstats_nstar_report_precuration}'
            busco_short_summary_txt: '${pre_curation_assembly_data.busco_short_summary_precuration}'
            merqury_qv: '${pre_curation_assembly_data.mercury_qv_precuration}'
            merqury_completeness_stats: '${pre_curation_assembly_data.merqury_completeness_stats_precuration}'

            busco_short_summary_txt: '${pre_curation_assembly_data.hap2_precuration_data.busco_short_summary_hap2_precuration}'
            merqury_qv: '${pre_curation_assembly_data.hap2_precuration_data.mercury_qv_hap2_precuration}'
            merqury_completeness_stats: '${pre_curation_assembly_data.hap2_precuration_data.merqury_completeness_stats_hap2_precuration}'

    Curated:
        pipeline: [GRIT_rapid_v2.0, HiGlass_v1.0]
        '${pre_curation_assembly_data.haplotype_selection}':
            gfastats--nstar-report_txt: '${curated_assembly_data.gfstats_nstar_report_curated}'
            busco_short_summary_txt: '${curated_assembly_data.busco_short_summary_curated}'
            merqury_qv: '${curated_assembly_data.mercury_qv_curated}'
            merqury_completeness_stats: '${curated_assembly_data.merqury_completeness_stats_curated}'

#else
# ASSEMBLY DATA
ASSEMBLIES:
    Pre-curation:
        pipeline: [Hifiasm_v0.19.4|HiC|l0, Purge_Dups_v1.2.6|, Bionano_vGalaxy_3.7.0, YaHS_v1.1]
        '${pre_curation_assembly_data.haplotype_selection}': 
            gfastats--nstar-report_txt: '${pre_curation_assembly_data.gfstats_nstar_report_precuration}'
            busco_short_summary_txt: '${pre_curation_assembly_data.busco_short_summary_precuration}'
            merqury_qv: '${pre_curation_assembly_data.mercury_qv_precuration}'
            merqury_completeness_stats: '${pre_curation_assembly_data.merqury_completeness_stats_precuration}'

    Curated:
        pipeline: [GRIT_rapid_v2.0, HiGlass_v1.0]
        '${pre_curation_assembly_data.haplotype_selection}':
            gfastats--nstar-report_txt: '${curated_assembly_data.gfstats_nstar_report_curated}'
            busco_short_summary_txt: '${curated_assembly_data.busco_short_summary_curated}'
            merqury_qv: '${curated_assembly_data.mercury_qv_curated}'
            merqury_completeness_stats: '${curated_assembly_data.merqury_completeness_stats_curated}'

            merqury_spectra_asm_png: '${curated_assembly_data.merqury_spectra_asm_curated}'
            hic_FullMap_png: '${curated_assembly_data.hic_FullMap_curated}'
            hic_FullMap_link: '${curated_assembly_data.hic_FullMap_link_curated}'
            blobplot_cont_png: '${curated_assembly_data.blobplot_cont_curated}'
#end if

# CURATION NOTES
NOTES:
    Obs_Haploid_num: '${curation_notes.obs_haploid_num}'
    Obs_Sex: '${curation_notes.obs_sex}'

            <param name="submitter" type="text" value="" optional="False" label="Enter the Submitter name"/>
            <param name="affiliation" type="text" value="" optional="False" label="Enter the Affiliation"/>
            <param name="tags" type="select" label="Select a valid tag"> 
                <option value="ERGA-BGE" selected="true">ERGA-BGE</option>
                <option value="ERGA-Pilot">ERGA-Pilot</option>
                <option value="ERGA-Satellite">ERGA-Satellite</option>
            </param>
        </section>

        <!-- Input parameters for Sequence Data Information -->
        <section name="sequencing_data" title="Sequencing Data Information">

            <param name="smudge_plot_summary" type="data" format="txt" optional="true" label="Summary file from Smudge Plot tool"/>
        </section>

        <!-- Input parameters for Assembly data precurated -->
        <section name="pre_curation_assembly_data" title="Pre-Curation Assembly Information">
            <param name="pipeline_tools_precuration" type="text" label="Input tool names along with version and paramters used" help="[Insert ToolA_v1.2.3|ParamX|ParamY, Insert ToolB_v2.3.4] valid input is empty or between brackets ToolName followed by _v followed by versionNumber followed by | followed by keyToolParameter"/>
            <param name="haplotype_selection" type="select"  label="Select a valid haplotype"> 
                <option value="hap1">hap1</option>
                <option value="pri">pri</option>
                <option value="collapsed">collapsed</option>
            </param>

            </conditional>
        </section>
        
        <!-- Input parameters for Assembly data Curated -->    
        <section name="curated_assembly_data" title="Curated Assembly Data Information">    
            <param name="pipeline_tools_curation" type="text" label="Input tool names along with version and paramters used" help="[Insert ToolA_v1.2.3|ParamX|ParamY, Insert ToolB_v2.3.4] valid input is empty or between brackets ToolName followed by _v followed by versionNumber followed by | followed by keyToolParameter"/>
            <param name="gfstats_nstar_report_curated" type="data" format="txt" label="Select curated gfastats--nstar report file"/>
            <param name="busco_short_summary_curated" type="data" format="txt" label="Select curated busco_short_summary.txt file"/>
            <param name="mercury_qv_curated" type="data" format="txt" label="Select curated Merqury results .qv file"/>
            <param name="merqury_completeness_stats_curated" type="data" format="txt" label="Select curated Merqury completeness.stats file"/>
            <param name="merqury_hap_spectra_cn_curated" type="data" format="png" label="Select Merqury HAP1 spectra-cn.ln.png file"/>

                    <param name="blobplot_cont_hap2_curated" type="data" format="png" label="Select blobplot contamination plot for hap2"/>
                </when>
            </conditional>
        </section>
        
        <!-- Input parameters for Curation notes --> 
        <section name="curation_notes" title="Curation Notes">
            <param name="obs_haploid_num" type="text" optional="False" label="Insert observed haploid number"/>
            <param name="obs_sex" type="select" label="Select observed sex" help="Example: XX, XY, X0, ZZ, ZW, NA">
                <option value="XX">XX</option>

                <param name="blobplot_cont_curated" value="blob1.png"/>
                <conditional name="hap2_curated_data">
                    <param name="hap2_exists_curated" value="no"/>
                </conditional>
            </section>
            <section name="curation_notes">
                <param name="obs_haploid_num" value="28"/>
                <param name="obs_sex" value="XX"/>
                <param name="interventions_per_gb" value="2"/>
                <param name="contam_notes" value="No presence of contaminants. Mitochondrial genome was removed from the assembly"/>

                    <param name="hic_FullMap_hap2_curated" value="pretext_snake2.png"/>
                    <param name="hic_FullMap_link_hap2_curated" value="https://box.fu-berlin.de/apps/files/something"/>
                    <param name="blobplot_cont_hap2_curated" value="blob2.png"/>
                </conditional>
            </section>
            <section name="curation_notes">
                <param name="obs_haploid_num" value="28"/>
                <param name="obs_sex" value="XX"/>
                <param name="interventions_per_gb" value="2"/>
                <param name="contam_notes" value="No presence of contaminants. Mitochondrial genome was removed from the assembly"/>

2:a34826ae0a73

#if $pre_curation_assembly_data.hap2_precuration_data.hap2_exists_precuration == "yes"
# ASSEMBLY DATA
ASSEMBLIES:
    Pre-curation:
        '${pre_curation_assembly_data.haplotype_selection}': 
            gfastats--nstar-report_txt: '${pre_curation_assembly_data.gfstats_nstar_report_precuration}'
            busco_short_summary_txt: '${pre_curation_assembly_data.busco_short_summary_precuration}'
            merqury_qv: '${pre_curation_assembly_data.mercury_qv_precuration}'
            merqury_completeness_stats: '${pre_curation_assembly_data.merqury_completeness_stats_precuration}'

            busco_short_summary_txt: '${pre_curation_assembly_data.hap2_precuration_data.busco_short_summary_hap2_precuration}'
            merqury_qv: '${pre_curation_assembly_data.hap2_precuration_data.mercury_qv_hap2_precuration}'
            merqury_completeness_stats: '${pre_curation_assembly_data.hap2_precuration_data.merqury_completeness_stats_hap2_precuration}'

    Curated:
        '${pre_curation_assembly_data.haplotype_selection}':
            gfastats--nstar-report_txt: '${curated_assembly_data.gfstats_nstar_report_curated}'
            busco_short_summary_txt: '${curated_assembly_data.busco_short_summary_curated}'
            merqury_qv: '${curated_assembly_data.mercury_qv_curated}'
            merqury_completeness_stats: '${curated_assembly_data.merqury_completeness_stats_curated}'

#else
# ASSEMBLY DATA
ASSEMBLIES:
    Pre-curation:
        '${pre_curation_assembly_data.haplotype_selection}': 
            gfastats--nstar-report_txt: '${pre_curation_assembly_data.gfstats_nstar_report_precuration}'
            busco_short_summary_txt: '${pre_curation_assembly_data.busco_short_summary_precuration}'
            merqury_qv: '${pre_curation_assembly_data.mercury_qv_precuration}'
            merqury_completeness_stats: '${pre_curation_assembly_data.merqury_completeness_stats_precuration}'

    Curated:
        '${pre_curation_assembly_data.haplotype_selection}':
            gfastats--nstar-report_txt: '${curated_assembly_data.gfstats_nstar_report_curated}'
            busco_short_summary_txt: '${curated_assembly_data.busco_short_summary_curated}'
            merqury_qv: '${curated_assembly_data.mercury_qv_curated}'
            merqury_completeness_stats: '${curated_assembly_data.merqury_completeness_stats_curated}'

            merqury_spectra_asm_png: '${curated_assembly_data.merqury_spectra_asm_curated}'
            hic_FullMap_png: '${curated_assembly_data.hic_FullMap_curated}'
            hic_FullMap_link: '${curated_assembly_data.hic_FullMap_link_curated}'
            blobplot_cont_png: '${curated_assembly_data.blobplot_cont_curated}'
#end if

# METHODS DATA
PIPELINES:
  Assembly:
    #for $repeat in $method_data.assembly_method_info:
    ${repeat.assembly_tools_info}
    #end for

  Curation:
    #for $repeat in $method_data.curation_method_info:
    ${repeat.curation_tools_info}
    #end for

# CURATION NOTES
NOTES:
    Obs_Haploid_num: '${curation_notes.obs_haploid_num}'
    Obs_Sex: '${curation_notes.obs_sex}'

            <param name="submitter" type="text" value="" optional="False" label="Enter the Submitter name"/>
            <param name="affiliation" type="text" value="" optional="False" label="Enter the Affiliation"/>
            <param name="tags" type="select" label="Select a valid tag"> 
                <option value="ERGA-BGE" selected="true">ERGA-BGE</option>
                <option value="ERGA-Pilot">ERGA-Pilot</option>
                <option value="ERGA-Community">ERGA-Community</option>
            </param>
        </section>

        <!-- Input parameters for Sequence Data Information -->
        <section name="sequencing_data" title="Sequencing Data Information">

            <param name="smudge_plot_summary" type="data" format="txt" optional="true" label="Summary file from Smudge Plot tool"/>
        </section>

        <!-- Input parameters for Assembly data precurated -->
        <section name="pre_curation_assembly_data" title="Pre-Curation Assembly Information">
            <param name="haplotype_selection" type="select"  label="Select a valid haplotype"> 
                <option value="hap1">hap1</option>
                <option value="pri">pri</option>
                <option value="collapsed">collapsed</option>
            </param>

            </conditional>
        </section>
        
        <!-- Input parameters for Assembly data Curated -->    
        <section name="curated_assembly_data" title="Curated Assembly Data Information">    
            <param name="gfstats_nstar_report_curated" type="data" format="txt" label="Select curated gfastats--nstar report file"/>
            <param name="busco_short_summary_curated" type="data" format="txt" label="Select curated busco_short_summary.txt file"/>
            <param name="mercury_qv_curated" type="data" format="txt" label="Select curated Merqury results .qv file"/>
            <param name="merqury_completeness_stats_curated" type="data" format="txt" label="Select curated Merqury completeness.stats file"/>
            <param name="merqury_hap_spectra_cn_curated" type="data" format="png" label="Select Merqury HAP1 spectra-cn.ln.png file"/>

                    <param name="blobplot_cont_hap2_curated" type="data" format="png" label="Select blobplot contamination plot for hap2"/>
                </when>
            </conditional>
        </section>
        
        <!-- Input parameters for Methods data -->
        <section name="method_data" title="Method Information">
            <repeat name='assembly_method_info' title="Specify the method used for Assembly" min="1" default="2">
                <param name="assembly_tools_info" type="text" label="Input tool names along with version and paramters used for assembly" optional="False" help="Specify ToolName:Tool_Version/Tool_parameters"/>
            </repeat>
            <repeat name='curation_method_info' title="Specify the method used for Curation" min="1" default="2">
                <param name="curation_tools_info" type="text" label="Input tool names along with version and paramters used for curation" optional="False" help="Specify ToolName:Tool_Version/Tool_parameters"/>
            </repeat>
        </section>

        <!-- Input parameters for Curation notes --> 
        <section name="curation_notes" title="Curation Notes">
            <param name="obs_haploid_num" type="text" optional="False" label="Insert observed haploid number"/>
            <param name="obs_sex" type="select" label="Select observed sex" help="Example: XX, XY, X0, ZZ, ZW, NA">
                <option value="XX">XX</option>

                <param name="blobplot_cont_curated" value="blob1.png"/>
                <conditional name="hap2_curated_data">
                    <param name="hap2_exists_curated" value="no"/>
                </conditional>
            </section>
            <expand macro="methods_tests"></expand>
            <section name="curation_notes">
                <param name="obs_haploid_num" value="28"/>
                <param name="obs_sex" value="XX"/>
                <param name="interventions_per_gb" value="2"/>
                <param name="contam_notes" value="No presence of contaminants. Mitochondrial genome was removed from the assembly"/>

                    <param name="hic_FullMap_hap2_curated" value="pretext_snake2.png"/>
                    <param name="hic_FullMap_link_hap2_curated" value="https://box.fu-berlin.de/apps/files/something"/>
                    <param name="blobplot_cont_hap2_curated" value="blob2.png"/>
                </conditional>
            </section>
            <expand macro="methods_tests"></expand>
            <section name="curation_notes">
                <param name="obs_haploid_num" value="28"/>
                <param name="obs_sex" value="XX"/>
                <param name="interventions_per_gb" value="2"/>
                <param name="contam_notes" value="No presence of contaminants. Mitochondrial genome was removed from the assembly"/>