Repository 'erga_ear'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/erga_ear

Changeset 1:b61022e1b807 (2024-07-09)
Previous changeset 0:8c99976de71e (2024-06-07) Next changeset 2:a34826ae0a73 (2024-08-30)
Commit message:
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit b7f4b9b05946009ced0c4faeadc7acca98a90131
modified:
macros.xml
make_EAR.xml
test-data/EAR.pdf
added:
test-data/EAR_2.pdf
b
diff -r 8c99976de71e -r b61022e1b807 macros.xml
--- a/macros.xml Fri Jun 07 14:23:49 2024 +0000
+++ b/macros.xml Tue Jul 09 07:48:46 2024 +0000
b
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.0.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">23.2</token>
     <xml name="creator">
         <creator>
b
diff -r 8c99976de71e -r b61022e1b807 make_EAR.xml
--- a/make_EAR.xml Fri Jun 07 14:23:49 2024 +0000
+++ b/make_EAR.xml Tue Jul 09 07:48:46 2024 +0000
[
b'@@ -1,5 +1,5 @@\n <tool id="make_ear" name="ERGA Assembly Reporting Tool (EAR)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">\n-    <description>A tool to compile assembly reports and stastics from assembly pipeline</description>\n+    <description>A tool to compile assembly reports and statistics from assembly pipeline</description>\n     <macros>\n         <import>macros.xml</import>\n     </macros>\n@@ -78,28 +78,28 @@\n \n #else\n # ASSEMBLY DATA\n-    ASSEMBLIES:\n-        Pre-curation:\n-            pipeline: [Hifiasm_v0.19.4|HiC|l0, Purge_Dups_v1.2.6|, Bionano_vGalaxy_3.7.0, YaHS_v1.1]\n-            \'${pre_curation_assembly_data.haplotype_selection}\': \n-                gfastats--nstar-report_txt: \'${pre_curation_assembly_data.gfstats_nstar_report_precuration}\'\n-                busco_short_summary_txt: \'${pre_curation_assembly_data.busco_short_summary_precuration}\'\n-                merqury_qv: \'${pre_curation_assembly_data.mercury_qv_precuration}\'\n-                merqury_completeness_stats: \'${pre_curation_assembly_data.merqury_completeness_stats_precuration}\'\n+ASSEMBLIES:\n+    Pre-curation:\n+        pipeline: [Hifiasm_v0.19.4|HiC|l0, Purge_Dups_v1.2.6|, Bionano_vGalaxy_3.7.0, YaHS_v1.1]\n+        \'${pre_curation_assembly_data.haplotype_selection}\': \n+            gfastats--nstar-report_txt: \'${pre_curation_assembly_data.gfstats_nstar_report_precuration}\'\n+            busco_short_summary_txt: \'${pre_curation_assembly_data.busco_short_summary_precuration}\'\n+            merqury_qv: \'${pre_curation_assembly_data.mercury_qv_precuration}\'\n+            merqury_completeness_stats: \'${pre_curation_assembly_data.merqury_completeness_stats_precuration}\'\n \n-        Curated:\n-            pipeline: [GRIT_rapid_v2.0, HiGlass_v1.0]\n-            \'${pre_curation_assembly_data.haplotype_selection}\':\n-                gfastats--nstar-report_txt: \'${curated_assembly_data.gfstats_nstar_report_curated}\'\n-                busco_short_summary_txt: \'${curated_assembly_data.busco_short_summary_curated}\'\n-                merqury_qv: \'${curated_assembly_data.mercury_qv_curated}\'\n-                merqury_completeness_stats: \'${curated_assembly_data.merqury_completeness_stats_curated}\'\n-                merqury_hap_spectra_cn_png: \'${curated_assembly_data.merqury_hap_spectra_cn_curated}\'\n-                merqury_spectra_cn_png:  \'${curated_assembly_data.merqury_spectra_cn_curated}\'   \n-                merqury_spectra_asm_png: \'${curated_assembly_data.merqury_spectra_asm_curated}\'\n-                hic_FullMap_png: \'${curated_assembly_data.hic_FullMap_curated}\'\n-                hic_FullMap_link: \'${curated_assembly_data.hic_FullMap_link_curated}\'\n-                blobplot_cont_png: \'${curated_assembly_data.blobplot_cont_curated}\'\n+    Curated:\n+        pipeline: [GRIT_rapid_v2.0, HiGlass_v1.0]\n+        \'${pre_curation_assembly_data.haplotype_selection}\':\n+            gfastats--nstar-report_txt: \'${curated_assembly_data.gfstats_nstar_report_curated}\'\n+            busco_short_summary_txt: \'${curated_assembly_data.busco_short_summary_curated}\'\n+            merqury_qv: \'${curated_assembly_data.mercury_qv_curated}\'\n+            merqury_completeness_stats: \'${curated_assembly_data.merqury_completeness_stats_curated}\'\n+            merqury_hap_spectra_cn_png: \'${curated_assembly_data.merqury_hap_spectra_cn_curated}\'\n+            merqury_spectra_cn_png:  \'${curated_assembly_data.merqury_spectra_cn_curated}\'   \n+            merqury_spectra_asm_png: \'${curated_assembly_data.merqury_spectra_asm_curated}\'\n+            hic_FullMap_png: \'${curated_assembly_data.hic_FullMap_curated}\'\n+            hic_FullMap_link: \'${curated_assembly_data.hic_FullMap_link_curated}\'\n+            blobplot_cont_png: \'${curated_assembly_data.blobplot_cont_curated}\'\n #end if\n \n # CURATION NOTES\n@@ -124,7 +124,7 @@\n                 <option value="X0">X0</option>\n                 <option value="ZZ">ZZ</option>\n                 <option value="ZW">ZW</option>\n-             '..b'\n+                </repeat>\n+                <repeat name="seq_data_info">\n+                    <param name="seq_data" value="Bionano: 10x"/>\n+                </repeat>\n+                <repeat name="seq_data_info">\n+                    <param name="seq_data" value="OmniC: 90x"/>\n+                </repeat>\n+            </section>\n+            <section name="genome_profiling_data">\n+                <param name="genome_scope_summary" value="genomescope_results_summary.txt"/>\n+                <param name="smudge_plot_summary" value="smudgeplot_verbose_summary.txt"/>\n+            </section>\n+            <section name="pre_curation_assembly_data">\n+                <param name="haplotype_selection" value="hap1"/>\n+                <param name="gfstats_nstar_report_precuration" value="ele_pre.asm1_gfastats.txt"/>\n+                <param name="busco_short_summary_precuration" value="short_summary.specific.mammalia_odb10.pre.asm1.txt"/>\n+                <param name="mercury_qv_precuration" value="ele_pre_merqOutput.qv"/>\n+                <param name="merqury_completeness_stats_precuration" value="ele_pre_merqOutput.completeness.stats"/>\n+                <conditional name="hap2_precuration_data">\n+                    <param name="hap2_exists_precuration" value="no"/>\n+                </conditional>\n+            </section>\n+            <section name="curated_assembly_data">\n+                <param name="gfstats_nstar_report_curated" value="ele.asm1_post_gfastats.txt"/>\n+                <param name="busco_short_summary_curated" value="short_summary.specific.mammalia_odb10.post.asm1.txt"/>\n+                <param name="mercury_qv_curated" value="ele_post_merqOutput.qv"/>\n+                <param name="merqury_completeness_stats_curated" value="ele_post_merqOutput.completeness.stats"/>\n+                <param name="merqury_hap_spectra_cn_curated" value="ele_post_merqOutput.ele_post.asm1.spectra-cn.ln.png"/>\n+                <param name="merqury_spectra_cn_curated" value="ele_post_merqOutput.spectra-cn.ln.png"/>\n+                <param name="merqury_spectra_asm_curated" value="ele_post_merqOutput.spectra-asm.ln.png"/>\n+                <param name="hic_FullMap_curated" value="pretext_snake1.png"/>\n+                <param name="hic_FullMap_link_curated" value="https://box.fu-berlin.de/apps/files/something"/>\n+                <param name="blobplot_cont_curated" value="blob1.png"/>\n+                <conditional name="hap2_curated_data">\n+                    <param name="hap2_exists_curated" value="no"/>\n+                </conditional>\n+            </section>\n+            <section name="curation_notes">\n+                <param name="obs_haploid_num" value="28"/>\n+                <param name="obs_sex" value="XX"/>\n+                <param name="interventions_per_gb" value="2"/>\n+                <param name="contam_notes" value="No presence of contaminants. Mitochondrial genome was removed from the assembly"/>\n+                <param name="other_notes" value="Large collapsed repeat in chr5, haplotypic inversion in chr12"/>\n+            </section>\n+            <output name="EAR_pdf" file="EAR.pdf" ftype="pdf" compare="sim_size"/>\n+            <output name="log" file="EAR_log"/>    \n+        </test>\n+        <!--- Test with 2 haplotypes information-->\n         <test expect_num_outputs="2">\n             <section name="sample_information">\n                 <param name="tolid" value="xgPhyFlav1"/>\n@@ -302,8 +363,7 @@\n                 <param name="contam_notes" value="No presence of contaminants. Mitochondrial genome was removed from the assembly"/>\n                 <param name="other_notes" value="Large collapsed repeat in chr5, haplotypic inversion in chr12"/>\n             </section>\n-            <output name="EAR_pdf" file="EAR.pdf" ftype="pdf" compare="sim_size"/>\n-            <output name="log" file="EAR_log"/>    \n+            <output name="EAR_pdf" file="EAR_2.pdf" ftype="pdf" compare="sim_size"/>\n         </test>\n     </tests>\n     <help><![CDATA[\n'
b
diff -r 8c99976de71e -r b61022e1b807 test-data/EAR.pdf
--- a/test-data/EAR.pdf Fri Jun 07 14:23:49 2024 +0000
+++ b/test-data/EAR.pdf Tue Jul 09 07:48:46 2024 +0000
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b
diff -r 8c99976de71e -r b61022e1b807 test-data/EAR_2.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/EAR_2.pdf Tue Jul 09 07:48:46 2024 +0000
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