--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srst2.xml	Mon Aug 22 19:12:11 2022 +0000
@@ -0,0 +1,339 @@
+<tool id="srst2" name="SRST2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Short Read Sequence Typing for Bacterial Pathogens</description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@FAST_A_Q_FORMATS@">fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
+    </macros>
+    <expand macro="requirements"/>
+    <version_command>srst2 --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+#if $input.selector == "single"
+#set ext=$input.single_input.datatype.file_ext
+    ln -s $input.single_input './input_read1.$ext' &&
+#else if $input.selector == "paired"
+#set ext_1=$input.paired_input1.datatype.file_ext
+#set ext_2=$input.paired_input2.datatype.file_ext
+    ln -s $input.paired_input1 './input_read1.$ext_1' &&
+    ln -s $input.paired_input2 './input_read2.$ext_2' &&
+#end if
+#for $i, $s in enumerate($prev_output)
+    #if $s
+        ln -s $s './$i-prev_output.txt' &&
+    #end if
+#end for
+#for $i, $s in enumerate($use_gene_db.gene_db)
+    #if $s
+        ln -s $s './$i-gene_db.fasta' &&
+    #end if
+#end for
+#if $use_mlst_db.selector == "yes"
+#set ext_3=$use_mlst_db.mlst_definitions.datatype.file_ext
+    ln -s $use_mlst_db.mlst_db './mlst_db.fasta' &&
+    ln -s $use_mlst_db.mlst_definitions './mlst_definitions.$ext_3' &&
+#end if
+srst2
+#if $input.selector == "single"
+    --input_se './input_read1.$ext'
+    --read_type ${input.read_type}
+#else if $input.selector == "paired"
+    --input_pe './input_read1.$ext_1' './input_read2.$ext_2'
+    $input.merge_paired
+    --forward _read1
+    --reverse _read2
+    --read_type ${input.read_type}
+#end if
+#if $use_mlst_db.selector == "yes"    
+    --mlst_db './mlst_db.fasta'
+    --mlst_definitions './mlst_definitions.$ext_3'
+    --mlst_delimiter '$use_mlst_db.mlst_delimiter'
+    --mlst_max_mismatch $use_mlst_db.mlst_max_mismatch
+    --min_depth $use_mlst_db.min_depth
+    --min_edge_depth $use_mlst_db.min_edge_depth    
+#end if
+#if $use_gene_db.selector == "yes" 
+    --gene_db
+    #for $i, $s in enumerate($use_gene_db.gene_db)
+        #if $s
+            '$i-gene_db.fasta'
+        #end if
+    #end for
+    $use_gene_db.no_gene_details
+    --gene_max_mismatch $use_gene_db.gene_max_mismatch
+    --min_coverage $use_gene_db.min_coverage
+    --max_divergence $use_gene_db.max_divergence
+#end if
+    --prob_err $prob_err
+#if $truncation_score_tolerance     
+    --truncation_score_tolerance $truncation_score_tolerance
+#end if
+#if $stop_after    
+    --stop_after $stop_after
+#end if
+    --max_unaligned_overlap $max_unaligned_overlap
+    --mapq $mapq
+    --baseq $baseq
+    --output 'output'
+#if $prev_output
+    --prev_output 
+    #for $i, $s in enumerate($prev_output)
+        #if $s
+            '$i-prev_output.txt'
+        #end if
+    #end for  
+#end if 
+#if 'log' in str($output_files_selector)
+    --log
+#end if
+#if 'save_scores' in str($output_files_selector)
+    --save_scores
+#end if
+#if 'report_new_consensus' in str($output_files_selector)
+    --report_new_consensus
+#end if
+#if 'report_all_consensus' in str($output_files_selector)
+    --report_all_consensus
+#end if
+#if 'keep_interim_alignment' in str($output_files_selector)
+    --keep_interim_alignment
+#end if
+#if 'report_new_consensus' in str($output_files_selector) and $use_gene_db.selector == "yes" and $use_mlst_db.selector == "yes"
+&& mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput
+#end if
+#if $use_gene_db.selector == "yes" and  $use_gene_db.no_gene_details
+&& mkdir -p geneTypingOutput/ && cp output__genes__*__results.txt geneTypingOutput && cp output__fullgenes__*__results.txt geneTypingOutput
+#end if
+#if 'save_scores' in str($output_files_selector)
+    && mkdir -p scoresOutput/ && cp *.scores scoresOutput
+#end if
+#if $input.selector == "single" or $input.selector == "paired"
+&& mkdir -p bowtie2Alignments/ && cp *.sorted.bam bowtie2Alignments
+&& mkdir -p samtoolsPileup/ && cp output__input.*.pileup samtoolsPileup
+#end if
+    ]]></command>
+    <inputs>
+        <conditional name="input">
+            <param name="selector" type="select" label="Reads files type for anaylsis">
+                <option value="single">Single-end</option>
+                <option value="paired">Paired-end</option>
+                <option value="only_compiling_previous_results">Only Compiling Previous SRST2 Results</option>
+            </param>
+            <when value="single">
+                <param name="single_input" type="data" format="@FAST_A_Q_FORMATS@" label="Single end read file(s) for analysing (may be gzipped)"/>
+                <expand macro="read_type_options" />  
+            </when>
+            <when value="paired">
+                <param name="paired_input1" type="data" format="@FAST_A_Q_FORMATS@" label="Paired end read files for analysing (may be gzipped)"/>
+                <param name="paired_input2" type="data" format="@FAST_A_Q_FORMATS@" label="Paired end read files for analysing (may be gzipped)"/>                
+                <param argument="--merge_paired" type="boolean" truevalue="--merge_paired" falsevalue="" checked="false" label="Do you want to merge the data to get a single result" help="Important only if all the input read sets belong to a single sample"/> 
+                <expand macro="read_type_options" />
+            </when>
+            <when value="only_compiling_previous_results">
+            </when>    
+        </conditional>
+        <conditional name="use_mlst_db">
+            <param name="selector" type="select" label="Do you want to provide an MLST database of all allele sequences for the MLST scheme?">
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param argument="--mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/>
+                <param argument="--mlst_definitions" type="data" format="tabular" label="ST definitions for MLST scheme" help="This is the file that tells you the ST number that is assigned to known combinations of alleles. Column 1 is the ST, and subsequent columns are the loci that make up the scheme."/>
+                <param argument="--mlst_delimiter" type="text" value="-" label="Character(s) separating gene name from allele number in MLST database" help="E.g.'-', as in arcc-1">           
+                    <sanitizer invalid_char="">
+                        <valid initial="string.letters,string.digits">
+                            <add value="\" />
+                            <add value="-" />
+                            <add value="/" />
+                            <add value="+" />
+                            <add value="=" />
+                            <add value=" " />
+                            <add value="_" />    
+                        </valid>
+                    </sanitizer>
+                    <validator type="regex">[A-Za-z0-9 =-_/+]+</validator>
+                </param>
+                <param argument="--mlst_max_mismatch" type="integer" value="10" label="Maximum number of mismatches per read for MLST allele calling"/>
+                <param argument="--min_depth" type="integer" value="5" label="Minimum mean depth to flag as dubious allele call"/>
+                <param argument="--min_edge_depth" type="integer" value="2" label="Minimum edge depth to flag as dubious allele call"/>            
+            </when>
+            <when value="no">
+            </when>
+        </conditional>
+        <conditional name="use_gene_db">
+            <param name="selector" type="select" label="Do you want to use a Gene database(s)?">
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param argument="--gene_db" type="data" optional="true" multiple="true" format="fasta" label="Gene database(s)" help="Fasta file/s for gene databases"/>
+                <param argument="--no_gene_details" type="boolean" truevalue="" falsevalue="--no_gene_details" checked="false" label="Do you want reporting of gene typing?"/>
+                <param argument="--gene_max_mismatch" type="integer" value="10" label="Maximum number of mismatches per read for gene detection and allele calling"/>
+                <param argument="--min_coverage" type="integer" value="90" label="Minimum %coverage cutoff for gene reporting"/>
+                <param argument="--max_divergence" type="integer" value="10" label="Maximum %divergence cutoff for gene reporting"/>            
+            </when>
+            <when value="no">
+            </when>
+        </conditional>
+        <param name="output_files_selector" type="select" label="Select all outputs you need" multiple="true">
+            <option value="log">Save the log</option>
+            <option value="save_scores">Report scores</option>
+            <option value="report_new_consensus">Report the consensus allele if a matching alleles is not found</option>
+            <option value="report_all_consensus">Report the consensus allele for the most likely allele</option>
+            <option value="keep_interim_alignment">Keep interim files (sam and unsorted bam)</option>
+        </param>
+        <param argument="--prob_err" type="float" min="0" max="1" value="0.01" label="Probability of sequencing error"/>
+        <param argument="--truncation_score_tolerance" optional="true" type="float" label="% increase in score allowed to choose non-truncated allele"/>
+        <param argument="--stop_after" type="integer" optional="true" label="Stop mapping after this number of reads have been mapped" help="Leave empty to map all"/>       
+        <param argument="--max_unaligned_overlap" type="integer" value="10" label="Read discarded from alignment" help="if either of its ends has unaligned overlap with the reference that is longer than this value"/>
+        <param argument="--mapq" type="integer" value="1" label="Samtools -q parameter (Minimum mapping quality)"/>
+        <param argument="--baseq" type="integer" value="20" label="Samtools -Q parameter (Minimum base quality)"/>
+        <param argument="--prev_output" type="data" format="tabular" multiple="true" optional="true" label="SRST2 results files to compile" help="Any new results from this run will also be incorporated"/>
+    </inputs>
+    <outputs> 
+        <data name="mlst_results" format="tabular" from_work_dir="output__mlst__mlst_db__results.txt" label="${tool.name} on ${on_string}: MLST Results">
+            <filter>use_mlst_db['selector'] == "yes"</filter>
+        </data>  
+        <collection name="gene_typing" type="list" label="${tool.name} on ${on_string}: Gene typing results files" >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutput" format="txt,tabular"/>
+            <filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter>
+        </collection>         
+        <data name="Compiled_gene_and_mlst_output" format="tabular" from_work_dir="output__compiledResults.txt" label="${tool.name} on ${on_string}: Compiled MLST and Gene databases Results">
+        </data>
+        <data name="all_consensus" format="fasta" from_work_dir="output.all_consensus_alleles.fasta" label="${tool.name} on ${on_string}: All consensus Results">
+            <filter>"report_all_consensus" in output_files_selector</filter>
+        </data>              
+        <collection name="new_consensus" type="list" label="${tool.name} on ${on_string}: New consensus Results" >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="allelesOutput" format="pileup"/>
+            <filter>"report_new_consensus" in output_files_selector</filter>
+        </collection>
+        <collection name="scores_ofEachAllele" type="list" label="${tool.name} on ${on_string}: Scores for each allele in the database(s)" >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="scoresOutput" format="tabular"/>
+            <filter>"save_scores" in output_files_selector</filter>
+        </collection>
+        <collection name="bowtie2_alignment_output" type="list" label="${tool.name} on ${on_string}: Bowtie2 alignment of reads to each input database" >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="bowtie2Alignments" format="bam"/>
+            <filter>input['selector'] == "single" or input['selector'] == "paired"</filter>        
+        </collection>
+        <collection name="samtools_pileup_alignment" type="list" label="${tool.name} on ${on_string}: Samtools pileup of the alignment to each input database" >
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="samtoolsPileup" format="pileup"/>
+            <filter>input['selector'] == "single" or input['selector'] == "paired"</filter>        
+        </collection>               
+        <data name="log_output" format="tabular" from_work_dir="output.log" label="${tool.name} on ${on_string}: Log file">
+            <filter>"log" in output_files_selector</filter>
+        </data>             
+    </outputs>
+    <tests>
+    <test expect_num_outputs="9">
+        <param name="prob_err" value="0.01"/>
+        <param name="max_unaligned_overlap" value="10"/>
+        <param name="mapq" value="1"/>
+        <param name="baseq" value="20"/>
+        <param name="output_files_selector" value="log,save_scores,report_new_consensus,report_all_consensus"/>
+        <conditional name="input">
+            <param name="selector" value="paired"/>
+            <param name="paired_input1" value="ERR024070_1_reduced_forward_reads.fastqsanger.gz"/>
+            <param name="paired_input2" value="ERR024070_2_reduced_reverse_reads.fastqsanger.gz"/>
+            <param name="merge_paired" value="false"/>
+            <param name="read_type" value="q"/>
+        </conditional>
+        <conditional name="use_mlst_db">
+            <param name="selector" value="yes"/>
+            <param name="mlst_db" value="Escherichia_coli1R.fasta"/>
+            <param name="mlst_definitions" value="profiles_csv"/>
+            <param name="mlst_delimiter" value="_"/>
+            <param name="mlst_max_mismatch" value="10"/>
+            <param name="min_depth" value="5"/>
+            <param name="min_edge_depth" value="2"/>
+        </conditional>
+        <conditional name="use_gene_db">
+            <param name="selector" value="yes"/>
+            <param name="gene_db" value="ARGannotR.fasta"/>
+            <param name="no_gene_details" value="true"/>
+            <param name="gene_max_mismatch" value="10"/>
+            <param name="min_coverage" value="90"/>
+            <param name="max_divergence" value="10"/>
+        </conditional>
+        <output name="mlst_results">
+            <assert_contents>
+                <has_text text="fumC"/>
+                <has_n_lines n="2"/>
+            </assert_contents>
+        </output>
+        <output_collection name="gene_typing" type="list">
+            <element name="output__fullgenes__0-gene_db__results.txt">
+                <assert_contents>
+                    <has_text text="AmpC1_Ecoli_Bla"/>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </element>
+            <element name="output__genes__0-gene_db__results.txt">
+                <assert_contents>
+                    <has_text text="AmpC1_Ecoli_Bla"/>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </element>
+        </output_collection>
+        <output name="Compiled_gene_and_mlst_output">
+            <assert_contents>
+                <has_text text="fumC"/>
+                <has_n_lines n="2"/>
+            </assert_contents>
+        </output>
+        <output name="all_consensus">
+            <assert_contents>
+                <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
+                <has_n_lines n="2"/>
+            </assert_contents>
+        </output>
+        <output_collection name="new_consensus" type="list">
+            <element name="49__AmpC1_Ecoli_Bla__AmpC1__1670.output__input.0-gene_db.pileup">
+                <assert_contents>
+                    <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
+                    <has_n_lines n="1196"/>
+                </assert_contents>
+            </element>
+        </output_collection>
+        <output_collection name="samtools_pileup_alignment" type="list">
+            <element name="output__input.0-gene_db.pileup">
+                <assert_contents>
+                    <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
+                    <has_n_lines n="1196"/>
+                </assert_contents>
+            </element>
+        </output_collection>
+        <output_collection name="bowtie2_alignment_output" type="list">
+            <element name="output__input.0-gene_db.sorted.bam">
+                <assert_contents>
+                    <has_size value="18500" delta="1000"/>
+                </assert_contents>
+            </element>
+        </output_collection>
+        <output name="log_output">
+            <assert_contents>
+                <has_text text="Building"/>
+                <has_n_lines n="52"/>
+            </assert_contents>
+        </output>
+    </test>
+    </tests>
+    <help><![CDATA[
+SRST2
+=====
+Short Read Sequence Typing for Bacterial Pathogens
+
+This program is designed to take Illumina sequence data, a MLST (Multi Locus Sequence Types) database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs (Serotypes) and/or reference genes
+
+Read more about the tool: https://holtlab.net/2014/12/27/behind-the-paper-srst2-for-short-read-sequence-typing-of-bacterial-pathogens/
+
+Input
+=====
+Learn more about all inputs and their formates: https://github.com/katholt/srst2#input-read-formats-and-options
+
+Output
+======
+Learn more about all outputs: https://github.com/katholt/srst2#output-files
+    ]]></help> 
+    <citations>
+        <citation type="doi">10.1186/s13073-014-0090-6</citation>
+    </citations>
+ </tool>
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