| Previous changeset 5:66617be450bd (2025-04-10) Next changeset 7:ca98fc5a5803 (2025-07-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 9670088b288a41d4f3e4fdee2d021fd50646b886 |
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modified:
macro.xml tooldistillator.xml |
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added:
test-data/coreprofiler/results.tsv |
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| diff -r 66617be450bd -r dfd6fa2637ba macro.xml --- a/macro.xml Thu Apr 10 15:02:10 2025 +0000 +++ b/macro.xml Tue Jun 03 07:21:16 2025 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">0.9.2</token> + <token name="@TOOL_VERSION@">0.9.3</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.05</token> <xml name="version_command"> |
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| diff -r 66617be450bd -r dfd6fa2637ba test-data/coreprofiler/results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coreprofiler/results.tsv Tue Jun 03 07:21:16 2025 +0000 |
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| @@ -0,0 +1,2 @@ +seq_id accB_S accC_S accD_S +tests/data/kp/genomes/10_04A025_hennart2022.fas 1 accC_S_6db3bfc0871923e1aedb4998b3c93b37 accD_S_2e603343825da09506bdc8ea287f5584 |
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| diff -r 66617be450bd -r dfd6fa2637ba tooldistillator.xml --- a/tooldistillator.xml Thu Apr 10 15:02:10 2025 +0000 +++ b/tooldistillator.xml Tue Jun 03 07:21:16 2025 +0000 |
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| b'@@ -131,6 +131,15 @@\n --checkm2_log_path \'$tool.select_tool.checkm2_log_path\'\n --checkm2_log_hid \'$tool.select_tool.checkm2_log_path.hid\'\n #end if\n+ #elif $tool.select_tool.tool_list == \'coreprofiler\':\n+ #if $tool.select_tool.profiles_json_path\n+ --profiles_json_path \'$tool.select_tool.profiles_json_path\'\n+ --profiles_json_hid \'$tool.select_tool.profiles_json_path.hid\'\n+ #end if\n+ #if $tool.select_tool.alleles_fna_path\n+ --alleles_fna_path \'$tool.select_tool.alleles_fna_path\'\n+ --alleles_fna_hid \'$tool.select_tool.alleles_fna_path.hid\'\n+ #end if\n #elif $tool.select_tool.tool_list == \'fastp\':\n #if $tool.select_tool.trimmed_forward_R1_path\n --trimmed_forward_R1_path \'$tool.select_tool.trimmed_forward_R1_path\'\n@@ -265,6 +274,7 @@\n <option value="bracken">Bracken</option>\n <option value="bwa">BWA</option>\n <option value="checkm2">CheckM2</option>\n+ <option value="coreprofiler">CoreProfiler</option>\n <option value="fastp">Fastp</option>\n <option value="fastqc">Fastqc</option>\n <option value="filtlong">Filtlong</option>\n@@ -342,12 +352,19 @@\n </when>\n <when value="checkm2">\n <param name="input" type="data" format="txt,tabular" multiple="false" label="CheckM2 quality report file" help="Tabular file from CheckM2 output"/>\n- <param argument="--diamond_results_path" type="data" format="txt,tabular" optional="true" multiple="false" label="CheckM2 Diamond results file" help="DIAMOND_RESULTS file for CheckM2"/>\n+ <param argument="--diamond_results_path" type="data" format="txt,tabular" optional="true" multiple="false" label="CheckM2 Diamond results file" help="DIAMOND_RESULTS file from CheckM2"/>\n <param argument="--protein_zip_path" type="data" format="zip,tar,tar.gz" optional="true" multiple="false" label="Archive file with protein files from CheckM2" help="Protein sequence fasta files in an archive file for CheckM2"/>\n <param argument="--checkm2_log_path" type="data" format="txt" multiple="false" optional="true" label="CheckM2 log file" help="Log file from CheckM2"/>\n <expand macro="analysis_software_version"/>\n <expand macro="reference_database_version"/>\n </when>\n+ <when value="coreprofiler">\n+ <param name="input" type="data" format="txt,tabular" multiple="false" label="CoreProfiler allele calling report file" help="Tabular file from CoreProfiler output"/>\n+ <param argument="--profiles_json_path" type="data" format="json" optional="true" multiple="false" label="Coreprofiler JSON results file" help="JSON file containing info about files with temporary alleles"/>\n+ <param argument="--alleles_fna_path" type="data" format="fasta" optional="true" multiple="false" label="Coreprofiler FASTA results file" help=" FASTA file with new alleles sequences if detected"/>\n+ <expand macro="analysis_software_version"/>\n+ <expand macro="reference_database_version"/>\n+ </when>\n <when value="fastp">\n <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/>\n <param argument="--trimmed_forward_R1_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R1" help="trimmed file R1"/>\n@@ -632,6 +649,16 @@\n </repeat>\n <repeat name="tools">\n <conditional name="select_tool">\n+ '..b'------+----------------+---------------------+------------------------------------------------------------+\n+| Fastp | 0.23.2 | output.json | |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| Fastqc | 0.12.1 | report.txt | report.html |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| Filtlong | 0.2.1 | input.fastq | |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| Flye | 2.9.1 | contig.fasta | contig.gfa, infos.tsv |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| Integronfinder2 | 2.0.2 | output.integrons | output.summary |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| ISEScan | 1.7.2.3 | output.tsv | is.fna, orf.faa, orf.fna |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| MultiQC | 1.11 | report.html | no optional files |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| PlasmidFinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| Polypolish | 0.5.0 | contig.fasta | |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| Quast | 5.2.0 | output.tsv | |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| RefSeqMasher | 0.1.2 | output.tsv | |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| Shovill | 1.1.0 | contigs.fasta | alignment.bam, contigs.gfa |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| Staramr | 0.9.1 | resfinder.tsv | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n+| tabular_file | 0 | output.tsv | |\n++-----------------+----------------+---------------------+------------------------------------------------------------+\n \n ** Options **\n \n' |