Mercurial > repos > bgruening > erga_ear
diff make_EAR.xml @ 0:8c99976de71e draft
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
| author | bgruening |
|---|---|
| date | Fri, 07 Jun 2024 14:23:49 +0000 |
| parents | |
| children | b61022e1b807 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/make_EAR.xml Fri Jun 07 14:23:49 2024 +0000 @@ -0,0 +1,319 @@ +<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> + <requirement type="package" version="24.4.0">pyaml</requirement> + <requirement type="package" version="2024.1">pytz</requirement> + <requirement type="package" version="2.32.3">requests</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/make_EAR.py' '$param_file' > '$log' + ]]></command> + <configfiles> + <configfile name="param_file"><![CDATA[ +# SAMPLE INFORMATION +ToLID: '${sample_information.tolid}' +Species: '${sample_information.species_name}' +Sex: '${sample_information.species_sex}' +Submitter: '${sample_information.submitter}' +Affiliation: '${sample_information.affiliation}' +Tags: '${sample_information.tags}' + +# SEQUENCING DATA +DATA: + #for $repeat in $sequencing_data.seq_data_info: + - ${repeat.seq_data} + #end for + +# GENOME PROFILING DATA +PROFILING: + GenomeScope: + genomescope_summary_txt: '${genome_profiling_data.genome_scope_summary}' + Smudgeplot: + smudgeplot_verbose_summary_txt: '${genome_profiling_data.smudge_plot_summary}' + +#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}' + hap2: + gfastats--nstar-report_txt: '${pre_curation_assembly_data.hap2_precuration_data.gfstats_nstar_report_hap2_precuration}' + busco_short_summary_txt: '${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: '${curated_assembly_data.merqury_completeness_stats_curated}' + merqury_hap_spectra_cn_png: '${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: '${curated_assembly_data.blobplot_cont_curated}' + hap2: + gfastats--nstar-report_txt: '${curated_assembly_data.hap2_curated_data.gfstats_nstar_report_hap2_curated}' + busco_short_summary_txt: '${curated_assembly_data.hap2_curated_data.busco_short_summary_hap2_curated}' + merqury_qv: '${curated_assembly_data.hap2_curated_data.mercury_qv_hap2_curated}' + merqury_completeness_stats: '${curated_assembly_data.hap2_curated_data.merqury_completeness_stats_hap2_curated}' + merqury_hap_spectra_cn_png: '${curated_assembly_data.hap2_curated_data.merqury_hap_spectra_cn_hap2_curated}' + merqury_spectra_cn_png: '${curated_assembly_data.hap2_curated_data.merqury_spectra_cn_hap2_curated}' + merqury_spectra_asm_png: '${curated_assembly_data.hap2_curated_data.merqury_spectra_asm_hap2_curated}' + hic_FullMap_png: '${curated_assembly_data.hap2_curated_data.hic_FullMap_hap2_curated}' + hic_FullMap_link: '${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}' + Obs_Sex: '${curation_notes.obs_sex}' + Interventions_per_Gb: '${curation_notes.interventions_per_gb}' + Contamination_notes: '${curation_notes.contam_notes}' + Other_notes: '${curation_notes.other_notes}' + + ]]></configfile> + </configfiles> + + <inputs> + <!-- Input parameters for Sample Information --> + <section name="sample_information" title="Sample Information" expanded="true"> + <param name="tolid" type="text" optional="False" value="" label="Input a ToLID"/> + <param name="species_name" type="text" optional="False" value="" label="Enter the Species name"/> + <param name="species_sex" type="select" label="Enter the Species sex"> + <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> + <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"> + <repeat name='seq_data_info' title="Add Sequence Data information" min="1" default="2"> + <param name="seq_data" type="text" label="Enter Sequencing data information" optional="False" help="Input Sequencing data information along with coverage scores if available. (Example Input: HiFi: 40X)"/> + </repeat> + </section> + + <!-- Input parameters for Genome Profiling Data --> + <section name="genome_profiling_data" title="Genome Profiling Information"> + <param name="genome_scope_summary" type="data" format="txt" label="Summary file from GenomeScope tool"/> + <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> + <param name="gfstats_nstar_report_precuration" type="data" format="txt" label="Select gfastats--nstar report file from gfstats tool"/> + <param name="busco_short_summary_precuration" type="data" format="txt" label="Select short summary report file from busco tool"/> + <param name="mercury_qv_precuration" type="data" format="txt" label="Select Merqury results .qv file"/> + <param name="merqury_completeness_stats_precuration" type="data" format="txt" label="Select Merqury results completeness.stats file"/> + <conditional name="hap2_precuration_data"> + <param name="hap2_exists_precuration" type="select" label="Do you have data for Hap2?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="gfstats_nstar_report_hap2_precuration" type="data" format="data" label="Select gfastats--nstar report tool from gfstats tool for Hap2"/> + <param name="busco_short_summary_hap2_precuration" type="data" format="txt" label="Select short summary from busco tool for Hap2"/> + <param name="mercury_qv_hap2_precuration" type="data" format="txt" label="Select Merqury results .qv file for Hap2"/> + <param name="merqury_completeness_stats_hap2_precuration" type="data" format="txt" label="Select Merqury results completeness.stats file for Hap2"/> + </when> + </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="merqury_spectra_cn_curated" type="data" format="png" label="Select Merqury results spectra-cn.ln.png file"/> + <param name="merqury_spectra_asm_curated" type="data" format="png" label="Select Merqury results spectra-asm.ln.png file"/> + <param name="hic_FullMap_curated" type="data" format="png" label="Select pretext FullMap plot"/> + <param name="hic_FullMap_link_curated" type="text" value="" label="Insert .pretext file web link" help="This can be copied from the dataset-download-button"/> + <param name="blobplot_cont_curated" type="data" format="png" label="Select blobplot contamination plot file"/> + + <conditional name="hap2_curated_data"> + <param name="hap2_exists_curated" type="select" label="Do you have data for Hap2?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="gfstats_nstar_report_hap2_curated" type="data" format="txt" label="Select curated gfastats--nstar report file for hap2"/> + <param name="busco_short_summary_hap2_curated" type="data" format="txt" label="Select curated busco_short_summary.txt file for hap2"/> + <param name="mercury_qv_hap2_curated" type="data" format="txt" label="Select curated Merqury results .qv file for hap2"/> + <param name="merqury_completeness_stats_hap2_curated" type="data" format="txt" label="Select curated Merqury results completeness.stats file for hap2"/> + <param name="merqury_hap_spectra_cn_hap2_curated" type="data" format="png" label="Select Merqury results HAP1 spectra-cn.ln.png file for hap2"/> + <param name="merqury_spectra_cn_hap2_curated" type="data" format="png" label="Select Merqury HAP2 spectra-cn.ln.png file"/> + <param name="merqury_spectra_asm_hap2_curated" type="data" format="png" label="Select curated Merqury results spectra-asm.ln.png file for hap2"/> + <param name="hic_FullMap_hap2_curated" type="data" format="png" label="Select pretext FullMap plot for hap2"/> + <param name="hic_FullMap_link_hap2_curated" type="text" value="" label="Insert .pretext file web link for hap2" help="This can be copied from the dataset-download-button"/> + <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> + <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="interventions_per_gb" type="text" label="Insert manual intervention during curation (GB)"/> + <param name="contam_notes" type="text" label="Insert contamination notes"/> + <param name="other_notes" type="text" label="Insert Other notes"/> + </section> + </inputs> + + <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="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="yes"/> + <param name="gfstats_nstar_report_hap2_precuration" value="ele_pre.asm2_gfastats.txt"/> + <param name="busco_short_summary_hap2_precuration" value="short_summary.specific.mammalia_odb10.pre.asm2.txt"/> + <param name="mercury_qv_hap2_precuration" value="ele_pre_merqOutput.qv"/> + <param name="merqury_completeness_stats_hap2_precuration" value="ele_pre_merqOutput.completeness.stats"/> + </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="yes"/> + <param name="gfstats_nstar_report_hap2_curated" value="ele.asm2_post_gfastats.txt"/> + <param name="busco_short_summary_hap2_curated" value="short_summary.specific.mammalia_odb10.post.asm2.txt"/> + <param name="mercury_qv_hap2_curated" value="ele_post_merqOutput.qv"/> + <param name="merqury_completeness_stats_hap2_curated" value="ele_post_merqOutput.completeness.stats"/> + <param name="merqury_hap_spectra_cn_hap2_curated" value="ele_post_merqOutput.ele_post.asm2.spectra-cn.ln.png"/> + <param name="merqury_spectra_cn_hap2_curated" value="ele_post_merqOutput.spectra-cn.ln.png"/> + <param name="merqury_spectra_asm_hap2_curated" value="ele_post_merqOutput.spectra-asm.ln.png"/> + <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"/> + <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 + +**What it does** + +**ERGA Assembly Reporting Tool (EAR)** is a tool that compiles various statistics and reports generated from Assembly pipeline tools and compiles them in to a summarized PDF document for reporting. + ]]></help> + <expand macro="citations"/> + <expand macro="creator"/> +</tool> \ No newline at end of file