Mercurial > repos > bgruening > erga_ear
annotate make_EAR.xml @ 1:b61022e1b807 draft
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit b7f4b9b05946009ced0c4faeadc7acca98a90131
author | bgruening |
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date | Tue, 09 Jul 2024 07:48:46 +0000 |
parents | 8c99976de71e |
children | a34826ae0a73 |
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8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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1 <tool id="make_ear" name="ERGA Assembly Reporting Tool (EAR)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> |
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b61022e1b807
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit b7f4b9b05946009ced0c4faeadc7acca98a90131
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2 <description>A tool to compile assembly reports and statistics from assembly pipeline</description> |
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8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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3 <macros> |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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4 <import>macros.xml</import> |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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5 </macros> |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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6 <requirements> |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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7 <requirement type="package" version="4.1.0">reportlab</requirement> |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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8 <requirement type="package" version="24.4.0">pyaml</requirement> |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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9 <requirement type="package" version="2024.1">pytz</requirement> |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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10 <requirement type="package" version="2.32.3">requests</requirement> |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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11 </requirements> |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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12 <command detect_errors="exit_code"><![CDATA[ |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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13 python '$__tool_directory__/make_EAR.py' '$param_file' > '$log' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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14 ]]></command> |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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15 <configfiles> |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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16 <configfile name="param_file"><![CDATA[ |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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17 # SAMPLE INFORMATION |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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18 ToLID: '${sample_information.tolid}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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19 Species: '${sample_information.species_name}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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20 Sex: '${sample_information.species_sex}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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21 Submitter: '${sample_information.submitter}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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22 Affiliation: '${sample_information.affiliation}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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23 Tags: '${sample_information.tags}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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24 |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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25 # SEQUENCING DATA |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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26 DATA: |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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27 #for $repeat in $sequencing_data.seq_data_info: |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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28 - ${repeat.seq_data} |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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29 #end for |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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30 |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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31 # GENOME PROFILING DATA |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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32 PROFILING: |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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33 GenomeScope: |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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34 genomescope_summary_txt: '${genome_profiling_data.genome_scope_summary}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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35 Smudgeplot: |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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36 smudgeplot_verbose_summary_txt: '${genome_profiling_data.smudge_plot_summary}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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37 |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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38 #if $pre_curation_assembly_data.hap2_precuration_data.hap2_exists_precuration == "yes" |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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39 # ASSEMBLY DATA |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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40 ASSEMBLIES: |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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41 Pre-curation: |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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42 pipeline: [Hifiasm_v0.19.4|HiC|l0, Purge_Dups_v1.2.6|, Bionano_vGalaxy_3.7.0, YaHS_v1.1] |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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43 '${pre_curation_assembly_data.haplotype_selection}': |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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44 gfastats--nstar-report_txt: '${pre_curation_assembly_data.gfstats_nstar_report_precuration}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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45 busco_short_summary_txt: '${pre_curation_assembly_data.busco_short_summary_precuration}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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46 merqury_qv: '${pre_curation_assembly_data.mercury_qv_precuration}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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47 merqury_completeness_stats: '${pre_curation_assembly_data.merqury_completeness_stats_precuration}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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48 hap2: |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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49 gfastats--nstar-report_txt: '${pre_curation_assembly_data.hap2_precuration_data.gfstats_nstar_report_hap2_precuration}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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50 busco_short_summary_txt: '${pre_curation_assembly_data.hap2_precuration_data.busco_short_summary_hap2_precuration}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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51 merqury_qv: '${pre_curation_assembly_data.hap2_precuration_data.mercury_qv_hap2_precuration}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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52 merqury_completeness_stats: '${pre_curation_assembly_data.hap2_precuration_data.merqury_completeness_stats_hap2_precuration}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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53 |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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54 Curated: |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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55 pipeline: [GRIT_rapid_v2.0, HiGlass_v1.0] |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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56 '${pre_curation_assembly_data.haplotype_selection}': |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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57 gfastats--nstar-report_txt: '${curated_assembly_data.gfstats_nstar_report_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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58 busco_short_summary_txt: '${curated_assembly_data.busco_short_summary_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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59 merqury_qv: '${curated_assembly_data.mercury_qv_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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60 merqury_completeness_stats: '${curated_assembly_data.merqury_completeness_stats_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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61 merqury_hap_spectra_cn_png: '${curated_assembly_data.merqury_hap_spectra_cn_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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62 merqury_spectra_cn_png: '${curated_assembly_data.merqury_spectra_cn_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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63 merqury_spectra_asm_png: '${curated_assembly_data.merqury_spectra_asm_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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64 hic_FullMap_png: '${curated_assembly_data.hic_FullMap_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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65 hic_FullMap_link: '${curated_assembly_data.hic_FullMap_link_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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66 blobplot_cont_png: '${curated_assembly_data.blobplot_cont_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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67 hap2: |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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68 gfastats--nstar-report_txt: '${curated_assembly_data.hap2_curated_data.gfstats_nstar_report_hap2_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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69 busco_short_summary_txt: '${curated_assembly_data.hap2_curated_data.busco_short_summary_hap2_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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70 merqury_qv: '${curated_assembly_data.hap2_curated_data.mercury_qv_hap2_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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71 merqury_completeness_stats: '${curated_assembly_data.hap2_curated_data.merqury_completeness_stats_hap2_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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72 merqury_hap_spectra_cn_png: '${curated_assembly_data.hap2_curated_data.merqury_hap_spectra_cn_hap2_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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73 merqury_spectra_cn_png: '${curated_assembly_data.hap2_curated_data.merqury_spectra_cn_hap2_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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74 merqury_spectra_asm_png: '${curated_assembly_data.hap2_curated_data.merqury_spectra_asm_hap2_curated}' |
8c99976de71e
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
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75 hic_FullMap_png: '${curated_assembly_data.hap2_curated_data.hic_FullMap_hap2_curated}' |
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76 hic_FullMap_link: '${curated_assembly_data.hap2_curated_data.hic_FullMap_link_hap2_curated}' |
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77 blobplot_cont_png: '${curated_assembly_data.hap2_curated_data.blobplot_cont_hap2_curated}' |
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78 |
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79 #else |
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80 # ASSEMBLY DATA |
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81 ASSEMBLIES: |
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82 Pre-curation: |
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83 pipeline: [Hifiasm_v0.19.4|HiC|l0, Purge_Dups_v1.2.6|, Bionano_vGalaxy_3.7.0, YaHS_v1.1] |
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84 '${pre_curation_assembly_data.haplotype_selection}': |
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85 gfastats--nstar-report_txt: '${pre_curation_assembly_data.gfstats_nstar_report_precuration}' |
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86 busco_short_summary_txt: '${pre_curation_assembly_data.busco_short_summary_precuration}' |
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87 merqury_qv: '${pre_curation_assembly_data.mercury_qv_precuration}' |
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88 merqury_completeness_stats: '${pre_curation_assembly_data.merqury_completeness_stats_precuration}' |
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89 |
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90 Curated: |
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91 pipeline: [GRIT_rapid_v2.0, HiGlass_v1.0] |
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92 '${pre_curation_assembly_data.haplotype_selection}': |
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93 gfastats--nstar-report_txt: '${curated_assembly_data.gfstats_nstar_report_curated}' |
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94 busco_short_summary_txt: '${curated_assembly_data.busco_short_summary_curated}' |
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95 merqury_qv: '${curated_assembly_data.mercury_qv_curated}' |
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96 merqury_completeness_stats: '${curated_assembly_data.merqury_completeness_stats_curated}' |
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97 merqury_hap_spectra_cn_png: '${curated_assembly_data.merqury_hap_spectra_cn_curated}' |
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98 merqury_spectra_cn_png: '${curated_assembly_data.merqury_spectra_cn_curated}' |
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99 merqury_spectra_asm_png: '${curated_assembly_data.merqury_spectra_asm_curated}' |
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100 hic_FullMap_png: '${curated_assembly_data.hic_FullMap_curated}' |
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101 hic_FullMap_link: '${curated_assembly_data.hic_FullMap_link_curated}' |
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102 blobplot_cont_png: '${curated_assembly_data.blobplot_cont_curated}' |
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103 #end if |
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104 |
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105 # CURATION NOTES |
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106 NOTES: |
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107 Obs_Haploid_num: '${curation_notes.obs_haploid_num}' |
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108 Obs_Sex: '${curation_notes.obs_sex}' |
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109 Interventions_per_Gb: '${curation_notes.interventions_per_gb}' |
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110 Contamination_notes: '${curation_notes.contam_notes}' |
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111 Other_notes: '${curation_notes.other_notes}' |
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112 |
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113 ]]></configfile> |
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114 </configfiles> |
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115 |
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116 <inputs> |
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117 <!-- Input parameters for Sample Information --> |
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118 <section name="sample_information" title="Sample Information" expanded="true"> |
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119 <param name="tolid" type="text" optional="False" value="" label="Input a ToLID"/> |
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120 <param name="species_name" type="text" optional="False" value="" label="Enter the Species name"/> |
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121 <param name="species_sex" type="select" label="Enter the Species sex"> |
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122 <option value="XX">XX</option> |
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123 <option value="XY">XY</option> |
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124 <option value="X0">X0</option> |
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125 <option value="ZZ">ZZ</option> |
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126 <option value="ZW">ZW</option> |
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127 <option value="NA">NA</option> |
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128 </param> |
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129 <param name="submitter" type="text" value="" optional="False" label="Enter the Submitter name"/> |
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130 <param name="affiliation" type="text" value="" optional="False" label="Enter the Affiliation"/> |
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131 <param name="tags" type="select" label="Select a valid tag"> |
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132 <option value="ERGA-BGE" selected="true">ERGA-BGE</option> |
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133 <option value="ERGA-Pilot">ERGA-Pilot</option> |
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134 <option value="ERGA-Satellite">ERGA-Satellite</option> |
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135 </param> |
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136 </section> |
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137 |
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138 <!-- Input parameters for Sequence Data Information --> |
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139 <section name="sequencing_data" title="Sequencing Data Information"> |
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140 <repeat name='seq_data_info' title="Add Sequence Data information" min="1" default="2"> |
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141 <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)"/> |
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142 </repeat> |
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143 </section> |
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144 |
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145 <!-- Input parameters for Genome Profiling Data --> |
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146 <section name="genome_profiling_data" title="Genome Profiling Information"> |
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147 <param name="genome_scope_summary" type="data" format="txt" label="Summary file from GenomeScope tool"/> |
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148 <param name="smudge_plot_summary" type="data" format="txt" optional="true" label="Summary file from Smudge Plot tool"/> |
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149 </section> |
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150 |
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151 <!-- Input parameters for Assembly data precurated --> |
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152 <section name="pre_curation_assembly_data" title="Pre-Curation Assembly Information"> |
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153 <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"/> |
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154 <param name="haplotype_selection" type="select" label="Select a valid haplotype"> |
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155 <option value="hap1">hap1</option> |
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156 <option value="pri">pri</option> |
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157 <option value="collapsed">collapsed</option> |
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158 </param> |
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159 <param name="gfstats_nstar_report_precuration" type="data" format="txt" label="Select gfastats--nstar report file from gfstats tool"/> |
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160 <param name="busco_short_summary_precuration" type="data" format="txt" label="Select short summary report file from busco tool"/> |
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161 <param name="mercury_qv_precuration" type="data" format="txt" label="Select Merqury results .qv file"/> |
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162 <param name="merqury_completeness_stats_precuration" type="data" format="txt" label="Select Merqury results completeness.stats file"/> |
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163 <conditional name="hap2_precuration_data"> |
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164 <param name="hap2_exists_precuration" type="select" label="Do you have data for Hap2?"> |
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165 <option value="no" selected="true">No</option> |
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166 <option value="yes">Yes</option> |
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167 </param> |
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168 <when value="no"/> |
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169 <when value="yes"> |
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170 <param name="gfstats_nstar_report_hap2_precuration" type="data" format="data" label="Select gfastats--nstar report tool from gfstats tool for Hap2"/> |
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171 <param name="busco_short_summary_hap2_precuration" type="data" format="txt" label="Select short summary from busco tool for Hap2"/> |
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172 <param name="mercury_qv_hap2_precuration" type="data" format="txt" label="Select Merqury results .qv file for Hap2"/> |
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173 <param name="merqury_completeness_stats_hap2_precuration" type="data" format="txt" label="Select Merqury results completeness.stats file for Hap2"/> |
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174 </when> |
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175 </conditional> |
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176 </section> |
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177 |
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178 <!-- Input parameters for Assembly data Curated --> |
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179 <section name="curated_assembly_data" title="Curated Assembly Data Information"> |
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180 <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"/> |
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181 <param name="gfstats_nstar_report_curated" type="data" format="txt" label="Select curated gfastats--nstar report file"/> |
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182 <param name="busco_short_summary_curated" type="data" format="txt" label="Select curated busco_short_summary.txt file"/> |
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183 <param name="mercury_qv_curated" type="data" format="txt" label="Select curated Merqury results .qv file"/> |
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184 <param name="merqury_completeness_stats_curated" type="data" format="txt" label="Select curated Merqury completeness.stats file"/> |
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185 <param name="merqury_hap_spectra_cn_curated" type="data" format="png" label="Select Merqury HAP1 spectra-cn.ln.png file"/> |
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186 <param name="merqury_spectra_cn_curated" type="data" format="png" label="Select Merqury results spectra-cn.ln.png file"/> |
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187 <param name="merqury_spectra_asm_curated" type="data" format="png" label="Select Merqury results spectra-asm.ln.png file"/> |
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188 <param name="hic_FullMap_curated" type="data" format="png" label="Select pretext FullMap plot"/> |
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189 <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"/> |
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190 <param name="blobplot_cont_curated" type="data" format="png" label="Select blobplot contamination plot file"/> |
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191 |
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192 <conditional name="hap2_curated_data"> |
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193 <param name="hap2_exists_curated" type="select" label="Do you have data for Hap2?"> |
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194 <option value="no" selected="true">No</option> |
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195 <option value="yes">Yes</option> |
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196 </param> |
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197 <when value="no"/> |
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198 <when value="yes"> |
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199 <param name="gfstats_nstar_report_hap2_curated" type="data" format="txt" label="Select curated gfastats--nstar report file for hap2"/> |
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200 <param name="busco_short_summary_hap2_curated" type="data" format="txt" label="Select curated busco_short_summary.txt file for hap2"/> |
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201 <param name="mercury_qv_hap2_curated" type="data" format="txt" label="Select curated Merqury results .qv file for hap2"/> |
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202 <param name="merqury_completeness_stats_hap2_curated" type="data" format="txt" label="Select curated Merqury results completeness.stats file for hap2"/> |
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203 <param name="merqury_hap_spectra_cn_hap2_curated" type="data" format="png" label="Select Merqury results HAP1 spectra-cn.ln.png file for hap2"/> |
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204 <param name="merqury_spectra_cn_hap2_curated" type="data" format="png" label="Select Merqury HAP2 spectra-cn.ln.png file"/> |
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205 <param name="merqury_spectra_asm_hap2_curated" type="data" format="png" label="Select curated Merqury results spectra-asm.ln.png file for hap2"/> |
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206 <param name="hic_FullMap_hap2_curated" type="data" format="png" label="Select pretext FullMap plot for hap2"/> |
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207 <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"/> |
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208 <param name="blobplot_cont_hap2_curated" type="data" format="png" label="Select blobplot contamination plot for hap2"/> |
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209 </when> |
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210 </conditional> |
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211 </section> |
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212 |
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213 <!-- Input parameters for Curation notes --> |
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214 <section name="curation_notes" title="Curation Notes"> |
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215 <param name="obs_haploid_num" type="text" optional="False" label="Insert observed haploid number"/> |
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216 <param name="obs_sex" type="select" label="Select observed sex" help="Example: XX, XY, X0, ZZ, ZW, NA"> |
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217 <option value="XX">XX</option> |
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218 <option value="XY">XY</option> |
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219 <option value="X0">X0</option> |
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220 <option value="ZZ">ZZ</option> |
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221 <option value="ZW">ZW</option> |
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222 <option value="NA">NA</option> |
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223 </param> |
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224 <param name="interventions_per_gb" type="text" label="Insert manual intervention during curation (GB)"/> |
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225 <param name="contam_notes" type="text" label="Insert contamination notes"/> |
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226 <param name="other_notes" type="text" label="Insert Other notes"/> |
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227 </section> |
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228 </inputs> |
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229 |
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230 <outputs> |
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231 <data name="EAR_pdf" format="pdf" from_work_dir="EAR.pdf" label="${tool.name} on ${on_string}: Output PDF" ></data> |
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232 <data name="log" format="txt" from_work_dir="EAR.log" label="${tool.name} on ${on_string}: Log file"/> |
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233 </outputs> |
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234 <tests> |
1
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235 <!--- Test with 1 haplotypes information--> |
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236 <test expect_num_outputs="2"> |
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237 <section name="sample_information"> |
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238 <param name="tolid" value="xgPhyFlav1"/> |
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239 <param name="species_name" value="Phyllidia flava"/> |
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240 <param name="species_sex" value="XX"/> |
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241 <param name="submitter" value="John Doe"/> |
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242 <param name="affiliation" value="Galaxy EU"/> |
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243 <param name="tags" value="ERGA-BGE"/> |
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244 </section> |
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245 <section name="sequencing_data"> |
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246 <repeat name="seq_data_info"> |
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247 <param name="seq_data" value="HiFi: 40x"/> |
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248 </repeat> |
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249 <repeat name="seq_data_info"> |
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250 <param name="seq_data" value="Bionano: 10x"/> |
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251 </repeat> |
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252 <repeat name="seq_data_info"> |
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253 <param name="seq_data" value="OmniC: 90x"/> |
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254 </repeat> |
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255 </section> |
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256 <section name="genome_profiling_data"> |
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257 <param name="genome_scope_summary" value="genomescope_results_summary.txt"/> |
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258 <param name="smudge_plot_summary" value="smudgeplot_verbose_summary.txt"/> |
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259 </section> |
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260 <section name="pre_curation_assembly_data"> |
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261 <param name="haplotype_selection" value="hap1"/> |
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262 <param name="gfstats_nstar_report_precuration" value="ele_pre.asm1_gfastats.txt"/> |
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263 <param name="busco_short_summary_precuration" value="short_summary.specific.mammalia_odb10.pre.asm1.txt"/> |
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264 <param name="mercury_qv_precuration" value="ele_pre_merqOutput.qv"/> |
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265 <param name="merqury_completeness_stats_precuration" value="ele_pre_merqOutput.completeness.stats"/> |
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266 <conditional name="hap2_precuration_data"> |
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267 <param name="hap2_exists_precuration" value="no"/> |
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268 </conditional> |
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269 </section> |
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270 <section name="curated_assembly_data"> |
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271 <param name="gfstats_nstar_report_curated" value="ele.asm1_post_gfastats.txt"/> |
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272 <param name="busco_short_summary_curated" value="short_summary.specific.mammalia_odb10.post.asm1.txt"/> |
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273 <param name="mercury_qv_curated" value="ele_post_merqOutput.qv"/> |
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274 <param name="merqury_completeness_stats_curated" value="ele_post_merqOutput.completeness.stats"/> |
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275 <param name="merqury_hap_spectra_cn_curated" value="ele_post_merqOutput.ele_post.asm1.spectra-cn.ln.png"/> |
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276 <param name="merqury_spectra_cn_curated" value="ele_post_merqOutput.spectra-cn.ln.png"/> |
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277 <param name="merqury_spectra_asm_curated" value="ele_post_merqOutput.spectra-asm.ln.png"/> |
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278 <param name="hic_FullMap_curated" value="pretext_snake1.png"/> |
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279 <param name="hic_FullMap_link_curated" value="https://box.fu-berlin.de/apps/files/something"/> |
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280 <param name="blobplot_cont_curated" value="blob1.png"/> |
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281 <conditional name="hap2_curated_data"> |
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282 <param name="hap2_exists_curated" value="no"/> |
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283 </conditional> |
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284 </section> |
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285 <section name="curation_notes"> |
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286 <param name="obs_haploid_num" value="28"/> |
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287 <param name="obs_sex" value="XX"/> |
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288 <param name="interventions_per_gb" value="2"/> |
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289 <param name="contam_notes" value="No presence of contaminants. Mitochondrial genome was removed from the assembly"/> |
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290 <param name="other_notes" value="Large collapsed repeat in chr5, haplotypic inversion in chr12"/> |
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291 </section> |
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292 <output name="EAR_pdf" file="EAR.pdf" ftype="pdf" compare="sim_size"/> |
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293 <output name="log" file="EAR_log"/> |
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294 </test> |
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295 <!--- Test with 2 haplotypes information--> |
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296 <test expect_num_outputs="2"> |
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297 <section name="sample_information"> |
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298 <param name="tolid" value="xgPhyFlav1"/> |
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299 <param name="species_name" value="Phyllidia flava"/> |
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300 <param name="species_sex" value="XX"/> |
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301 <param name="submitter" value="John Doe"/> |
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302 <param name="affiliation" value="Galaxy EU"/> |
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303 <param name="tags" value="ERGA-BGE"/> |
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304 </section> |
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305 <section name="sequencing_data"> |
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306 <repeat name="seq_data_info"> |
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307 <param name="seq_data" value="HiFi: 40x"/> |
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308 </repeat> |
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309 <repeat name="seq_data_info"> |
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310 <param name="seq_data" value="Bionano: 10x"/> |
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311 </repeat> |
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312 <repeat name="seq_data_info"> |
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313 <param name="seq_data" value="OmniC: 90x"/> |
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314 </repeat> |
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315 </section> |
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316 <section name="genome_profiling_data"> |
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317 <param name="genome_scope_summary" value="genomescope_results_summary.txt"/> |
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318 <param name="smudge_plot_summary" value="smudgeplot_verbose_summary.txt"/> |
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319 </section> |
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320 <section name="pre_curation_assembly_data"> |
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321 <param name="haplotype_selection" value="hap1"/> |
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322 <param name="gfstats_nstar_report_precuration" value="ele_pre.asm1_gfastats.txt"/> |
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323 <param name="busco_short_summary_precuration" value="short_summary.specific.mammalia_odb10.pre.asm1.txt"/> |
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324 <param name="mercury_qv_precuration" value="ele_pre_merqOutput.qv"/> |
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325 <param name="merqury_completeness_stats_precuration" value="ele_pre_merqOutput.completeness.stats"/> |
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326 <conditional name="hap2_precuration_data"> |
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327 <param name="hap2_exists_precuration" value="yes"/> |
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328 <param name="gfstats_nstar_report_hap2_precuration" value="ele_pre.asm2_gfastats.txt"/> |
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329 <param name="busco_short_summary_hap2_precuration" value="short_summary.specific.mammalia_odb10.pre.asm2.txt"/> |
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330 <param name="mercury_qv_hap2_precuration" value="ele_pre_merqOutput.qv"/> |
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331 <param name="merqury_completeness_stats_hap2_precuration" value="ele_pre_merqOutput.completeness.stats"/> |
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332 </conditional> |
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333 </section> |
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334 <section name="curated_assembly_data"> |
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335 <param name="gfstats_nstar_report_curated" value="ele.asm1_post_gfastats.txt"/> |
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336 <param name="busco_short_summary_curated" value="short_summary.specific.mammalia_odb10.post.asm1.txt"/> |
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337 <param name="mercury_qv_curated" value="ele_post_merqOutput.qv"/> |
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338 <param name="merqury_completeness_stats_curated" value="ele_post_merqOutput.completeness.stats"/> |
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339 <param name="merqury_hap_spectra_cn_curated" value="ele_post_merqOutput.ele_post.asm1.spectra-cn.ln.png"/> |
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340 <param name="merqury_spectra_cn_curated" value="ele_post_merqOutput.spectra-cn.ln.png"/> |
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341 <param name="merqury_spectra_asm_curated" value="ele_post_merqOutput.spectra-asm.ln.png"/> |
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342 <param name="hic_FullMap_curated" value="pretext_snake1.png"/> |
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343 <param name="hic_FullMap_link_curated" value="https://box.fu-berlin.de/apps/files/something"/> |
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344 <param name="blobplot_cont_curated" value="blob1.png"/> |
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345 <conditional name="hap2_curated_data"> |
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346 <param name="hap2_exists_curated" value="yes"/> |
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347 <param name="gfstats_nstar_report_hap2_curated" value="ele.asm2_post_gfastats.txt"/> |
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348 <param name="busco_short_summary_hap2_curated" value="short_summary.specific.mammalia_odb10.post.asm2.txt"/> |
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349 <param name="mercury_qv_hap2_curated" value="ele_post_merqOutput.qv"/> |
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350 <param name="merqury_completeness_stats_hap2_curated" value="ele_post_merqOutput.completeness.stats"/> |
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351 <param name="merqury_hap_spectra_cn_hap2_curated" value="ele_post_merqOutput.ele_post.asm2.spectra-cn.ln.png"/> |
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352 <param name="merqury_spectra_cn_hap2_curated" value="ele_post_merqOutput.spectra-cn.ln.png"/> |
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353 <param name="merqury_spectra_asm_hap2_curated" value="ele_post_merqOutput.spectra-asm.ln.png"/> |
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354 <param name="hic_FullMap_hap2_curated" value="pretext_snake2.png"/> |
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355 <param name="hic_FullMap_link_hap2_curated" value="https://box.fu-berlin.de/apps/files/something"/> |
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356 <param name="blobplot_cont_hap2_curated" value="blob2.png"/> |
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357 </conditional> |
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358 </section> |
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359 <section name="curation_notes"> |
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360 <param name="obs_haploid_num" value="28"/> |
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361 <param name="obs_sex" value="XX"/> |
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362 <param name="interventions_per_gb" value="2"/> |
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363 <param name="contam_notes" value="No presence of contaminants. Mitochondrial genome was removed from the assembly"/> |
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364 <param name="other_notes" value="Large collapsed repeat in chr5, haplotypic inversion in chr12"/> |
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365 </section> |
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366 <output name="EAR_pdf" file="EAR_2.pdf" ftype="pdf" compare="sim_size"/> |
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367 </test> |
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368 </tests> |
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369 <help><![CDATA[ |
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370 |
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371 .. class:: infomark |
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372 |
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373 **What it does** |
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374 |
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375 **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. |
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376 ]]></help> |
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377 <expand macro="citations"/> |
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378 <expand macro="creator"/> |
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379 </tool> |