--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tb_profiler_profile.xml	Tue Oct 21 10:24:35 2025 +0000
@@ -0,0 +1,298 @@
+<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09" license="AGPL-3.0-or-later">
+    <description>Infer strain types and drug resistance markers from sequences</description>
+  
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <xrefs>
+        <xref type="bio.tools">tb-profiler</xref>
+    </xrefs>
+
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
+    </requirements>
+
+    <expand macro="version_command"/>
+    
+    <command detect_errors="exit_code"><![CDATA[
+        #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
+            #if str($fastq_or_bam.input_select.value) == "paired_fastq"
+                #set r1_ext = $fastq_or_bam.read1.extension
+                #set r2_ext = $fastq_or_bam.read2.extension
+                ln -s '$fastq_or_bam.read1' fastq_r1.'$r1_ext' &&
+                ln -s '$fastq_or_bam.read2' fastq_r2.'$r2_ext' &&
+            #else if str($fastq_or_bam.input_select.value) == "single_fastq"
+                #set r1_ext = $fastq_or_bam.fastq.extension
+                ln -s '$fastq_or_bam.fastq' fastq_r1.'$r1_ext' &&
+            #else if str($fastq_or_bam.input_select.value) == "paired_collection_fastq"
+                #set r1_ext = $fastq_or_bam.fastq_collection.forward.extension
+                #set r2_ext = $fastq_or_bam.fastq_collection.reverse.extension
+                ln -s '$fastq_or_bam.fastq_collection.forward' fastq_r1.'$r1_ext' &&
+                ln -s '$fastq_or_bam.fastq_collection.reverse' fastq_r2.'$r2_ext' &&
+            #end if
+        #else if str($fastq_or_bam.input_select.value) == "bam"
+            ln -s '$fastq_or_bam.bam_input' input.bam &&
+        #end if
+
+        tb-profiler profile
+            --platform '${platform.value}'
+            ${spoligotype}
+        #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
+            -1 fastq_r1.'$r1_ext'
+        #end if
+        #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq")
+            -2 fastq_r2.'$r1_ext'
+        #else if str($fastq_or_bam.input_select.value) == "bam"
+            --bam input.bam
+        #end if
+
+            --threads "\${GALAXY_SLOTS:-1}"
+        #if $advanced.options == 'yes'
+            --mapper '${advanced.mapper}'
+            --caller '${advanced.caller}'
+            --depth '${advanced.vf.min_depth_hard},${advanced.vf.min_depth_soft}'
+            --af '${advanced.vf.min_af_hard},${advanced.vf.min_af_soft}'
+            --strand '${advanced.vf.min_read_hard},${advanced.vf.min_read_soft}'
+            --sv-depth '${advanced.vf.min_sv_depth_hard},${advanced.vf.min_sv_depth_soft}'
+            --sv-af '${advanced.vf.min_sv_af_hard},${advanced.vf.min_sv_af_soft}'
+            --sv-len '${advanced.vf.max_sv_len_hard},${advanced.vf.max_sv_len_soft}'
+            ${advanced.suspect}
+            ${advanced.no_trim}
+            ${advanced.no_coverage_qc}
+            ${advanced.no_samclip}
+            ${advanced.no_delly}
+        #end if
+
+        #if $output_format == "pdf"
+            --pdf
+        #else if $output_format == "txt"
+            --txt
+        #end if
+        && mv results/tbprofiler.results.json $results_json
+        #if str($fastq_or_bam.input_select) != "bam"
+            && mv bam/tbprofiler.bam '${output_bam}'
+        #end if
+        && bcftools view -Ov -o '${output_vcf}' vcf/tbprofiler.targets.vcf.gz
+        #if $output_format == "pdf"
+            && mv results/tbprofiler.results.pdf '${output_pdf}'
+        #else if $output_format == "txt"
+            && mv results/tbprofiler.results.txt '${output_txt}'
+        #end if 
+
+    ]]>    </command>
+    <inputs>
+        <param name="platform" type="select" label="Platform">
+            <option value="illumina" selected="true">Illumina</option>
+            <option value="nanopore">Nanopore</option>
+            <option value="pacbio">PacBio</option>
+        </param>
+        <conditional name="fastq_or_bam">
+            <param name="input_select" type="select" label="Input File Type">
+                <option value="paired_fastq">Paired Fastq</option>
+                <option value="paired_collection_fastq">Paired Collection Fastq</option>
+                <option value="single_fastq">Single Fastq</option>
+                <option value="bam">BAM</option>
+            </param>
+            <when value="paired_fastq">
+                <param name="read1" type="data" format="fastq" label="Read1" help="First read file (default: None)"/>
+                <param name="read2" type="data" format="fastq" optional="true" label="Read2" help="Second read file (default: None)"/>
+            </when>
+            <when value="paired_collection_fastq">
+                <param label="Reads (collection)" name="fastq_collection" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
+            </when>
+            <when value="single_fastq">
+                <param label="Reads" name="fastq" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
+            </when>
+            <when value="bam">
+                <param name="bam_input" type="data" format="bam" label="Bam" help="Warning!!!: The BAM files must have been created using the ensembl version of the genome."/>
+            </when>
+        </conditional>
+        <param argument="--spoligotype" type="boolean" label="Perform in-silico spoligotyping" checked="false" truevalue="--spoligotype" falsevalue="" 
+            help="Uses spacers of CRISPR region to call a spoligotype."/>
+        <param name="output_format" label="Output format" type="select">
+            <option value="txt" selected="true">Text</option>
+            <option value="pdf">PDF</option>
+        </param>
+        <conditional name="advanced">
+            <param label="Select advanced options" type="select" name="options">
+                <option value="yes">Yes</option>
+                <option value="no" selected="true">No</option>
+            </param>
+            <when value="no">
+            </when>
+            <when value="yes">
+                <param argument="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
+                    <option value="bwa" selected="true">bwa</option>
+                    <option value="minimap2">minimap2</option>
+                    <option value="bowtie2">bowtie2</option>
+                    <option value="bwa-mem2">bwa-mem2</option>
+                </param>
+                <param argument="caller" label="Variant caller" help="Variant calling tool to use" type="select">
+                    <option value="freebayes" selected="true">freebayes</option>
+                    <option value="bcftools">bcftools</option>
+                    <option value="gatk">gatk</option>
+                    <option value="pilon">pilon</option>
+                    <option value="lofreq">lofreq</option>
+                </param>
+                <section name="vf" title="Variant Filters">
+                    <param name="min_depth_hard" argument="--depth" label="Min Depth (hard cutoff)" type="integer" value="0" min="0"
+                        help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 0)"/>
+                    <param name="min_depth_soft" argument="--depth" label="Min Depth (soft cutoff)" type="integer" value="10" min="0"
+                        help="Minimum depth required to call variant. Variants at positions lower than this depth and above the hard cutoff will be marked as QC fail (default: 10)"/>
+                    <param name="min_af_hard" argument="--af" type="float" value="0" label="Minimum allele frequency to call variants (hard cutoff)" min="0.0" max="1.0" 
+                        help="Minimum allele frequency to call variants (default: 0)" />
+                    <param name="min_af_soft" argument="--af" type="float" value="0.1" label="Minimum allele frequency to call variants (soft cutoff)" min="0.0" max="1.0"
+                        help="Variants with an allele frequency lower than this (and higher than the hard cutoff) will be marked as QC fail (default 0.1)" />
+                    <param name="min_read_hard" argument="--strand" type="integer" value="0" label="Mininum read number per strand (hard cutoff)" min="0"
+                        help="Minimum read number per strand to call variants (default: 0)" />
+                    <param name="min_read_soft" argument="--strand" type="integer" value="3" label="Mininum read number per strand (soft cutoff)" min="0"
+                        help="Minimum read number per strand to report variants (default: 3). Variants with number of reads on each strand below this (and above the hard cutoff) will be marked as QC fail" />
+                    <param name="min_sv_depth_hard" argument="--sv-depth" type="integer" value="0" label="Min Depth for SV (hard cutoff)" min="0"
+                        help="Minimum depth required to call structural variants (default: 0)" />
+                    <param name="min_sv_depth_soft" argument="--sv-depth" type="integer" value="10" label="Min Depth for SV (soft cutoff)" min="0"
+                        help="Minimum depth required to call structural variants. Variants at positions lower than this depth and above the hard cutoff will be marked as QC fail" />
+                    <param name="min_sv_af_hard" argument="--sv-af" type="float" value="0.5" label="Min SV allele frequency (hard cutoff)" min="0.0" max="1.0"
+                        help="Minimum allele frequency to call structural variants (default: 0.5)" />
+                    <param name="min_sv_af_soft" argument="--sv-af" type="float" value="0.9" label="Min SV allele frequency (soft cutoff)" min="0.0" max="1.0"
+                        help="Variants with an allele frequency lower than this (and higher than the hard cutoff) will be marked as QC fail (default 0.9)" />
+                    <param name="max_sv_len_hard" argument="--sv-len" type="integer" value="100000" label="Max SV length (hard cutoff)" min="0"
+                        help="Maximum length (length) of structural variants to call (default: 100000)" />
+                    <param name="max_sv_len_soft" argument="--sv-len" type="integer" value="50000" label="Max SV length (soft cutoff)" min="0"
+                        help="Structural variants with length higher than this (and lower than the hard cutoff) will be marked as QC fail (default: 50000)" />
+                </section>
+                <param argument="--suspect" label="Use ML predictions of resistance from the SUSPECT tool suite" type="boolean" checked="False" truevalue="--suspect" falsevalue="" 
+                    help="The SUSPECT tools offer ML-based predictions of RIF, PZA and BDQ resistance. Note that this uses a web service thus requires an Internet connection."/>
+                <param argument="--no_trim" label="Do not trim reads using trimmomatic" checked="false" type="boolean" truevalue="--no_trim" falsevalue="" />
+                <param argument="--no_coverage_qc" label="Don't collect flagstats" type="boolean" truevalue="--no_coverage_qc" falsevalue="" />
+                <param argument="--no_samclip" label="Don't removed clipped reads from variant calling" type="boolean" truevalue="--no_samclip" falsevalue="" />
+                <param argument="--no_delly" label="Don't run delly for SV calling" type="boolean" truevalue="--no_delly" falsevalue="" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>
+        <data format="vcf" name="output_vcf" label="${tool.name} VCF on ${on_string}" />
+        <data format="bam" name="output_bam" label="${tool.name} BAM on ${on_string}">
+            <filter>fastq_or_bam['input_select'] != 'bam'</filter>
+        </data>
+        <data format="pdf" name="output_pdf" label="${tool.name} PDF report on ${on_string}">
+            <filter>output_format == 'pdf'</filter>
+        </data>
+        <data format="txt" name="output_txt" label="${tool.name} report on ${on_string}">
+            <filter>output_format == 'txt'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="4">
+            <conditional name="fastq_or_bam">
+                <param name="input_select" value="single_fastq"/>
+                <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
+            </conditional>
+            <param name="output_format" value="txt" />
+            <param name="platform" value="illumina" />
+            <conditional name="advanced">
+                <param name="options" value="no" />
+            </conditional>
+            <output name="output_txt">
+                <assert_contents>
+                    <has_line line="Drug-resistance: RR-TB" />
+                    <has_line line="lineage2.2.2&#009;100.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
+                    <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
+                    <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;43&#009;1.000&#009;rifampicin&#009;Assoc w R" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="3">
+            <conditional name="fastq_or_bam">   
+                <param name="input_select" value="bam"/>
+                <param name="bam_input" ftype="bam" value="rif_resistant.bam" />
+            </conditional>
+            <param name="output_format" value="txt" />
+            <param name="platform" value="illumina" />
+            <conditional name="advanced">
+                <param name="options" value="no" />
+            </conditional>
+            <output name="output_txt">
+                <assert_contents>
+                    <has_line line="Drug-resistance: RR-TB" />
+                    <has_line line="lineage2.2.2&#009;100.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
+                    <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
+                    <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;43&#009;1.000&#009;rifampicin&#009;Assoc w R" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="4">
+            <conditional name="fastq_or_bam">
+                <param name="input_select" value="single_fastq"/>
+                <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
+            </conditional>
+            <param name="output_format" value="txt" />
+            <param name="platform" value="illumina" />
+            <conditional name="advanced">
+                <param name="options" value="yes" />
+                <section name="vf">
+                    <param name="min_depth_hard" value="40" />
+                    <param name="min_depth_soft" value="50" />
+                </section>
+            </conditional>
+            <output name="output_txt">
+                <assert_contents>
+                    <has_line line="lineage2.2.2&#009;100.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
+                    <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;43&#009;1.000&#009;rifampicin&#009;Assoc w R" />
+                </assert_contents>
+            </output>
+            <output name="results_json">
+                <assert_contents>
+                    <has_text text='"filter": "soft_fail",' />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="4">
+            <conditional name="fastq_or_bam">
+                <param name="input_select" value="single_fastq"/>
+                <param name="fastq" ftype="fastq.gz" value="rpoB_and_crispr.fastq.gz" />
+            </conditional>            
+            <param name="output_format" value="txt" />
+            <param name="platform" value="illumina" />
+            <param name="spoligotype" value="true" />
+            <conditional name="advanced">
+                <param name="options" value="no" />
+            </conditional>
+            <output name="output_txt">
+                <assert_contents>
+                    <has_line line="Octal: 000000000000771" />
+                    <has_line line="Drug-resistance: RR-TB" />
+                    <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
+                    <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;35&#009;1.000&#009;rifampicin&#009;Assoc w R" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[    
+Summary
+=======
+
+The pipeline aligns reads to the H37Rv reference using BWA, bowtie2 or minimap2 and then calls variants 
+(using bcftools, GATK4 or freebayes). These variants are then compared to a drug-resistance database. 
+TB-Profiler also predicts the number of reads supporting drug resistance variants as an insight into
+hetero-resistance (not applicable for MinION data).
+
+Produces a JSON output file by default.
+
+In the Advanced options, you can select the mapper and variant caller to use, as well as set a number of filtering parameters.
+Each of these typically has a "hard" and a "soft" cutoff. If a variant value is below the "hard" cutoff it is discarded, if
+it is between the "hard" and "soft" values it is removed from the final predictions but added to the "qc_fail_variants" section
+of the output.
+
+One of the advanced options is to use the SUSPECT tool suite to predict resistance to `rifampicin (RIF)`_, `pyrazinamide (PZA)`_
+and `bedaquiline (BDQ)`_.
+
+.. _rifampicin (RIF): https://www.nature.com/articles/s41598-020-74648-y
+.. _pyrazinamide (PZA): https://www.nature.com/articles/s41598-020-58635-x
+.. _bedaquiline (BDQ): https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0217169
+    ]]>    </help>
+    <citations>
+        <citation type="doi">10.1186/s13073-019-0650-x</citation>
+    </citations>
+</tool>