diff make_EAR.xml @ 1:82450f7907ef draft

planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176

--- a/make_EAR.xml	Thu Jul 04 12:43:34 2024 +0000
+++ b/make_EAR.xml	Fri Aug 30 09:27:17 2024 +0000
@@ -39,7 +39,6 @@
 # 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: '${pre_curation_assembly_data.busco_short_summary_precuration}'
@@ -52,7 +51,6 @@
             merqury_completeness_stats: '${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: '${curated_assembly_data.busco_short_summary_curated}'
@@ -80,7 +78,6 @@
 # ASSEMBLY DATA
 ASSEMBLIES:
     Pre-curation:
-        pipeline: [Hifiasm_v0.19.4|HiC|l0, Purge_Dups_v1.2.6|, Bionano_vGalaxy_3.7.0, YaHS_v1.1]
         '${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}'
@@ -88,7 +85,6 @@
             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: '${curated_assembly_data.busco_short_summary_curated}'
@@ -102,6 +98,18 @@
             blobplot_cont_png: '${curated_assembly_data.blobplot_cont_curated}'
 #end if
 
+# METHODS DATA
+PIPELINES:
+  Assembly:
+    #for $repeat in $method_data.assembly_method_info:
+    ${repeat.assembly_tools_info}
+    #end for
+
+  Curation:
+    #for $repeat in $method_data.curation_method_info:
+    ${repeat.curation_tools_info}
+    #end for
+
 # CURATION NOTES
 NOTES:
     Obs_Haploid_num: '${curation_notes.obs_haploid_num}'
@@ -131,7 +139,7 @@
             <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>
+                <option value="ERGA-Community">ERGA-Community</option>
             </param>
         </section>
 
@@ -150,7 +158,6 @@
 
         <!-- 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>
@@ -177,7 +184,6 @@
         
         <!-- 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"/>
@@ -210,6 +216,16 @@
             </conditional>
         </section>
         
+        <!-- Input parameters for Methods data -->
+        <section name="method_data" title="Method Information">
+            <repeat name='assembly_method_info' title="Specify the method used for Assembly" min="1" default="2">
+                <param name="assembly_tools_info" type="text" label="Input tool names along with version and paramters used for assembly" optional="False" help="Specify ToolName:Tool_Version/Tool_parameters"/>
+            </repeat>
+            <repeat name='curation_method_info' title="Specify the method used for Curation" min="1" default="2">
+                <param name="curation_tools_info" type="text" label="Input tool names along with version and paramters used for curation" optional="False" help="Specify ToolName:Tool_Version/Tool_parameters"/>
+            </repeat>
+        </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"/>
@@ -282,6 +298,7 @@
                     <param name="hap2_exists_curated" value="no"/>
                 </conditional>
             </section>
+            <expand macro="methods_tests"></expand>
             <section name="curation_notes">
                 <param name="obs_haploid_num" value="28"/>
                 <param name="obs_sex" value="XX"/>
@@ -356,6 +373,7 @@
                     <param name="blobplot_cont_hap2_curated" value="blob2.png"/>
                 </conditional>
             </section>
+            <expand macro="methods_tests"></expand>
             <section name="curation_notes">
                 <param name="obs_haploid_num" value="28"/>
                 <param name="obs_sex" value="XX"/>