| Previous changeset 1:b61022e1b807 (2024-07-09) Next changeset 3:3dd6be0cd8dd (2024-10-15) |
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Commit message:
planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e293d14e82a903a4cab64dd72dfa3f3798466176 |
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modified:
macros.xml make_EAR.py make_EAR.xml test-data/EAR.pdf test-data/EAR_2.pdf |
| b |
| diff -r b61022e1b807 -r a34826ae0a73 macros.xml --- a/macros.xml Tue Jul 09 07:48:46 2024 +0000 +++ b/macros.xml Fri Aug 30 09:27:31 2024 +0000 |
| b |
| @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">1.0.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">24.08.26</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">23.2</token> <xml name="creator"> <creator> @@ -21,4 +21,26 @@ </citation> </citations> </xml> + <xml name="methods_tests"> + <section name="method_data"> + <repeat name="assembly_method_info"> + <param name="assembly_tools_info" value="Hifiasm: 0.19.4/HiC/l0"/> + </repeat> + <repeat name="assembly_method_info"> + <param name="assembly_tools_info" value="purge_dups: 1.2.6/"/> + </repeat> + <repeat name="assembly_method_info"> + <param name="assembly_tools_info" value="Bionano_solve: Galaxy_3.7.0"/> + </repeat> + <repeat name="assembly_method_info"> + <param name="assembly_tools_info" value="YaHS: 1.1"/> + </repeat> + <repeat name="curation_method_info"> + <param name="curation_tools_info" value="GRIT_Rapid: 2.0"/> + </repeat> + <repeat name="curation_method_info"> + <param name="curation_tools_info" value="HiGlass: 1.0"/> + </repeat> + </section> + </xml> </macros> \ No newline at end of file |
| b |
| diff -r b61022e1b807 -r a34826ae0a73 make_EAR.py --- a/make_EAR.py Tue Jul 09 07:48:46 2024 +0000 +++ b/make_EAR.py Fri Aug 30 09:27:31 2024 +0000 |
| [ |
| b'@@ -1,6 +1,5 @@\n \n import argparse\n-import glob\n import logging\n import math\n import os\n@@ -22,7 +21,7 @@\n # CAUTION: This is for the Galaxy version!\n # by Diego De Panis\n # ERGA Sequencing and Assembly Committee\n-EAR_version = "v24.05.20_glxy_beta"\n+EAR_version = "v24.08.26"\n \n \n def make_report(yaml_file):\n@@ -120,19 +119,9 @@\n fifth_column_value = target_line.split(\'\\t\')[4].strip()\n return fifth_column_value\n except Exception as e:\n- logging.warning(f"Error reading {file_path}: {str(e)}")\n+ logging.error(f"Error reading {file_path} for tool {tool} and haplotype {haplotype}: {str(e)}")\n return \'\'\n \n- # Getting kmer plots for curated asm\n- def get_png_files(dir_path):\n- png_files = glob.glob(f"{dir_path}/*.ln.png")\n- if len(png_files) < 4:\n- logging.warning(f"Warning: Less than 4 png files found in {dir_path}. If this is diploid, some images may be missing.")\n- # fill missing with None\n- while len(png_files) < 4:\n- png_files.append(None)\n- return png_files[:4]\n-\n # get unique part in file names\n def find_unique_parts(file1, file2):\n # Split filenames into parts\n@@ -141,7 +130,6 @@\n # Find unique parts\n unique_parts1 = [part for part in parts1 if part not in parts2]\n unique_parts2 = [part for part in parts2 if part not in parts1]\n-\n return \' \'.join(unique_parts1), \' \'.join(unique_parts2)\n \n # extract BUSCO values\n@@ -274,33 +262,34 @@\n # Parse pipeline and generate "tree"\n def generate_pipeline_tree(pipeline_data):\n tree_lines = []\n- indent = " " * 2 # Adjust indent spacing as needed\n-\n- for tool_version_param in pipeline_data:\n- parts = tool_version_param.split(\'|\')\n- tool_version = parts[0]\n- tool, version = tool_version.split(\'_v\') if \'_v\' in tool_version else (tool_version, "NA")\n+ indent = " " * 2 # Adjust indent spacing\n \n- # Handle parameters: join all but the first (which is tool_version) with \', \'\n- param_text = \', \'.join(parts[1:]) if len(parts) > 1 else "NA"\n+ if isinstance(pipeline_data, dict):\n+ for tool, version_param in pipeline_data.items():\n+ # Tool line\n+ tool_line = f"- <b>{tool}</b>"\n+ tree_lines.append(tool_line)\n \n- # Tool line\n- tool_line = f"- <b>{tool}</b>"\n- tree_lines.append(tool_line)\n+ # Convert version_param to string and split\n+ version_param_str = str(version_param)\n+ parts = version_param_str.split(\'/\')\n+ version = parts[0]\n+ params = [p for p in parts[1:] if p] # This will remove empty strings\n \n- # Version line\n- version_line = f"{indent*2}|_ <i>ver:</i> {version}"\n- tree_lines.append(version_line)\n+ # Version line\n+ version_line = f"{indent * 2}|_ <i>ver:</i> {version}"\n+ tree_lines.append(version_line)\n \n- # Param line(s)\n- if param_text != "NA":\n- for param in param_text.split(\',\'):\n- param = param.strip()\n- param_line = f"{indent*2}|_ <i>key param:</i> {param if param else \'NA\'}"\n+ # Param line(s)\n+ if params:\n+ for param in params:\n+ param_line = f"{indent * 2}|_ <i>key param:</i> {param}"\n+ tree_lines.append(param_line)\n+ else:\n+ param_line = f"{indent * 2}|_ <i>key param:</i> NA"\n tree_lines.append(param_line)\n- else:\n- param_line = f"{indent*2}|_ <i>key param:</i> NA"\n- tree_lines.append(param_line)\n+ else:\n+ tree_lines.append("Invalid pipeline data form'..b"l.', 'BUSCO frag.', 'BUSCO miss.']}\n for asm_stage, stage_properties in asm_data.items():\n- asm_stage_elements = [element for element in stage_properties.keys() if element != 'pipeline']\n+ asm_stage_elements = list(stage_properties.keys())\n for i, haplotypes in enumerate(asm_stage_elements):\n haplotype_properties = stage_properties[haplotypes]\n if isinstance(haplotype_properties, dict):\n@@ -580,7 +574,7 @@\n styles.add(ParagraphStyle(name='subTitleStyle', fontName='Courier', fontSize=16))\n styles.add(ParagraphStyle(name='normalStyle', fontName='Courier', fontSize=12))\n styles.add(ParagraphStyle(name='midiStyle', fontName='Courier', fontSize=10))\n- styles.add(ParagraphStyle(name='LinkStyle', fontName='Courier', fontSize=10, textColor='blue', underline=True))\n+ # styles.add(ParagraphStyle(name='LinkStyle', fontName='Courier', fontSize=10, textColor='blue', underline=True))\n styles.add(ParagraphStyle(name='treeStyle', fontName='Courier', fontSize=10, leftIndent=12))\n styles.add(ParagraphStyle(name='miniStyle', fontName='Courier', fontSize=8))\n styles.add(ParagraphStyle(name='FileNameStyle', fontName='Courier', fontSize=6))\n@@ -659,7 +653,7 @@\n \n # Iterate over haplotypes in the Curated category to get data for EBP metrics\n curated_assemblies = yaml_data.get('ASSEMBLIES', {}).get('Curated', {})\n- haplotype_names = [key for key in curated_assemblies.keys() if key != 'pipeline']\n+ haplotype_names = list(curated_assemblies.keys())\n \n for haplotype in haplotype_names:\n properties = curated_assemblies[haplotype]\n@@ -756,7 +750,7 @@\n # Store BUSCO version and lineage information from each file in list\n busco_info_list = []\n for asm_stages, stage_properties in asm_data.items():\n- for haplotype_keys, haplotype_properties in stage_properties.items():\n+ for i, haplotype_properties in stage_properties.items():\n if isinstance(haplotype_properties, dict):\n if 'busco_short_summary_txt' in haplotype_properties:\n busco_version, lineage_info = extract_busco_info(haplotype_properties['busco_short_summary_txt'])\n@@ -787,9 +781,9 @@\n tool_count = 0\n \n # Add title and images for each step\n- for idx, (asm_stages, stage_properties) in enumerate(asm_data.items(), 1):\n+ for asm_stages, stage_properties in asm_data.items():\n if asm_stages == 'Curated':\n- tool_elements = [element for element in stage_properties.keys() if element != 'pipeline']\n+ tool_elements = list(stage_properties.keys())\n \n images_with_names = []\n \n@@ -825,7 +819,7 @@\n \n # Add images and names to the elements in pairs\n for i in range(0, len(images_with_names), 4): # Process two images (and their names) at a time\n- elements_to_add = images_with_names[i:i + 4]\n+ elements_to_add = images_with_names[i: i + 4]\n \n # Create table for the images and names\n table = Table(elements_to_add)\n@@ -856,7 +850,6 @@\n \n # Iterate over haplotypes in the Curated category to get K-mer spectra images\n curated_assemblies = yaml_data.get('ASSEMBLIES', {}).get('Curated', {})\n- haplotype_names = [key for key in curated_assemblies.keys() if key != 'pipeline']\n \n # Get paths for spectra files\n spectra_files = {\n@@ -974,9 +967,9 @@\n tool_count = 0\n \n # Add title and images for each step\n- for idx, (asm_stages, stage_properties) in enumerate(asm_data.items(), 1):\n+ for asm_stages, stage_properties in asm_data.items():\n if asm_stages == 'Curated': # Check if the current stage is 'Curated'\n- tool_elements = [element for element in stage_properties.keys() if element != 'pipeline']\n+ tool_elements = list(stage_properties.keys())\n \n for haplotype in tool_elements:\n haplotype_properties = stage_properties[haplotype]\n" |
| b |
| diff -r b61022e1b807 -r a34826ae0a73 make_EAR.xml --- a/make_EAR.xml Tue Jul 09 07:48:46 2024 +0000 +++ b/make_EAR.xml Fri Aug 30 09:27:31 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"/> |
| b |
| diff -r b61022e1b807 -r a34826ae0a73 test-data/EAR.pdf --- a/test-data/EAR.pdf Tue Jul 09 07:48:46 2024 +0000 +++ b/test-data/EAR.pdf Fri Aug 30 09:27:31 2024 +0000 |
| [ |
| @@ -153,7 +153,7 @@ endobj 20 0 obj << -/Author (\(anonymous\)) /CreationDate (D:20240704122313+00'00') /Creator (\(unspecified\)) /Keywords () /ModDate (D:20240704122313+00'00') /Producer (ReportLab PDF Library - www.reportlab.com) +/Author (\(anonymous\)) /CreationDate (D:20240829084627+00'00') /Creator (\(unspecified\)) /Keywords () /ModDate (D:20240829084627+00'00') /Producer (ReportLab PDF Library - www.reportlab.com) /Subject (\(unspecified\)) /Title (\(anonymous\)) /Trapped /False >> endobj @@ -164,10 +164,10 @@ endobj 22 0 obj << -/Filter [ /ASCII85Decode /FlateDecode ] /Length 1481 +/Filter [ /ASCII85Decode /FlateDecode ] /Length 1471 >> stream 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