# HG changeset patch
# User iuc
# Date 1748935276 0
# Node ID dfd6fa2637bad64729383966524e687f1e8f53d4
# Parent  66617be450bda1533455a0f5d202439bb4b4b230
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 9670088b288a41d4f3e4fdee2d021fd50646b886

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
@@ -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">
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
@@ -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
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
@@ -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 **