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planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 3be367228b531c346c10700f07d57ae44394be36-dirty

<tool id="panaroo" name="Panaroo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>A Bacterial Pangenome Analysis Pipeline</description>
    <macros>
          <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <stdio>
        <exit_code range="1:" />
        <regex match="System..*Exception"
           source="both"
           level="fatal"
           description="Error encountered" />
    </stdio>
    <command><![CDATA[

         mkdir outdir &&
	    
	 #import re
	 #set input_directory = 'input_directory'
	 mkdir $input_directory &&
	 #for $gff in $gff_input_collection:
	    #set identifier = re.sub('[^\s\w\-\\.]','_',str($gff.element_identifier))
	    ln -fs '$gff' '$input_directory/$identifier' &&
	 #end for

	 panaroo 
	 -t \${GALAXY_SLOTS:-2}
         #if str($gen_code) != 'None':
           --codon-table $gen_code
	 #end if
         #if str($advanced.adv_options_selector) == "set":
	     #if $advanced.remove_invalid_gene
		 $advanced.remove_invalid_gene
	     #end if
	     -c '$advanced.matching_option.seq_threshold'
	     -f '$advanced.matching_option.peptide_threshold'
	     --len_dif_percent '$advanced.matching_option.length_diff_cutoff'
	     $advanced.matching_option.merge_paralogs
	     --search_radius '$advanced.refind_option.search_radius'
	     --refind_prop_match '$advanced.refind_option.refind_prop_match'
	     --refind-mode '$advanced.refind_option.refind_mode'
	     --min_trailing_support '$advanced.graph_correction_option.min_trailing_support'
	     --trailing_recursive '$advanced.graph_correction_option.trailing_recursive'
	     --edge_support_threshold '$advanced.graph_correction_option.edge_support_threshold'
	     --remove_by_consensus '$advanced.graph_correction_option.remove_by_consensus'
	     --high_var_flag '$advanced.graph_correction_option.high_var_flag'
	     --min_edge_support_sv '$advanced.graph_correction_option.min_edge_support_sv'
	     $advanced.graph_correction_option.all_seq_in_graph
	     $advanced.graph_correction_option.no_clean_edges
	
	     #if $advanced.gene_alignment_option.a != 'None'
		-a '$advanced.gene_alignment_option.a'
	     #end if

	     #if '$advanced.gene_alignment_option.aligner' == 'mafft'
                --aligner mafft
	     #else
               --aligner '$advanced.gene_alignment_option.aligner'
	     #end if
	     #if $advanced.gene_alignment_option.core_subset != ''
		--core_subset $advanced.gene_alignment_option.core_subset
	     #end if
         #end if
	 -i $input_directory/*.gff 
	 -o outdir 
	 --clean-mode $mode 
	 > '$log' &&
	 mv outdir/gene_presence_absence.Rtab outdir/gene_presence_absence_rtab.Rtab &&
	 2>&1  

    ]]></command>
    <inputs>
	<param name="gff_input_collection" type="data_collection" format="gff" collection_type="list" label="GFF Input Collection" help="A list of gff files (i.e prokka)"/>
	<param name="mode" type="select" label="The stringency mode at which to run panaroo" help="--clean-mode">
            <expand macro="clean_mode"/>
    	</param>
	<param name="gen_code" type="select" label="the codon table user for translation" help="default: 11">
            <expand macro="genetic_code"/>
    	</param>
        <conditional name="advanced">
            <param name="adv_options_selector" type="select" label="Set advanced options?" help="Provides additional controls">
                <option value="set">Set</option>
                <option value="do_not_set" selected="True">Do not set</option>
            </param>
	    <when value="set">
		 <param name="remove_invalid_gene" argument="--remove-invalid-genes" type="boolean" truevalue="--remove-invalid-genes" falsevalue=""  label="removes annotations that do not conform to the expected Prokka format such as those including premature stop codons" help="--remove-invalid-genes"/>

                 <section name="matching_option" title="Matching" expanded="false">
                   <param name="seq_threshold" argument="--threshold" type="float" value="0.98" label="sequence identity threshold" help="default: 0.98"/>
                   <param name="peptide_threshold" argument="--family_threshold" type="float" value="0.7" label="protein family sequence identity threshold" help="default: 0.7"/>
                   <param name="length_diff_cutoff" argument="--len_dif_percent" type="float" value="0.98" label="length difference cutoff" help="default: 0.98"/>
                   <param name="merge_paralogs" type="boolean" truevalue="--merge_paralogs" falsevalue="" checked="false" label="do not split paralogs" help="--merge_paralogs"/>
	   	 </section>

                 <section name="refind_option" title="Refind" expanded="false">
                   <param argument="--search_radius" type="integer" value="5000" label="Search radius" help="--search_radius (default: 5000)"/>
                   <param argument="--refind_prop_match" type="float" value="0.75" label="Gene proportion match" help="default: 0.75"/>
		   <param argument="--refind_mode" type="select" label="The stringency mode at which to re-find genes" help="default: default">
			  <expand macro="refind_mode_option"/>
	   	   </param>
                 </section>

                 <section name="graph_correction_option" title="Graph Correction" expanded="false">
                   <param argument="--min_trailing_support" type="integer" value="2" label="Minimum cluster size to keep a gene called at the end of a contig" help="--min_traiiing_support [relexed mode : 2 is used]"/>
                   <param argument="--trailing_recursive" type="integer" value="1" label="Number of times to perform recursive trimming of low support nodes near the end of contigs" help="--trailing_recursive [relaxed mode: 1 is used]"/>
                   <param name="edge_support_threshold" type="integer" value="1" label="Edge support threshold" help="--edge_support_threshold [ Minimal edge 1 is used ]"/>
		   <param name="len_outlier_proportion" type="float" value="0.01" label="Length outlier support proportion" help="--length_outlier_support_proportion [default: 0.01]"/>
		   <param name="remove_by_consensus" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Remove consensus" help="--remove_by_consensus [default: False]"/>
		   <param name="high_var_flag" type="integer" value="5" label="Highly variable gene region" help="--high_var_flag [default: 5]"/>
		   <param name="min_edge_support_sv" type="integer" value="2" label="Minimum edge support structural variants" help="--min_edge_support_sv [relaxed mode: 2 is used]"/>
		   <param argument="--all_seq_in_graph" type="boolean" truevalue="--all_seq_in_graph" falsevalue="" label="Retains all DNA sequence" help="--all_seq_in_graph [default: off]"/>
		   <param argument="--no_clean_edges" type="boolean" truevalue="--no_clean_edges" falsevalue="" label="Edge filtering in the final output graph" help="--no_clean_edges [default: off]"/>
	   	</section>
	
		<section name="gene_alignment_option" title="Gene Alignment" expanded="false">
		    <param argument="-a" type="select" label="Output alignments of core genes or all genes." help="-a [optional: core or pan; default: None">
                        <expand macro="gene_alignment"/>
                   </param>
		   <param argument="--aligner" type="select" label="Specify an aligner" help="--aligner [mafft|prank|clustal][default: mafft]">
			<expand macro="gene_aligner"/>
		   </param>
		   <param name="codons" type="boolean" truevalue="true" falsevalue="false"  checked="false" label="Generate codon alignments" help="--codons"/>
		   <param name="core_threshold" type="float" value="0.95" label="Core-genome sample threshold" help="--core_threshold [default: 0.95]"/>
		   <param argument="--core_subset" type="integer" value=""  optional="true" label="Subset of the core genome to these many genes" help="--core_subset [default: all]"/>
		   <param name="core_entropy" type="float" value="0.1" label="Set the Block Mapping and Gathering with Entropy" help="--core_entropy_filter (threshold can be between 0.0 and 1.0) [default: Tukey outlier method]"/>
		</section>
	    </when>
            <when value="do_not_set"/>
        </conditional>
    </inputs>
    <outputs>
        <collection name="output" type="list" label="${tool.name} on ${on_string}: Pangenome output">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;clstr)" directory="outdir" format="txt" visible="false" />
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;txt)" directory="outdir" format="txt" visible="false" />
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;gml)" directory="outdir" format="txt" visible="false" />
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;Rtab)" directory="outdir" format="tabular" visible="false" />
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;csv)" directory="outdir" format="csv" visible="false" />
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fasta)" directory="outdir" format="fasta" visible="false" />
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fa)" directory="outdir" format="fasta" visible="false" />
             <filter>advanced['adv_options_selector'] != 'set'</filter>
       </collection>
	<collection name="output_advance" type="list" label="${tool.name} on ${on_string}: Pangenome output (advance)">
	     <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;clstr)" directory="outdir" format="txt" visible="false" />
	     <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;txt)" directory="outdir" format="txt" visible="false" />
	     <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;gml)" directory="outdir" format="txt" visible="false" />
	     <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;Rtab)" directory="outdir" format="tabular" visible="false" />
	     <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;csv)" directory="outdir" format="csv" visible="false" />
	     <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fasta)" directory="outdir" format="fasta" visible="false" />
	     <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fa)" directory="outdir" format="fasta" visible="false" />
	     <filter>advanced['adv_options_selector'] == 'set' and advanced['gene_alignment_option']['a'] == 'None'</filter>
       </collection>
        <collection name="output_pangenome" type="list" label="${tool.name} on ${on_string}: Pangenome alignment output">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;clstr)" directory="outdir" format="txt" visible="false" />
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;txt)" directory="outdir" format="txt" visible="false" />
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;gml)" directory="outdir" format="txt" visible="false" />
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;Rtab)" directory="outdir" format="tabular" visible="false" />
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;csv)" directory="outdir" format="csv" visible="false" />
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fasta)" directory="outdir" format="fasta" visible="false" />
	     <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fa)" directory="outdir" format="fasta" visible="false" />
	     <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;aln)" directory="outdir" format="aln" visible="false" />
	     <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;embl)" directory="outdir" format="embl" visible="false" />
             <filter>advanced['adv_options_selector'] == 'set' and advanced['gene_alignment_option']['a'] != 'None' </filter>
       </collection>
       <collection name="output_pangenome_fasta" type="list" label="${tool.name} on ${on_string}: Pangenom alignment fasta">
	     <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fas)" directory="outdir/aligned_gene_sequences" format="fasta" visible="false" />  
             <filter>advanced['adv_options_selector'] == 'set' and advanced['gene_alignment_option']['a'] != 'None'</filter>
       </collection>
       <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/>
    </outputs>
    <tests>
	  <!-- run panaroo with default parameters (i.e panaroo -t 2 -i *.gff -o default \-\-clean-mode strict \-\-remove-invalid-genes) -->
         <test expect_num_outputs="2">
            <param name="gen_code" value="11"/>
            <param name="mode" value="strict"/>
            <param name="adv_options_selector" value="do_not_set"/>
            <param name="gff_input_collection">
                <collection type="list">
                    <element name="gff10.gff" value="10_small.gff"/>
                    <element name="gff11.gff" value="11_small.gff"/>
                </collection>
            </param>
            <output_collection name="output" count="13"/>
            <output name="log">
                 <assert_contents>
                      <has_text text="pre-processing gff3 files..."/>
                 </assert_contents>
            </output>
        </test>
	 <test expect_num_outputs="2">
	    <param name="gen_code" value="11"/>
	    <param name="mode" value="strict"/>
	    <param name="adv_options_selector" value="set"/>
	    <param name="a" value="None"/>
	    <param name="gff_input_collection">
		<collection type="list">
		    <element name="gff10.gff" value="10_small.gff"/>
		    <element name="gff11.gff" value="11_small.gff"/>
		</collection>
	    </param>
	    <output_collection name="output_advance" count="13"/>
	    <output name="log">
		 <assert_contents>
		      <has_text text="pre-processing gff3 files..."/>
		 </assert_contents>
            </output>
    	</test>
	<test expect_num_outputs="3">
	   <param name="gen_code" value="11"/>
	   <param name="mode" value="strict"/>
	   <param name="adv_options_selector" value="set"/>
	   <param name="a" value="core"/>
	   <param name="gff_input_collection">
		<collection type="list">
		    <element name="gff10.gff" value="10_small.gff"/>
		    <element name="gff11.gff" value="11_small.gff"/>
	        </collection>
           </param>
	   <output_collection name="output_pangenome" count="18"/>
	   <output_collection name="output_pangenome_fasta" count="251"/>
	   <output name="log">
		  <assert_contents>
		       <has_text text="pre-processing gff3 files..."/>
		 </assert_contents>
	   </output>
	</test>
    </tests>
    <help><![CDATA[
Panaroo_ is A Bacterial Pangenome Analysis Pipeline.

**INPUTS**
Panaroo now supports multiple input formats. To use non-standard GFF3 files you must profile the input file as a list in a text file (one per line). Separate GFF and FASTA files can be provided per isolate by providing each file delimited by a space or a tab. Genbank file formats are also supported with extensions '.gbk', '.gb' or '.gbff'. These must compliant with Genbank/ENA/DDJB. This can be forced in Prokka by specifying the --compliance parameter.

  - a list of gff format in a collection

**OUTPUTS**

  - combined_protein_cdhit_out.txt
  - combined_protein_cdhit_out.txt.clstr
  - pre_filt_graph.gml
  - gene_data.csv
  - combined_protein_CDS.fasta
  - combined_DNA_CDS.fasta
  - gene_presence_absence_rtab.Rtab
  - gene_presence_absence_roary.csv
  - gene_presence_absence.csv
  - summary_statistics.txt
  - pan_genome_reference.fa
  - struct_presence_absence.Rtab
  - final_graph.gml

**OUTPUTS with Advance parameters**

  - combined_protein_cdhit_out.txt
  - combined_protein_cdhit_out.txt.clstr
  - pre_filt_graph.gml
  - gene_data.csv
  - combined_protein_CDS.fasta
  - combined_DNA_CDS.fasta
  - gene_presence_absence_rtab.Rtab
  - gene_presence_absence_roary.csv
  - gene_presence_absence.csv
  - summary_statistics.txt
  - pan_genome_reference.fa
  - struct_presence_absence.Rtab
  - final_graph.gml
  - core_gene_alignment
  - core_gene_alignment_filtered
  - core_alignment_filtered_header
  - core_alignment_header
  - a collection of fasta files

.. _Panaroo: https://gthlab.au/panaroo/#/gettingstarted/quickstart

    ]]></help>
    <citations>
        <citation type="doi">10.1186/s13059-020-02090-4</citation>
    </citations>
</tool>