# HG changeset patch
# User iuc
# Date 1737542090 0
# Node ID 6fdee3720de7fc36f9447cc0f9993da51bbe560f

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ppanggolin commit f51871dfce652ad0bbb9d4967d02338d03b9e2a3

diff -r 000000000000 -r 6fdee3720de7 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Jan 22 10:34:50 2025 +0000
@@ -0,0 +1,19 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.2.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1371/journal.pcbi.1007732</citation> 
+        </citations>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">ppanggolin</requirement>
+        </requirements>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">ppanggolin</xref>
+        </xrefs>
+    </xml>
+</macros>
diff -r 000000000000 -r 6fdee3720de7 ppanggolin_all.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ppanggolin_all.xml	Wed Jan 22 10:34:50 2025 +0000
@@ -0,0 +1,324 @@
+<tool id="ppanggolin_all" name="PPanGGOLiN all" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
+    <description>generates a partitioned pangenome</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+
+    <command detect_errors="exit_code"><![CDATA[
+        
+        mkdir -p "./tmp_ppanggolin/all" &&
+        mkdir -p "./tmp_ppanggolin/organism_list" &&
+        mkdir -p "./tmp_ppanggolin/ln_input_genomes" &&
+        
+        touch "./tmp_ppanggolin/organism_list/organism.list" &&
+        
+        #set extension_input_files = ""
+        #for $counter_input_files, $file in enumerate($genomes):
+            #if $counter_input_files == 0:
+            	#set extension_input_files = $file.ext
+            #else:
+                #if $file.ext != $extension_input_files:
+                    #raise Exception("All the genome files must be of the same datatype, either all genbank files or all fasta files.")
+            	#end if
+            #end if
+            
+            #set base_name = str($file.element_identifier).replace(" ", "_")
+            echo -e '${base_name}\t${file}' >> "./tmp_ppanggolin/organism_list/organism.list" &&
+            
+        #end for
+
+        ppanggolin all
+
+        #if $extension_input_files == "fasta":
+            --fasta
+        #elif $extension_input_files == "genbank":
+            --anno
+        #end if
+        "./tmp_ppanggolin/organism_list/organism.list"
+        
+        -o ./tmp_ppanggolin/all
+        --force
+        --cpu "\${GALAXY_SLOTS:-4}"
+        
+        --coverage $coverage
+        --identity $identity
+        --translation_table $translation_table
+        
+        
+        #if str($nb_of_partitions) != "":
+            --nb_of_partitions $nb_of_partitions
+        #end if
+        
+        $do_defrag
+        
+
+        #if "output_functional_modules" in $advanced_pangenome_optional_files:
+		&& cat ./tmp_ppanggolin/all/functional_modules.tsv > '${functional_modules}'
+        #end if
+        #if "output_modules_RGP_lists" in $advanced_pangenome_optional_files:
+		&& cat ./tmp_ppanggolin/all/modules_RGP_lists.tsv > '${modules_RGP_lists}'
+        #end if
+        #if "output_modules_spots" in $advanced_pangenome_optional_files:
+		&& cat ./tmp_ppanggolin/all/modules_spots.tsv > '${modules_spots}'
+        #end if
+        #if "output_modules_in_genomes" in $advanced_pangenome_optional_files:
+		&& cat ./tmp_ppanggolin/all/modules_in_genomes.tsv > '${modules_in_genomes}'
+        #end if
+        #if "output_modules_summary" in $advanced_pangenome_optional_files:
+		&& cat ./tmp_ppanggolin/all/modules_summary.tsv > '${modules_summary}'
+        #end if
+        #if "output_spot_borders" in $advanced_pangenome_optional_files:
+		&& cat ./tmp_ppanggolin/all/spot_borders.tsv > '${spot_borders}'
+        #end if
+        #if "output_spots" in $advanced_pangenome_optional_files:
+		&& cat ./tmp_ppanggolin/all/spots.tsv > '${spots}'
+        #end if
+        #if "output_summarize_spots" in $advanced_pangenome_optional_files:
+		&& cat ./tmp_ppanggolin/all/summarize_spots.tsv > '${summarize_spots}'
+        #end if
+        #if "output_border_protein_genes" in $advanced_pangenome_optional_files:
+		&& cat ./tmp_ppanggolin/all/border_protein_genes.fasta > '${border_protein_genes}'
+        #end if
+        
+        #if "output_tile_plot" in $advanced_pangenome_optional_files:
+        	&& cat ./tmp_ppanggolin/all/tile_plot.html > '${tile_plot}'
+        #end if
+        #if "output_ushaped_plot" in $advanced_pangenome_optional_files:
+        	&& cat ./tmp_ppanggolin/all/Ushaped_plot.html > '${Ushaped_plot}'
+        #end if
+        
+        #if "output_pangenomeGraph_json" in $advanced_pangenome_optional_files:
+            && cat ./tmp_ppanggolin/all/pangenomeGraph.json > '${pangenomeGraph_json}'
+        #end if
+        #if "output_pangenomeGraph_gexf" in $advanced_pangenome_optional_files:
+            && cat ./tmp_ppanggolin/all/pangenomeGraph.gexf > '${pangenomeGraph_gexf}'
+        #end if
+        #if "output_pangenomeGraph_light_gexf" in $advanced_pangenome_optional_files:
+            && cat ./tmp_ppanggolin/all/pangenomeGraph_light.gexf > '${pangenomeGraph_light_gexf}'
+        #end if
+        
+        #if "output_matrix" in $advanced_pangenome_optional_files:
+		&& cat ./tmp_ppanggolin/all/matrix.csv > '${matrix}'
+        #end if
+        #if "output_mean_persistent_duplication" in $advanced_pangenome_optional_files:
+		&& cat ./tmp_ppanggolin/all/mean_persistent_duplication.tsv > '${mean_persistent_duplication}'
+        #end if
+        #if "output_gene_families" in $advanced_pangenome_optional_files:
+		&& cat ./tmp_ppanggolin/all/gene_families.tsv > '${gene_families}'
+        #end if
+        #if "output_gene_presence_absence" in $advanced_pangenome_optional_files:
+		&& cat ./tmp_ppanggolin/all/gene_presence_absence.Rtab > '${gene_presence_absence}'
+        #end if
+        
+        
+        && cat ./tmp_ppanggolin/all/regions_of_genomic_plasticity.tsv > '${regions_of_genomic_plasticity}'
+        && cat ./tmp_ppanggolin/all/pangenome.h5 > '${pangenome_h5}'
+        && cat ./tmp_ppanggolin/all/genomes_statistics.tsv > '${genomes_statistics}'
+        
+        
+    ]]></command>
+
+    <inputs>
+    
+        <param name="genomes" type="data" multiple="true"  min="2" label="Select genome files" format="fasta,genbank" help="All the genome files must be of similar format, either all genbank files or all fasta files. Processing of at least 15 genomes files is recommended, a minimum of 2 genomes files is mandatory. Space is not allowed in filename.">
+        </param>
+        
+        <param argument="--identity" type="float" value="0.8" min="0" max="1" label="Minimum alignment identity"/>
+        <param argument="--coverage" type="float" value="0.8" min="0" max="1" label="Minimum alignment coverage"/>
+        
+        <param argument="--nb_of_partitions" type="integer" max="20" label="Number of classes used to partition the pangenome" optional="true" help="If empty value (default), it will be automatically determined. Otherwise, the value needs to be between 2 and 20 and it is advised to set a value of 3. See the link for the documentation in the help section for more details.">
+            <validator type="expression" message="Value needs to be empty or an integer between 2 and 20">value == "" or int(value) >= 2</validator>
+        </param>
+         
+        <param argument="--translation_table" type="select" label="Translation table">
+            <option value="1">1 - Standard Code</option>
+            <option value="2">2 - Vertebrate Mitochondrial</option>
+            <option value="3">3 - Yeast Mitochondrial</option>
+            <option value="4">4 - Mold, Protozoan, and Coelenterate Mitochondrial</option>
+            <option value="5">5 - Invertebrate Mitochondrial</option>
+            <option value="6">6 - Ciliate Nuclear</option>
+            <option value="9">9 - Echinoderm Mitochondrial</option>
+            <option value="10">10 - Euplotid Nuclear</option>
+            <option value="11">11 - Bacterial and Plant Plastid</option>
+            <option value="12">12 - Alternative Yeast Nuclear</option>
+            <option value="13">13 - Ascidian Mitochondrial</option>
+            <option value="14">14 - Flatworm Mitochondrial</option>
+            <option value="15">15 - Blepharisma Nuclear</option>
+            <option value="16">16 - Chlorophycean Mitochondrial</option>
+            <option value="21">21 - Trematode Mitochondrial</option>
+            <option value="22">22 - Scenedesmus obliquus Mitochondrial</option>
+            <option value="23">23 - Thraustochytrium Mitochondrial</option>
+            <option value="24">24 - Pterobranchia Mitochondrial</option>
+            <option value="25">25 - Candidate Division SR1 and Gracilibacteria</option>
+            <option value="26">26 - Pachysolen tannophilus Nuclear</option>
+            <option value="27">27 - Karyorelict Nuclear</option>
+            <option value="28">28 - Condylostoma Nuclear</option>
+            <option value="29">29 - Mesodinium Nuclear</option>
+            <option value="30">30 - Peritrich Nuclear</option>
+            <option value="31">31 - Blastocrithidia Nuclear</option>
+            <option value="32">32 - Balanophoraceae Plastid</option>
+            <option value="33">33 - Cephalodiscidae Mitochondrial</option>
+        </param>
+        <param name="do_defrag" type="boolean" checked="true" label="Gene family defragmentation" truevalue="" falsevalue="--no_defrag"/>
+        
+
+        <param name="advanced_pangenome_optional_files" type="select" label="Add the following pangenome output files in the Galaxy history" multiple="true" optional="true" display="checkboxes" >
+        	<!-- Basic files -->
+            <option value="output_gene_presence_absence" selected="true">Gene presence absence</option>
+            <option value="output_gene_families" selected="true">Gene families</option>
+            <option value="output_mean_persistent_duplication" selected="true">Mean persistent duplication</option>
+            <option value="output_matrix" selected="true">Matrix</option>
+        	<!-- plot files -->
+            <option value="output_Ushaped_plot" selected="true">Ushaped plot</option>
+            <option value="output_tile_plot" selected="true">Tile plot</option>
+        	<!-- graph files -->
+            <option value="output_pangenomeGraph_light_gexf" selected="true">PanGenome Graph Light (Gexf)</option>
+            <option value="output_pangenomeGraph_gexf" selected="true">PanGenome Graph (Gexf)</option>
+            <option value="output_pangenomeGraph_json" selected="true">PanGenome Graph (Json)</option>
+        	<!-- advanced files -->
+            <option value="output_summarize_spots" selected="true">Summarize spots</option>
+            <option value="output_spots" selected="true">Spots</option>
+            <option value="output_spot_borders" selected="true">Spot borders</option>
+            <option value="output_border_protein_genes" selected="true">Border protein genes</option>
+            <option value="output_modules_summary" selected="true">Modules summary</option>
+            <option value="output_modules_in_genomes" selected="true">Modules in genomes</option>
+            <option value="output_modules_spots" selected="true">Modules spots</option>
+            <option value="output_modules_RGP_lists" selected="true">Modules RGP lists</option>
+            <option value="output_functional_modules" selected="true">Functional modules</option>
+        </param>
+
+    </inputs>
+
+    <outputs>
+    
+        <data name="functional_modules" format="tsv" label="PPanGGOLiN all on ${on_string}: Functional modules" >
+          <filter>advanced_pangenome_optional_files and "output_functional_modules" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="modules_RGP_lists" format="tsv" label="PPanGGOLiN all on ${on_string}: Modules RGP lists" >
+          <filter>advanced_pangenome_optional_files and "output_modules_RGP_lists" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="modules_spots" format="tsv" label="PPanGGOLiN all on ${on_string}: Modules spots" >
+          <filter>advanced_pangenome_optional_files and "output_modules_spots" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="modules_in_genomes" format="tsv" label="PPanGGOLiN all on ${on_string}: Modules in genomes" >
+          <filter>advanced_pangenome_optional_files and "output_modules_in_genomes" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="modules_summary" format="tsv" label="PPanGGOLiN all on ${on_string}: Modules summary" >
+          <filter>advanced_pangenome_optional_files and "output_modules_summary" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="border_protein_genes" format="fasta" label="PPanGGOLiN all on ${on_string}: Border protein genes" >
+          <filter>advanced_pangenome_optional_files and "output_border_protein_genes" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="spot_borders" format="tsv" label="PPanGGOLiN all on ${on_string}: Spot borders" >
+          <filter>advanced_pangenome_optional_files and "output_spot_borders" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="spots" format="tsv" label="PPanGGOLiN all on ${on_string}: Spots" >
+          <filter>advanced_pangenome_optional_files and "output_spots" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="summarize_spots" format="tsv" label="PPanGGOLiN all on ${on_string}: Summarized spots" >
+          <filter>advanced_pangenome_optional_files and "output_summarize_spots" in advanced_pangenome_optional_files</filter>
+        </data>
+        
+        <data name="pangenomeGraph_json" format="json" label="PPanGGOLiN all on ${on_string}: PanGenome Graph (JSON)" >
+          <filter>advanced_pangenome_optional_files and "output_pangenomeGraph_json" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="pangenomeGraph_gexf" format="xml" label="PPanGGOLiN all on ${on_string}: PanGenome Graph (GEXF)" >
+          <filter>advanced_pangenome_optional_files and "output_pangenomeGraph_gexf" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="pangenomeGraph_light_gexf" format="xml" label="PPanGGOLiN all on ${on_string}: PanGenome Graph Light (GEXF)" >
+          <filter>advanced_pangenome_optional_files and "output_pangenomeGraph_light_gexf" in advanced_pangenome_optional_files</filter>
+        </data>
+
+        
+        <data name="tile_plot" format="html" label="PPanGGOLiN all on ${on_string}: Tile plot" >
+          <filter>advanced_pangenome_optional_files and "output_tile_plot" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="Ushaped_plot" format="html" label="PPanGGOLiN all on ${on_string}: U-shaped plot" >
+          <filter>advanced_pangenome_optional_files and "output_Ushaped_plot" in advanced_pangenome_optional_files</filter>
+        </data>
+        
+        <data name="matrix" format="csv" label="PPanGGOLiN all on ${on_string}: Matrix" >
+          <filter>advanced_pangenome_optional_files and "output_matrix" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="mean_persistent_duplication" format="tsv" label="PPanGGOLiN all on ${on_string}: Mean persistent duplication" >
+          <filter>advanced_pangenome_optional_files and "output_mean_persistent_duplication" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="gene_families" format="tsv" label="PPanGGOLiN all on ${on_string}: Gene families" >
+          <filter>advanced_pangenome_optional_files and "output_gene_families" in advanced_pangenome_optional_files</filter>
+        </data>
+        <data name="gene_presence_absence" format="tsv" label="PPanGGOLiN all on ${on_string}: Gene presence/absence matrix" >
+          <filter>advanced_pangenome_optional_files and "output_gene_presence_absence" in advanced_pangenome_optional_files</filter>
+        </data>
+        
+        
+        <data name="regions_of_genomic_plasticity" format="tsv" label="PPanGGOLiN all on ${on_string}: Regions of genomic plasticity" />
+        <data name="pangenome_h5" format="h5" label="PPanGGOLiN all on ${on_string}: PanGenome HDF5 file" />
+        <data name="genomes_statistics" format="tsv" label="PPanGGOLiN all on ${on_string}: Genome statistics" />
+        
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="21">
+            <param name="nb_of_partitions" value="3"/>
+            <param name="coverage" value="0.8"/>
+            <param name="identity" value="0.8"/>
+            <param name="translation_table" value="1"/>
+            <param name="genomes" value="fasta/AP028611_984801_1194801.fasta.gz,fasta/CP107038_1022972_1232972.fasta.gz,fasta/CP113115_1290693_1440693.fasta.gz,fasta/LN831051_1254175_1464175.fasta.gz,fasta/NC_012467_959209_1169209.fasta.gz" ftype="fasta"/>
+            <output name="genomes_statistics" >
+                <assert_contents>
+                    <has_text text="#soft_core=" />
+                    <has_text text="#duplication_margin=" />
+                </assert_contents>
+            </output>
+            <output name="regions_of_genomic_plasticity" >
+                <assert_contents>
+                    <has_text text="region" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="21">
+            <param name="nb_of_partitions" value="3"/>
+            <param name="coverage" value="0.8"/>
+            <param name="identity" value="0.8"/>
+            <param name="translation_table" value="1"/>
+            <param name="genomes" value="genbank/AP028611_984801_1194801.gb.gz,genbank/CP107038_1022972_1232972.gb.gz,genbank/CP113115_1290693_1440693.gb.gz,genbank/LN831051_1254175_1464175.gb.gz,genbank/NC_012467_959209_1169209.gb.gz" ftype="genbank"/>
+            <output name="genomes_statistics" >
+                <assert_contents>
+                    <has_text text="#soft_core=" />
+                    <has_text text="#duplication_margin=" />
+                </assert_contents>
+            </output>
+            <output name="regions_of_genomic_plasticity" >
+                <assert_contents>
+                    <has_text text="region" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_failure="true">
+            <param name="nb_of_partitions" value="3"/>
+            <param name="coverage" value="0.8"/>
+            <param name="identity" value="0.8"/>
+            <param name="translation_table" value="1"/>
+            <param name="genomes" value="genbank/AP028611_984801_1194801.gb.gz,genbank/CP107038_1022972_1232972.gb.gz,genbank/CP113115_1290693_1440693.gb.gz,fasta/AP028611_984801_1194801.fasta.gz,fasta/CP107038_1022972_1232972.fasta.gz,fasta/CP113115_1290693_1440693.fasta.gz" ftype="genbank"/>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+    
+        PPanGGOLiN_ (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either assembled 
+        genomic DNA sequences or provided genome annotations. PPanGGOLiN builds pangenomes through a graphical model and a statistical method to partition gene 
+        families in persistent, shell and cloud genomes. It integrates both information on protein-coding genes and their genomic neighborhood to build a graph 
+        of gene families where each node is a gene family, and each edge is a relation of genetic contiguity. 
+
+	The `ppanggolin all` command generates a partitioned pangenome graph with predicted RGP, spots and modules. Please see the documentation_ on how parameters can be tuned for this command.
+
+        .. _PPanGGOLiN: https://github.com/labgem/PPanGGOLiN
+        .. _documentation: https://ppanggolin.readthedocs.io/en/latest/user/QuickUsage/quickAnalyses.html
+        
+    ]]></help>
+
+    <expand macro="citation"/>
+    
+</tool>
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