comparison make_EAR.xml @ 1:b61022e1b807 draft

planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit b7f4b9b05946009ced0c4faeadc7acca98a90131

0:8c99976de71e

<tool id="make_ear" name="ERGA Assembly Reporting Tool (EAR)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
    <description>A tool to compile assembly reports and stastics from assembly pipeline</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="4.1.0">reportlab</requirement>

            hic_FullMap_link: '${curated_assembly_data.hap2_curated_data.hic_FullMap_link_hap2_curated}'
            blobplot_cont_png: '${curated_assembly_data.hap2_curated_data.blobplot_cont_hap2_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: '${curated_assembly_data.merqury_completeness_stats_curated}'
                merqury_hap_spectra_cn_png: '${curated_assembly_data.merqury_hap_spectra_cn_curated}'
                merqury_spectra_cn_png:  '${curated_assembly_data.merqury_spectra_cn_curated}'   
                merqury_spectra_asm_png: '${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}'

                <option value="XX">XX</option>
                <option value="XY">XY</option>
                <option value="X0">X0</option>
                <option value="ZZ">ZZ</option>
                <option value="ZW">ZW</option>
                <option value="NA">Not Available</option>
            </param>
            <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>

    <outputs>
        <data name="EAR_pdf" format="pdf" from_work_dir="EAR.pdf" label="${tool.name} on ${on_string}: Output PDF" ></data> 
        <data name="log" format="txt" from_work_dir="EAR.log" label="${tool.name} on ${on_string}: Log file"/>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <section name="sample_information">
                <param name="tolid" value="xgPhyFlav1"/>
                <param name="species_name" value="Phyllidia flava"/>
                <param name="species_sex" value="XX"/>

                <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="other_notes" value="Large collapsed repeat in chr5, haplotypic inversion in chr12"/>
            </section>
            <output name="EAR_pdf" file="EAR.pdf" ftype="pdf" compare="sim_size"/>
            <output name="log" file="EAR_log"/>    
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

1:b61022e1b807

<tool id="make_ear" name="ERGA Assembly Reporting Tool (EAR)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
    <description>A tool to compile assembly reports and statistics from assembly pipeline</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="4.1.0">reportlab</requirement>

            hic_FullMap_link: '${curated_assembly_data.hap2_curated_data.hic_FullMap_link_hap2_curated}'
            blobplot_cont_png: '${curated_assembly_data.hap2_curated_data.blobplot_cont_hap2_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: '${curated_assembly_data.merqury_completeness_stats_curated}'
            merqury_hap_spectra_cn_png: '${curated_assembly_data.merqury_hap_spectra_cn_curated}'
            merqury_spectra_cn_png:  '${curated_assembly_data.merqury_spectra_cn_curated}'   
            merqury_spectra_asm_png: '${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}'

                <option value="XX">XX</option>
                <option value="XY">XY</option>
                <option value="X0">X0</option>
                <option value="ZZ">ZZ</option>
                <option value="ZW">ZW</option>
                <option value="NA">NA</option>
            </param>
            <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>

    <outputs>
        <data name="EAR_pdf" format="pdf" from_work_dir="EAR.pdf" label="${tool.name} on ${on_string}: Output PDF" ></data> 
        <data name="log" format="txt" from_work_dir="EAR.log" label="${tool.name} on ${on_string}: Log file"/>
    </outputs>
    <tests>
        <!--- Test with 1 haplotypes information-->
        <test expect_num_outputs="2">
            <section name="sample_information">
                <param name="tolid" value="xgPhyFlav1"/>
                <param name="species_name" value="Phyllidia flava"/>
                <param name="species_sex" value="XX"/>
                <param name="submitter" value="John Doe"/>
                <param name="affiliation" value="Galaxy EU"/>
                <param name="tags" value="ERGA-BGE"/>
            </section>
            <section name="sequencing_data">
                <repeat name="seq_data_info">
                    <param name="seq_data" value="HiFi: 40x"/>
                </repeat>
                <repeat name="seq_data_info">
                    <param name="seq_data" value="Bionano: 10x"/>
                </repeat>
                <repeat name="seq_data_info">
                    <param name="seq_data" value="OmniC: 90x"/>
                </repeat>
            </section>
            <section name="genome_profiling_data">
                <param name="genome_scope_summary" value="genomescope_results_summary.txt"/>
                <param name="smudge_plot_summary" value="smudgeplot_verbose_summary.txt"/>
            </section>
            <section name="pre_curation_assembly_data">
                <param name="haplotype_selection" value="hap1"/>
                <param name="gfstats_nstar_report_precuration" value="ele_pre.asm1_gfastats.txt"/>
                <param name="busco_short_summary_precuration" value="short_summary.specific.mammalia_odb10.pre.asm1.txt"/>
                <param name="mercury_qv_precuration" value="ele_pre_merqOutput.qv"/>
                <param name="merqury_completeness_stats_precuration" value="ele_pre_merqOutput.completeness.stats"/>
                <conditional name="hap2_precuration_data">
                    <param name="hap2_exists_precuration" value="no"/>
                </conditional>
            </section>
            <section name="curated_assembly_data">
                <param name="gfstats_nstar_report_curated" value="ele.asm1_post_gfastats.txt"/>
                <param name="busco_short_summary_curated" value="short_summary.specific.mammalia_odb10.post.asm1.txt"/>
                <param name="mercury_qv_curated" value="ele_post_merqOutput.qv"/>
                <param name="merqury_completeness_stats_curated" value="ele_post_merqOutput.completeness.stats"/>
                <param name="merqury_hap_spectra_cn_curated" value="ele_post_merqOutput.ele_post.asm1.spectra-cn.ln.png"/>
                <param name="merqury_spectra_cn_curated" value="ele_post_merqOutput.spectra-cn.ln.png"/>
                <param name="merqury_spectra_asm_curated" value="ele_post_merqOutput.spectra-asm.ln.png"/>
                <param name="hic_FullMap_curated" value="pretext_snake1.png"/>
                <param name="hic_FullMap_link_curated" value="https://box.fu-berlin.de/apps/files/something"/>
                <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="other_notes" value="Large collapsed repeat in chr5, haplotypic inversion in chr12"/>
            </section>
            <output name="EAR_pdf" file="EAR.pdf" ftype="pdf" compare="sim_size"/>
            <output name="log" file="EAR_log"/>    
        </test>
        <!--- Test with 2 haplotypes information-->
        <test expect_num_outputs="2">
            <section name="sample_information">
                <param name="tolid" value="xgPhyFlav1"/>
                <param name="species_name" value="Phyllidia flava"/>
                <param name="species_sex" value="XX"/>

                <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="other_notes" value="Large collapsed repeat in chr5, haplotypic inversion in chr12"/>
            </section>
            <output name="EAR_pdf" file="EAR_2.pdf" ftype="pdf" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark