diff tooldistillator.xml @ 1:65a69de1e294 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834

--- a/tooldistillator.xml	Tue Apr 30 08:42:33 2024 +0000
+++ b/tooldistillator.xml	Fri May 24 10:47:33 2024 +0000
@@ -20,7 +20,16 @@
         '$tool.select_tool.input'
         --analysis_software_version '$tool.select_tool.analysis_software_version'
         --reference_database_version '$tool.select_tool.reference_database_version'
-        #if $tool.select_tool.tool_list == 'bakta'
+        #if $tool.select_tool.tool_list == 'amrfinderplus':
+            #if $tool.select_tool.point_mutation_report_path
+                --point_mutation_report_path '$tool.select_tool.point_mutation_report_path'
+                --point_mutation_report_hid '$tool.select_tool.point_mutation_report_path.hid'
+            #end if
+            #if $tool.select_tool.nucleotide_sequence_path
+                --nucleotide_sequence_path '$tool.select_tool.nucleotide_sequence_path'
+                --nucleotide_sequence_hid '$tool.select_tool.nucleotide_sequence_path.hid'
+            #end if
+        #elif $tool.select_tool.tool_list == 'bakta'
             #if $tool.select_tool.annotation_tabular_path
                 --annotation_tabular_path '$tool.select_tool.annotation_tabular_path'
                 --annotation_tabular_hid '$tool.select_tool.annotation_tabular_path.hid'
@@ -191,21 +200,22 @@
             <repeat name="tools" title="Tool" min="0">
                 <conditional name="select_tool">
                     <param name="tool_list" type="select" label="Available tools">
-                        <option value="abricate">abricate</option>
-                        <option value="bakta">bakta</option>
-                        <option value="bandage">bandage</option>
-                        <option value="bracken">bracken</option>
-                        <option value="fastp">fastp</option>
-                        <option value="integronfinder2">integronfinder2</option>
-                        <option value="isescan">isescan</option>
-                        <option value="kraken2">kraken2</option>
+                        <option value="abricate">Abricate</option>
+                        <option value="amrfinderplus">AMRFinderPlus</option>
+                        <option value="bakta">Bakta</option>
+                        <option value="bandage">Bandage</option>
+                        <option value="bracken">Bracken</option>
+                        <option value="fastp">Fastp</option>
+                        <option value="integronfinder2">Integronfinder2</option>
+                        <option value="isescan">ISEScan</option>
+                        <option value="kraken2">Kraken2</option>
                         <option value="multiqc">MultiQC</option>
-                        <option value="plasmidfinder">plasmidfinder</option>
-                        <option value="quast">quast</option>
-                        <option value="recentrifuge">recentrifuge</option>
-                        <option value="refseqmasher">refseqmasher</option>
-                        <option value="shovill">shovill</option>
-                        <option value="staramr">staramr</option>
+                        <option value="plasmidfinder">PlasmidFinder</option>
+                        <option value="quast">Quast</option>
+                        <option value="recentrifuge">Recentrifuge</option>
+                        <option value="refseqmasher">RefSeqMasher</option>
+                        <option value="shovill">Shovill</option>
+                        <option value="staramr">Staramr</option>
                         <option value="tabular_file">tabular_generic_file</option>
                     </param>
                     <when value="abricate">
@@ -213,6 +223,13 @@
                         <expand macro="analysis_software_version"/>
                         <expand macro="reference_database_version"/>
                     </when>
+                    <when value="amrfinderplus">
+                        <param name="input" type="data" format="tabular" multiple="false" label="AMRFinderPlus report file" help="Tabular file from AMRFinderPlus output"/>
+                        <param argument="--point_mutation_report_path" type="data" format="tabular" multiple="false" optional="true" label="AMRFinderPlus point mutation report file" help="AMRFinderPlus Tabular point mutation report file"/>
+                        <param argument="--nucleotide_sequence_path" type="data" format="fasta" multiple="false" optional="true" label="AMRFinderPlus nucleotide identified sequence fasta file" help="AMRFinderPlus nucleotide identified sequence fasta file"/>
+                        <expand macro="analysis_software_version"/>
+                        <expand macro="reference_database_version"/>
+                    </when>
                     <when value="bakta">
                         <param name="input" type="data" format="json" multiple="false" label="Bakta report file" help="Json file from bakta output"/>
                         <param argument="--annotation_tabular_path" type="data" format="tabular" multiple="false" optional="true" label="Bakta annotation file" help="Tabular annotation file"/>
@@ -419,6 +436,16 @@
                 </repeat>
                 <repeat name="tools">
                     <conditional name="select_tool">
+                        <param name="tool_list" value="amrfinderplus"/>
+                        <param name="input" value="amrfinderplus/AMRFinderPlus_report.tsv" ftype="tabular"/>
+                        <param name="point_mutation_report_path" value="amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv" ftype="tabular"/>
+                        <param name="nucleotide_sequence_path" value="amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta" ftype="fasta"/>
+                        <param name="analysis_software_version" value="3.11.26"/>
+                        <param name="reference_database_version" value="v3.11-2023-04-17.1"/>
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
                         <param name="tool_list" value="bakta"/>
                         <param name="input" value="bakta/bakta.json" ftype="json"/>
                         <param name="annotation_tabular_path" value="bakta/bakta_annotation.tsv" ftype="tabular"/>
@@ -568,22 +595,23 @@
                     </conditional>
                 </repeat>
             </section>
-            <output_collection name="output_json" type="list" count="15">
+            <output_collection name="output_json" type="list" count="16">
                 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
-                <expand macro="element_assert" name="bakta_1_output" text="hypothetical protein"/>
-                <expand macro="element_assert" name="bandage_2_output" text="3042326"/>
-                <expand macro="element_assert" name="bracken_3_output" text="Staphylococcus_aureus"/>
-                <expand macro="element_assert" name="fastp_4_output" text="705053822"/>
-                <expand macro="element_assert" name="integronfinder2_5_output" text="2353.0"/>
-                <expand macro="element_assert" name="isescan_6_output" text="IS200/IS605"/>
-                <expand macro="element_assert" name="kraken2_7_output" text="Enterococcus_faecalis"/>
-                <expand macro="element_assert" name="plasmidfinder_8_output" text="repUS40_1_repB"/>
-                <expand macro="element_assert" name="quast_9_output" text="2944723"/>
-                <expand macro="element_assert" name="recentrifuge_10_output" text="6.4917947578"/>
-                <expand macro="element_assert" name="refseqmasher_11_output" text="GCF_000519925.1"/>
-                <expand macro="element_assert" name="shovill_12_output" text="436224"/>
-                <expand macro="element_assert" name="staramr_13_output" text="10_Enterococcus_faecalis_S17_L001"/>
-                <expand macro="element_assert" name="tabular_file_14_output" text="NP_814691"/>
+                <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"/>
+                <expand macro="element_assert" name="bandage_3_output" text="3042326"/>
+                <expand macro="element_assert" name="bracken_4_output" text="Staphylococcus_aureus"/>
+                <expand macro="element_assert" name="fastp_5_output" text="705053822"/>
+                <expand macro="element_assert" name="integronfinder2_6_output" text="2353.0"/>
+                <expand macro="element_assert" name="isescan_7_output" text="IS200/IS605"/>
+                <expand macro="element_assert" name="kraken2_8_output" text="Enterococcus_faecalis"/>
+                <expand macro="element_assert" name="plasmidfinder_9_output" text="repUS40_1_repB"/>
+                <expand macro="element_assert" name="quast_10_output" text="2944723"/>
+                <expand macro="element_assert" name="recentrifuge_11_output" text="6.4917947578"/>
+                <expand macro="element_assert" name="refseqmasher_12_output" text="GCF_000519925.1"/>
+                <expand macro="element_assert" name="shovill_13_output" text="436224"/>
+                <expand macro="element_assert" name="staramr_14_output" text="10_Enterococcus_faecalis_S17_L001"/>
+                <expand macro="element_assert" name="tabular_file_15_output" text="NP_814691"/>
             </output_collection>
         </test>
 
@@ -596,12 +624,15 @@
 This tool here is extracting information from output files of specific tools and exposing it as JSON files
 ** Tool input**
 
-ToolDistillator can use several input type from at least 14 different tools :
+ToolDistillator can use several input type from at least 15 different tools :
 
 +----------------+----------------+-------------------+------------------------------------------------------------+
 | 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         |                                                            |
@@ -616,13 +647,13 @@
 +----------------+----------------+-------------------+------------------------------------------------------------+
 | Kraken2        | 2.1.2          |  taxonomy.tsv     | reads_assignation.txt                                      |
 +----------------+----------------+-------------------+------------------------------------------------------------+
-| Plasmidfinder  | 2.1.6          |  output.json      | genome_hits.fasta, plasmid_hits.fasta                      |
+| PlasmidFinder  | 2.1.6          |  output.json      | genome_hits.fasta, plasmid_hits.fasta                      |
 +----------------+----------------+-------------------+------------------------------------------------------------+
 | Quast          | 5.2.0          |  output.tsv       |                                                            |
 +----------------+----------------+-------------------+------------------------------------------------------------+
 | Recentrifuge   | 1.10.0         |  data.tsv         | report.html, stat.tsv                                      |
 +----------------+----------------+-------------------+------------------------------------------------------------+
-| Refseqmasher   | 0.1.2          |  output.tsv       |                                                            |
+| RefSeqMasher   | 0.1.2          |  output.tsv       |                                                            |
 +----------------+----------------+-------------------+------------------------------------------------------------+
 | Shovill        | 1.1.0          |  contigs.fasta    | alignment.bam, contigs.gfa                                 |
 +----------------+----------------+-------------------+------------------------------------------------------------+