--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abromics_galaxy_json_extractor.xml	Sun Jun 04 17:16:20 2023 +0000
@@ -0,0 +1,404 @@
+<tool id="abromics_galaxy_json_extractor" name="abromics_galaxy_json_extractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Result extractor to json format
+    </description>
+    <macros>
+        <import>macro.xml</import>
+    </macros>
+    <expand macro='edam'/>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+
+    <command detect_errors="aggressive"><![CDATA[
+        mkdir "abromics_extracted_folder" &&
+#*=================================================================
+    Paramaters to add Database and tool version if available
+=================================================================*#
+#set $software_with_database = str("abricate,bakta,bracken,kraken2,plasmidfinder,recentrifuge").split(",")
+#set $counter = len($tool_section.tools)-1
+#*======================================================
+    Loop to include some different tool in one time
+======================================================*#
+#for $i, $tool in enumerate( $tool_section.tools )
+    abromics_extract
+    "$tool.select_tool.tool_list"
+    --hid $tool.select_tool.input.hid
+    "$tool.select_tool.input"
+    --analysis_software_version "$tool.select_tool.analysis_software_version"
+    #if str($tool.select_tool.tool_list) in str($software_with_database)
+        --reference_database_version "$tool.select_tool.reference_database_version"
+    #end if
+    #if "$tool.select_tool.tool_list" == "bakta"
+        --summary_result_path "$tool.select_tool.summary_result_path"
+        --nucleotide_annotation_path "$tool.select_tool.nucleotide_annotation_path"
+        --amino_acid_annotation_path "$tool.select_tool.amino_acid_annotation_path"
+        --gff_file_path "$tool.select_tool.gff_file_path"
+    #elif "$tool.select_tool.tool_list" == "bracken"
+        --kraken_report_path "tool.select_tool.kraken_report_path"
+        --threshold "tool.select_tool.threshold"
+        --read_length "tool.select_tool.read_length"
+        --level "tool.select_tool.level"
+    #elif"$tool.select_tool.tool_list" == "integronfinder2"
+        --summary_file_path "tool.select_tool.summary_file_path"
+    #elif "$tool.select_tool.tool_list" == "isescan"
+        --orf_fna_file "tool.select_tool.orf_fna_file"
+        --orf_faa_file "tool.select_tool.orf_faa_file"
+        --is_fna_file "tool.select_tool.is_fna_file"
+    #elif "$tool.select_tool.tool_list" == "kraken2"
+        --seq_classification_file_path "tool.select_tool.seq_classification_file_path"
+    #elif "$tool.select_tool.tool_list" == "plasmidfinder"
+        --genome_hit_file_path "tool.select_tool.genome_hit_file_path"
+        --plasmid_sequence_file_path "tool.select_tool.plasmid_sequence_file_path"
+    #elif "$tool.select_tool.tool_list" == "recentrifuge"
+        --rcf_stat_file_path "tool.select_tool.rcf_stat_file_path"
+        --rcf_html_path "tool.select_tool.rcf_html_path"
+    #elif "$tool.select_tool.tool_list" == "shovill"
+        --contig_graph_path "tool.select_tool.contig_graph_path"
+        --bam_file_path "tool.select_tool.bam_file_path"
+    #elif "$tool.select_tool.tool_list" == "staramr"
+        --mlst_file_path "tool.select_tool.mlst_file_path"
+        --plasmidfinder_file_path "tool.select_tool.plasmidfinder_file_path"
+        --pointfinder_file_path "tool.select_tool.pointfinder_file_path"
+        --setting_file_path "tool.select_tool.setting_file_path"
+    #elif "$tool.select_tool.tool_list" == "tabular_file"
+        --analysis_software_name "tool.select_tool.analysis_software_name"
+    #end if
+    -o "abromics_extracted_folder/$($tool.select_tool.tool_list)_$(i)_output.json" 
+    | tee "$logfile" 
+    #if $i < $counter
+        &&
+    #end if
+#end for
+
+        ]]>
+    </command>
+    <inputs>
+        <section name="tool_section" title="Available tools" expanded="true">
+            <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="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">
+                        <param name="input" type="data" format="tabular" multiple="false" label="Abricate report file" help="Tabular file from abricate output"/>
+                        <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="--summary_result_path" type="data" format="txt" multiple="false" optional="true" label="Bakta summary file" help="Summary file from bakta output"/>
+                        <param argument="--nucleotide_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta nucleotide file" help="Nucleotide sequence annotation file"/>
+                        <param argument="--amino_acid_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta amino acide file" help="Amino acid sequence annotation file"/>
+                        <param argument="--gff_file_path" type="data" format="gff3" multiple="false" optional="true" label="Bakta annotation file" help="Annotation file"/>
+                        <expand macro="analysis_software_version"/>
+                        <expand macro="reference_database_version"/>
+                    </when>
+                    <when value="bandage">
+                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Bandage report file" help="Tabular file from bandage output"/>
+                        <expand macro="analysis_software_version"/>
+                    </when>
+                    <when value="bracken">
+                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Bracken report file" help="Tabular file from bracken output"/>
+                        <expand macro="analysis_software_version"/>
+                        <expand macro="reference_database_version"/>
+                        <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" label="Kraken re-estimated report" help="New kraken report from bracken tool"/>
+                        <param argument="--threshold" type="integer" min="0" optional="true" label="PRIOR on read numbers" help="Prior of read for estimation, default is 0"/>
+                        <param argument="--read_length" type="integer" min="0" optional="true" label="Read length"/>
+                        <param argument="--level" type="select" label="Taxonomic level estimation" help="Level of final abundance (from Domain to subspecies, default on species)">
+                            <option value="D">Domain</option>
+                            <option value="P">Phylum</option>
+                            <option value="C">Class</option>
+                            <option value="O">Order</option>
+                            <option value="F">Family</option>
+                            <option value="G">Genus</option>
+                            <option value="S">Species</option>
+                            <option value="S+">Subspecies</option>
+                        </param>
+                    </when>
+                    <when value="fastp">
+                        <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/>
+                        <expand macro="analysis_software_version"/>
+                    </when>
+                    <when value="integronfinder2">
+                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/>
+                        <param argument="--summary_file_path" type="data" format="txt,tabular" multiple="false" label="Summary report" help="Summary file from integronfinder2"/>
+                        <expand macro="analysis_software_version"/>
+                    </when>
+                    <when value="isescan">
+                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Isescan report" help="IseScan file from integronfinder2"/>
+                        <param argument="--orf_fna_file" type="data" format="fasta" optional="true" multiple="false" label="ORF fna file" help="Nuleotide sequence to the ORFs"/>
+                        <param argument="--orf_faa_file" type="data" format="fasta" optional="true" multiple="false" label="ORF faa file" help="Amino acid sequence to the ORFs"/>
+                        <param argument="--is_fna_file" type="data" format="fasta" optional="true" multiple="false" label="IS fna file" help="Nuleotide sequence to the inserted elements"/>
+                        <expand macro="analysis_software_version"/>
+                    </when>
+                    <when value="kraken2">
+                        <param name="input" type="data" format="txt,tabular" multiple="false" label="kraken report" help="Taxonomic assignation file from kraken2"/>
+                        <param argument="--seq_classification_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Sequence assignation" help="Reads assignation file"/>
+                        <expand macro="analysis_software_version"/>
+                        <expand macro="reference_database_version"/>
+                    </when>
+                    <when value="plasmidfinder">
+                        <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/>
+                        <param argument="--genome_hit_file_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/>
+                        <param argument="--plasmid_sequence_file_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/>
+                        <expand macro="analysis_software_version"/>
+                        <expand macro="reference_database_version"/>
+                    </when>
+                    <when value="quast">
+                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/>
+                        <expand macro="analysis_software_version"/>
+                    </when>
+                    <when value="recentrifuge">
+                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Recentrifuge data file"/>
+                        <param argument="--rcf_stat_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Recentrifuge stat file"/>
+                        <param argument="--rcf_html_path" type="data" format="html" optional="true" multiple="false" label="Recentrifuge html report file"/>
+                        <expand macro="analysis_software_version"/>
+                        <expand macro="reference_database_version"/>
+                    </when>
+                    <when value="refseqmasher">
+                        <param name="input" type="data" format="txt,tabular" multiple="false" label="RefsesMasher results"/>
+                        <expand macro="analysis_software_version"/>
+                    </when>
+                    <when value="shovill">
+                        <param name="input" type="data" format="fasta" multiple="false" label="Contigs file" help="Contig fasta file from assembly"/>
+                        <param argument="--contig_graph_path" type="data" format="txt" optional="true" multiple="false" label="Contig graph file" help="Graphic file assembly"/>
+                        <param argument="--bam_file_path" type="data" format="bam" optional="true" multiple="false" label="Bam file" help="Alignemnt file in bam format"/>
+                        <expand macro="analysis_software_version"/>
+
+                    </when>
+                    <when value="staramr">
+                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Resfinder report" help="Resfinder result from starAMR"/>
+                        <param argument="--mlst_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="MLST results" help="mlst scheme file result from starAMR"/>
+                        <param argument="--plasmidfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Plasmid results" help="Plasmidfinder result from starAMR"/>
+                        <param argument="--pointfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Pointfinder results" help="PointFinder result from starAMR"/>
+                        <param argument="--setting_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Setting informations" help="Settings file from starAMR"/>
+                        <expand macro="analysis_software_version"/>
+                    </when>
+                    <when value="tabular_file">
+                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Tabular file type" help="Generic result file in tabular format with header"/>
+                        <param argument="--analysis_software_name" type="text" multiple="false" label="Tool name" help="Tool name which generated the result file"/>
+                        <expand macro="analysis_software_version"/>
+                    </when>
+                </conditional>
+            </repeat>
+        </section>
+        <param name="log" type="boolean" truevalue="true"  falsevalue="" label="Add log" help="Activate/Deactivate the log"/>
+    </inputs>
+    <outputs>
+        <collection name="output_json" type="list" label="${tool.name} on ${on_string}: abromics formated json results">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.json" format="json" directory="abromics_extracted_folder" />
+        </collection>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
+            <filter> log == True </filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2"> <!-- TEST_1 abricate with logfile -->
+            <section name="tool_section">
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="abricate"/>
+                        <param name="input" value="abricate/report.tsv" ftype="tabular"/>
+                        <param name="analysis_software_version" value="1.0"/>
+                        <param name="reference_database_version" value="2.0" />
+                    </conditional>
+                </repeat>
+            </section>
+            <param name="log" value="true"/>
+            <output_collection name="output_json" type="list">
+                <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
+            </output_collection>
+            <output name="logfile" value="abricate_logfile.txt"/>
+        </test>
+        <test expect_num_outputs="1"> <!-- TEST_2 bakta all files -->
+            <section name="tool_section">
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="bakta"/>
+                        <param name="input" value="bakta/bakta.json" ftype="json"/>
+                        <param name="summary_result_path" value="bakta/bakta_summary.txt" ftype="txt"/>
+                        <param name="nucleotide_annotation_path" value="bakta/bakta_nucleotide.fasta" ftype="fasta"/>
+                        <param name="amino_acid_annotation_path" value="bakta/bakta_aminoacid.faa" ftype="fasta"/>
+                        <param name="gff_file_path" value="bakta/bakta_annotation.gff3" ftype="gff3"/>
+                        <param name="reference_database_version" value="1.6.1"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <output_collection name="output_json" type="list" count="1">
+                <expand macro="element_assert" name="bakta_0_output" text="UniRef50_A0A0H2ZNL3"/>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="1"> <!-- TEST_3 All tool in repeat -->
+            <section name="tool_section">
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="abricate"/>
+                        <param name="input" value="abricate/report.tsv" ftype="tabular"/>
+                        <param name="analysis_software_version" value="1.0"/>
+                        <param name="reference_database_version" value="2.0" />
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="bakta"/>
+                        <param name="input" value="bakta/bakta.json" ftype="json"/>
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="bandage"/>
+                        <param name="input" value="bandage/bandage_info.txt" ftype="txt"/>
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="bracken"/>
+                        <param name="input" value="bracken/bracken_report.tsv" ftype="tabular"/>
+                        <param name="bracken/bracken_kraken_report" ftype="tabular" />
+                        <param name="threshold" value="0" />
+                        <param name="read_length" value="100"/>
+                        <param name="level" value="S"/>
+                    </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"/>
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="integronfinder2"/>
+                        <param name="input" value="integronfinder2/results.integrons" ftype="tabular"/>
+                        <param name="summary_file_path" value="integronfinder2/results.summary" ftype="tabular"/>
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="isescan"/>
+                        <param name="input" value="isescan/results.tsv" ftype="tabular"/>
+                        <param name="orf_fna_file" value="isescan/orf.fna" ftype="fasta"/>
+                        <param name="orf_faa_file" value="isescan/orf.faa" ftype="fasta"/>
+                        <param name="is_fna_file" value="isescan/is.fna" ftype="fasta"/>
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="kraken2"/>
+                        <param name="input" value="kraken2/taxonomy_report.tsv" ftype="tabular"/>
+                        <param name="seq_classification_file_path" value="kraken2/taxonomy_result.tsv" ftype="tabular"/>
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="plasmidfinder"/>
+                        <param name="input" value="plasmidfinder/plasmidfinder_result.json" ftype="json"/>
+                        <param name="genome_hit_file_path" value="plasmidfinder/genome_hit.fasta" ftype="fasta"/>
+                        <param name="plasmid_sequence_file_path" value="plasmidfinder/plasmid_hit.fasta" ftype="fasta"/>
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="quast"/>
+                        <param name="input" value="quast/quast_result.tsv" ftype="tabular"/>
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="recentrifuge"/>
+                        <param name="input" value="recentrifuge/rcf_data.tsv" ftype="tabular"/>
+                        <param name="rcf_stat_file_path" value="recentrifuge/rcf_stat.tsv" ftype="tabular"/>
+                        <param name="rcf_html_path" value="recentrifuge/rcf_report.html"/>
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="refseqmasher"/>
+                        <param name="input" value="refseqmasher/refsesqmasher.tsv" ftype="tabular"/>
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="shovill"/>
+                        <param name="input" value="shovill/contigs.fa" ftype="fasta"/>
+                        <param name="contig_graph_path" value="shovill/contigs.gfa" ftype="txt"/>
+                        <param name="bam_file_path" value="shovill/alignment.bam" ftype="bam"/>
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="staramr"/>
+                        <param name="input" value="staramr/resfinder.tsv" ftype="tabular"/>
+                        <param name="mlst_file_path" value="staramr/mlst.tsv" ftype="tabular"/>
+                        <param name="plasmidfinder_file_path" value="staramr/plasmidfinder.tsv" ftype="tabular"/>
+                        <param name="pointfinder_file_path" value="staramr/pointfinder.tsv" ftype="tabular"/>
+                        <param name="setting_file_path" value="staramr/settings.txt" ftype="tabular"/>
+                    </conditional>
+                </repeat>
+                <repeat name="tools">
+                    <conditional name="select_tool">
+                        <param name="tool_list" value="tabular_file"/>
+                        <param name="input" value="tabular_file/report.tsv" ftype="tabular"/>
+                    </conditional>
+                </repeat>
+            </section>
+            <output_collection name="output_json" type="list" count="15">
+                <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
+                <expand macro="element_assert" name="bakta_1_output" text="UniRef50_A0A0H2ZNL3"/>
+                <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_ATCC_29212"/>
+                <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"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[**What it does**
+        ** Tool input**
+        abromics_galaxy_json_extractor can use several input type from at least 14 different tools :
+        | Tools          | Version        | Default input file| Optional files                                             |
+        | -:             |   :-:          |  :-               | :-                                                         |
+        | Abricate       | 1.0.1          |  output.tsv       |                                                            |
+        | 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                                               |
+        | Fastp          | 0.23.2         |  output.json      |                                                            |
+        | 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                                      |
+        | 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       |                                                            |
+        | 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     | no optional files                                          |
+
+        ** Options **
+        You can add a tool version and a database version for related tools.
+        For some tools you can add optional files previously produced by the tool
+            ]]></help>
+    <expand macro="citations"/>
+</tool>