Mercurial > repos > iuc > tooldistillator
changeset 6:dfd6fa2637ba draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 9670088b288a41d4f3e4fdee2d021fd50646b886
| author | iuc |
|---|---|
| date | Tue, 03 Jun 2025 07:21:16 +0000 |
| parents | 66617be450bd |
| children | |
| files | macro.xml test-data/coreprofiler/results.tsv tooldistillator.xml |
| diffstat | 3 files changed, 99 insertions(+), 67 deletions(-) [+] |
line wrap: on
line diff
--- a/macro.xml Thu Apr 10 15:02:10 2025 +0000 +++ b/macro.xml Tue Jun 03 07:21:16 2025 +0000 @@ -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">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coreprofiler/results.tsv Tue Jun 03 07:21:16 2025 +0000 @@ -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
--- a/tooldistillator.xml Thu Apr 10 15:02:10 2025 +0000 +++ b/tooldistillator.xml Tue Jun 03 07:21:16 2025 +0000 @@ -131,6 +131,15 @@ --checkm2_log_path '$tool.select_tool.checkm2_log_path' --checkm2_log_hid '$tool.select_tool.checkm2_log_path.hid' #end if + #elif $tool.select_tool.tool_list == 'coreprofiler': + #if $tool.select_tool.profiles_json_path + --profiles_json_path '$tool.select_tool.profiles_json_path' + --profiles_json_hid '$tool.select_tool.profiles_json_path.hid' + #end if + #if $tool.select_tool.alleles_fna_path + --alleles_fna_path '$tool.select_tool.alleles_fna_path' + --alleles_fna_hid '$tool.select_tool.alleles_fna_path.hid' + #end if #elif $tool.select_tool.tool_list == 'fastp': #if $tool.select_tool.trimmed_forward_R1_path --trimmed_forward_R1_path '$tool.select_tool.trimmed_forward_R1_path' @@ -265,6 +274,7 @@ <option value="bracken">Bracken</option> <option value="bwa">BWA</option> <option value="checkm2">CheckM2</option> + <option value="coreprofiler">CoreProfiler</option> <option value="fastp">Fastp</option> <option value="fastqc">Fastqc</option> <option value="filtlong">Filtlong</option> @@ -342,12 +352,19 @@ </when> <when value="checkm2"> <param name="input" type="data" format="txt,tabular" multiple="false" label="CheckM2 quality report file" help="Tabular file from CheckM2 output"/> - <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"/> + <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"/> <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"/> <param argument="--checkm2_log_path" type="data" format="txt" multiple="false" optional="true" label="CheckM2 log file" help="Log file from CheckM2"/> <expand macro="analysis_software_version"/> <expand macro="reference_database_version"/> </when> + <when value="coreprofiler"> + <param name="input" type="data" format="txt,tabular" multiple="false" label="CoreProfiler allele calling report file" help="Tabular file from CoreProfiler output"/> + <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"/> + <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"/> + <expand macro="analysis_software_version"/> + <expand macro="reference_database_version"/> + </when> <when value="fastp"> <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/> <param argument="--trimmed_forward_R1_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R1" help="trimmed file R1"/> @@ -632,6 +649,16 @@ </repeat> <repeat name="tools"> <conditional name="select_tool"> + <param name="tool_list" value="coreprofiler"/> + <param name="input" value="coreprofiler/results.tsv" ftype="tabular"/> + <conditional name="origin"> + <param name="origin" value="true"/> + <param name="analysis_software_version" value="1.1.1"/> + </conditional> + </conditional> + </repeat> + <repeat name="tools"> + <conditional name="select_tool"> <param name="tool_list" value="fastp"/> <param name="input" value="fastp/fastp_report.json" ftype="json"/> <param name="trimmed_forward_R1_path" value="fastp/trimmed_R1.fastq.gz"/> @@ -806,7 +833,7 @@ </conditional> </repeat> </section> - <output_collection name="output_json" type="list" count="21"> + <output_collection name="output_json" type="list" count="22"> <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/> <expand macro="element_assert" name="amrfinderplus_1_output" text="mercury resistance transcriptional regulator MerR"/> <expand macro="element_assert" name="bakta_2_output" text="hypothetical protein"/> @@ -814,20 +841,21 @@ <expand macro="element_assert" name="bracken_4_output" text="Staphylococcus_aureus"/> <expand macro="element_assert" name="bwa_5_output" text="bwa_report"/> <expand macro="element_assert" name="checkm2_6_output" text="UniRef100_B5R745"/> - <expand macro="element_assert" name="fastp_7_output" text="705053822"/> - <expand macro="element_assert" name="fastqc_8_output" text="Sequences flagged as poor quality"/> - <expand macro="element_assert" name="filtlong_9_output" text="filtlong_report"/> - <expand macro="element_assert" name="flye_10_output" text="contig_2"/> - <expand macro="element_assert" name="integronfinder2_11_output" text="2353.0"/> - <expand macro="element_assert" name="isescan_12_output" text="IS200/IS605"/> - <expand macro="element_assert" name="kraken2_13_output" text="Enterococcus_faecalis"/> - <expand macro="element_assert" name="plasmidfinder_14_output" text="repUS40_1_repB"/> - <expand macro="element_assert" name="polypolish_15_output" text="320811"/> - <expand macro="element_assert" name="quast_16_output" text="2944723"/> - <expand macro="element_assert" name="recentrifuge_17_output" text="6.4917947578"/> - <expand macro="element_assert" name="refseqmasher_18_output" text="GCF_000519925.1"/> - <expand macro="element_assert" name="shovill_19_output" text="436224"/> - <expand macro="element_assert" name="tabular_file_20_output" text="NP_814691"/> + <expand macro="element_assert" name="coreprofiler_7_output" text="accC_S_6db3bfc0871923e1aedb4998b3c93b37"/> + <expand macro="element_assert" name="fastp_8_output" text="705053822"/> + <expand macro="element_assert" name="fastqc_9_output" text="Sequences flagged as poor quality"/> + <expand macro="element_assert" name="filtlong_10_output" text="filtlong_report"/> + <expand macro="element_assert" name="flye_11_output" text="contig_2"/> + <expand macro="element_assert" name="integronfinder2_12_output" text="2353.0"/> + <expand macro="element_assert" name="isescan_13_output" text="IS200/IS605"/> + <expand macro="element_assert" name="kraken2_14_output" text="Enterococcus_faecalis"/> + <expand macro="element_assert" name="plasmidfinder_15_output" text="repUS40_1_repB"/> + <expand macro="element_assert" name="polypolish_16_output" text="320811"/> + <expand macro="element_assert" name="quast_17_output" text="2944723"/> + <expand macro="element_assert" name="recentrifuge_18_output" text="6.4917947578"/> + <expand macro="element_assert" name="refseqmasher_19_output" text="GCF_000519925.1"/> + <expand macro="element_assert" name="shovill_20_output" text="436224"/> + <expand macro="element_assert" name="tabular_file_21_output" text="NP_814691"/> </output_collection> </test> </tests> @@ -840,57 +868,59 @@ ** Tool input** -ToolDistillator can use several input type from at least 22 different tools and 1 generic tool for tabular file: +ToolDistillator can use several input type from at least 23 different tools and 1 generic tool for tabular file: -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Tools | Version | Default input file| Optional files | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Abricate | 1.0.1 | output.tsv | | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| AMRFinderPlus | 3.11.26 | report.tsv | point_mutation_report.tsv, nucleotide_sequence.fasta | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Bakta | 1.7.0 | output.json | protein.faa, nucleotide.fna, annotation.gff3, summary.txt | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Bandage | 0.8.1 | info.txt | | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Bracken | 2.8 | output.tsv | taxonomy.tsv | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| BWA | 2.2.1 | input1.bam | input2.bam | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| CheckM2 |1.0.2 | quality_report.tsv| DIAMOND_RESULTS.tsv, protein_files.zip, checkm2.log | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Fastp | 0.23.2 | output.json | | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Fastqc | 0.12.1 | report.txt | report.html | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Filtlong | 0.2.1 | input.fastq | | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Flye | 2.9.1 | contig.fasta | contig.gfa, infos.tsv | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Integronfinder2| 2.0.2 | output.integrons | output.summary | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| ISEScan | 1.7.2.3 | output.tsv | is.fna, orf.faa, orf.fna | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| MultiQC | 1.11 | report.html | no optional files | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| PlasmidFinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Polypolish | 0.5.0 | contig.fasta | | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Quast | 5.2.0 | output.tsv | | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| RefSeqMasher | 0.1.2 | output.tsv | | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Shovill | 1.1.0 | contigs.fasta | alignment.bam, contigs.gfa | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| Staramr | 0.9.1 | resfinder.tsv | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv | -+----------------+----------------+-------------------+------------------------------------------------------------+ -| tabular_file | 0 | output.tsv | | -+----------------+----------------+-------------------+------------------------------------------------------------+ ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Tools | Version | Default input file | Optional files | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Abricate | 1.0.1 | output.tsv | | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| AMRFinderPlus | 3.11.26 | report.tsv | point_mutation_report.tsv, nucleotide_sequence.fasta | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Bakta | 1.7.0 | output.json | protein.faa, nucleotide.fna, annotation.gff3, summary.txt | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Bandage | 0.8.1 | info.txt | | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Bracken | 2.8 | output.tsv | taxonomy.tsv | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| BWA | 2.2.1 | input1.bam | input2.bam | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| CheckM2 |1.0.2 | quality_report.tsv | DIAMOND_RESULTS.tsv, protein_files.zip, checkm2.log | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| CoreProfiler | 1.1.1 | calling_results.tsv | profiles_w_tmp_alleles.json, new_alleles.fasta | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Fastp | 0.23.2 | output.json | | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Fastqc | 0.12.1 | report.txt | report.html | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Filtlong | 0.2.1 | input.fastq | | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Flye | 2.9.1 | contig.fasta | contig.gfa, infos.tsv | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Integronfinder2 | 2.0.2 | output.integrons | output.summary | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| ISEScan | 1.7.2.3 | output.tsv | is.fna, orf.faa, orf.fna | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| MultiQC | 1.11 | report.html | no optional files | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| PlasmidFinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Polypolish | 0.5.0 | contig.fasta | | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Quast | 5.2.0 | output.tsv | | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| RefSeqMasher | 0.1.2 | output.tsv | | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Shovill | 1.1.0 | contigs.fasta | alignment.bam, contigs.gfa | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| Staramr | 0.9.1 | resfinder.tsv | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv | ++-----------------+----------------+---------------------+------------------------------------------------------------+ +| tabular_file | 0 | output.tsv | | ++-----------------+----------------+---------------------+------------------------------------------------------------+ ** Options **