diff make_EAR.xml @ 1:b61022e1b807 draft default tip

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

--- a/make_EAR.xml	Fri Jun 07 14:23:49 2024 +0000
+++ b/make_EAR.xml	Tue Jul 09 07:48:46 2024 +0000
@@ -1,5 +1,5 @@
 <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>
+    <description>A tool to compile assembly reports and statistics from assembly pipeline</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -78,28 +78,28 @@
 
 #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: '${pre_curation_assembly_data.merqury_completeness_stats_precuration}'
+ASSEMBLIES:
+    Pre-curation:
+        pipeline: [Hifiasm_v0.19.4|HiC|l0, Purge_Dups_v1.2.6|, Bionano_vGalaxy_3.7.0, YaHS_v1.1]
+        '${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: '${curated_assembly_data.blobplot_cont_curated}'
+    Curated:
+        pipeline: [GRIT_rapid_v2.0, HiGlass_v1.0]
+        '${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
@@ -124,7 +124,7 @@
                 <option value="X0">X0</option>
                 <option value="ZZ">ZZ</option>
                 <option value="ZW">ZW</option>
-                <option value="NA">Not Available</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"/>
@@ -232,6 +232,67 @@
         <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"/>
@@ -302,8 +363,7 @@
                 <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"/>    
+            <output name="EAR_pdf" file="EAR_2.pdf" ftype="pdf" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[