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−<tool id="draw_amr_matrix" name="PIMA: draw AMR matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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−    <description>of genes and drugs</description>
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−    <macros>
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−        <import>macros.xml</import>
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−    </macros>
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−    <expand macro="requirements"/>
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−    <command detect_errors="exit_code"><![CDATA[
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−#import re
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−
+
−mkdir amr_feature_hits_dir &&
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−mkdir mutations_dir &&
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−mkdir output_dir &&
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−
+
−#if $reference_source.reference_source_selector == 'history':
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−    ln -f -s '$reference_source.ref_file' reference.fa &&
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−#else:
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−    ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
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−#end if
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−
+
−#for $i in $amr_feature_hits:
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−    #set file_name = $i.file_name
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−    #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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−    ln -s '$file_name' 'amr_feature_hits_dir/$identifier' &&
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−#end for
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−
+
−python '$__tool_directory__/draw_amr_matrix.py'
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−--amr_feature_hits_dir 'amr_feature_hits_dir'
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−#if str($amr_deletions_file) != 'None':
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−    --amr_deletions_file '$amr_deletions_file'
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−#end if
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−#if str($amr_mutations_file) != 'None':
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−    --amr_mutations_file '$amr_mutations_file'
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−#end if
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−#if str($amr_mutation_regions_file) != 'None':
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−    --amr_mutation_regions_file '$amr_mutation_regions_file'
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−    --region_mutations_output_file '$region_mutations_output_file'
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−#end if
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−--amr_gene_drug_file '$amr_gene_drug_file'
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−--reference_genome reference.fa
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−--mutations_dir 'mutations_dir'
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−--output_dir 'output_dir'
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−#if str($output_process_log) == 'yes':
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−    && mv 'process_log' '$process_log'
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−#end if
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−]]></command>
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−    <inputs>
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−        <conditional name="reference_source">
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−            <param name="reference_source_selector" type="select" label="Select a reference genome from your history or use a cached genome index?">
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−                <option value="cached">Use a cached genome index</option>
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−                <option value="history">Select a genome from the history and build the index</option>
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−            </param>
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−            <when value="cached">
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−                <param name="ref_file" type="select" label="Using reference genome" help="Select reference genome">
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−                    <options from_data_table="all_fasta">
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−                        <filter type="sort_by" column="2"/>
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−                        <validator type="no_options" message="No reference genomes are available"/>
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−                    </options>
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−                </param>
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−            </when>
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−            <when value="history">
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−                <param name="ref_file" type="data" format="fasta,fastq" label="Select the reference sequence" help="You can upload a FASTA file and use it as reference"/>
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−            </when>
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−        </conditional>
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−        <param argument="--amr_feature_hits" format="bed" type="data_collection" collection_type="list" label="Collection of feature hits BED files"/>
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−        <param argument="--amr_deletions_file" type="data" format="bed" optional="true" label="AMR deletions file" help="Optional, leave blank to ignore"/>
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−        <param argument="--amr_mutations_file" type="data" format="tabular,tsv" optional="true" label="AMR mutations file" help="Optional, leave blank to ignore"/>
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−        <param argument="--amr_mutation_regions_file" type="data" format="bed" optional="true" label="AMR mutation regions BED file" help="Optional, leave blank to ignore"/>
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−        <param argument="--amr_gene_drug_file" type="data" format="tabular,tsv" label="AMR gene drugs file"/>
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−        <param name="output_process_log" type="select" display="radio" label="Output process log file?">
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−            <option value="no" selected="true">No</option>
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−            <option value="yes">Yes</option>
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−        </param>
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−    </inputs>
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−    <outputs>
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−        <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
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−            <filter>output_process_log == 'yes'</filter>
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−        </data>
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−        <data name="region_mutations_output_file" format="tsv" label="${tool.name} on ${on_string} (region mutations)">
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−            <filter>amr_mutation_regions_file not in [None, 'None']</filter>
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−        </data>
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−        <collection name="amr_matrix_png" type="list" format="png">
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−            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;png)" directory="output_dir"/>
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−        </collection>
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−    </outputs>
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−    <tests>
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−        <test>
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−            <param name="reference_source_selector" value="history"/>
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−            <param name="ref_file" ftype="fasta" value="ref_genome.fasta"/>
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−            <param name="amr_feature_hits">
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−                <collection type="list">
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−                    <element name="amr_pima_md.bed" value="amr_pima_md.bed"/>
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−                </collection>
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−            </param>
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−            <param name="amr_gene_drug_file" value="amr_gene_drug.tsv" ftype="tsv"/>
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−            <output_collection name="amr_matrix_png" type="list" count="1">
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−                <element name="contig_1" ftype="png">
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−                    <assert_contents>
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−                        <has_size value="25383" delta="100"/>
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−                    </assert_contents>
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−                </element>
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−            </output_collection>
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−        </test>
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−    </tests>
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−    <help>
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−**What it does**
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−
+
−Accepts a collection of best AMR feature hits, an optional AMR deletions BED file, an optional AMR mutations TSV file and a AMR gene
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−drug mappings file and draws an AMR matrix.
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−    </help>
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−    <expand macro="citations"/>
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−</tool>
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−