--- a/tb_profiler_profile.xml	Tue Apr 02 09:03:16 2019 -0400
+++ b/tb_profiler_profile.xml	Thu Apr 04 13:52:45 2019 -0400
@@ -4,82 +4,164 @@
         <requirement type="package" version="2.1.0">tb-profiler</requirement>
     </requirements>
     <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}'
 
-            #if $fastq_or_bam.input_select.value == "fastq":
-                --read1 '${read1}'
-
-                #if $read2:
-                    --read2 '${read2}'
-                #end if
+        #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
 
-            #else if $fastq_or_bam.input_select.value == "bam":
-                --bam '${bam_input}'
-            #end if 
+            --threads "\${GALAXY_SLOTS:-1}"
+        #if $advanced.options == 'yes'
+            --call_method '${advanced.call_method}'
+            --min_gene_frac '${advanced.min_gene_frac}'
+            --mapper '${advanced.mapper}'
+            --min_depth '${advanced.min_depth}'
+        #end if
 
-            --call_method '${call_method}'
-            --min_depth '${min_depth}'
-            --threads "\${GALAXY_SLOTS:-1}"
-            --mapper '${mapper}'
-            --min_gene_frac '${min_gene_frac}'
-
-            #if $txt:
-                --txt
-            #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.csq.bcf
+        #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="minION">minION</option>
+            <option value="minION">MinION</option>
         </param>
         <conditional name="fastq_or_bam">
             <param name="input_select" type="select" label="Input File Type">
-                <option value="fastq">fastq</option>
-                <option value="bam">bam</option>
+                <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="fastq">
+            <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>
+            <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 name="call_method" type="select" label="Call Method" help="Level of quality stringency required. (default: low)">
-            <option value="low" selected="true">low</option>
-            <option value="high">high</option>
-            <option value="optimise">optimise</option>
+        <param name="output_format" label="Output format" type="select">
+            <option value="txt">Text</option>
+            <option value="pdf">PDF</option>
         </param>
-        <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
-        <param name="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>
-        </param>
-        <param name="min_gene_frac" label="Minimum Gene Fraction" type="float" value="0.9" help="Used to infer a deletion if the fraction of a gene covered falls below this value. Also used to see if sample is high quality to continue by checking the fraction for rpoB (where deletion should not occur). (default: 0.9)"/>
-        <param name="txt" label="Generate text file ouput" type="boolean" value="false" help="Create reader-friendly text output in addition to standard JSON output (default: False)"/>
+        <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 label="Quality required for calls to be accepted" type="select" argument="--call_method">
+                    <option value="low" selected="true">Low</option>
+                    <option value="high">High</option>
+                    <option value="optimise">Optimise</option>
+                </param>
+                <param label="Minimum coverage fraction to infer deletion" type="float"
+                        help="Used to infer a deletion if the fraction of a gene covered falls below this value."
+                        argument="--min_gene_frac" value="0.9" />
+
+                <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
+                <param name="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>
+                </param>
+                <param name="min_gene_frac" label="Minimum Gene Fraction" type="float" value="0.9" help="Used to infer a deletion if the fraction of a gene covered falls below this value. Also used to see if sample is high quality to continue by checking the fraction for rpoB (where deletion should not occur). (default: 0.9)" />
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>
-        <data name="results_txt" format="txt" from_work_dir="results/tbprofiler.results.txt" label="${tool.name} on ${on_string}: Results.txt">
-            <filter>txt</filter>
+        <data format="vcf" name="output_vcf" label="${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="1">
-            <param name="read1" value="rif_resistant.fastq.gz"/>
-            <output name="results_json" value="results_1.json"/>
+        <test>
+            <param name="input_select" value="single_fastq"/>
+            <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
+            <param name="output_format" value="txt" />
+            <param name="platform" value="Illumina" />
+            <param name="options" value="no" />
+            <output name="output_txt">
+                <assert_contents>
+                    <has_line line="Drug-resistance: Drug-resistant" />
+		    <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
+                    <has_line line="rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
+                    <has_line line="763031&#009;Rv0667&#009;c.3225T>C&#009;1.000" />
+                </assert_contents>
+            </output>
         </test>
-        <test expect_num_outputs="2">
-            <param name="read1" value="rif_resistant.fastq.gz"/>
-            <param name="txt" value="true"/>
-            <param name="call_method" value="high"/>
-            <param name="min_depth" value="11"/>
-            <output name="results_json" value="results_2.json"/>
-            <output name="results_txt" value="results_2.txt"/>
+        <test>
+            <param name="input_select" value="bam"/>
+            <param name="bam_input" ftype="bam" value="rif_resistant.bam" />
+            <param name="output_format" value="txt" />
+            <param name="platform" value="Illumina" />
+            <param name="options" value="no" />
+            <output name="output_txt">
+                <assert_contents>
+                    <has_line line="Drug-resistance: Drug-resistant" />
+		    <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
+                    <has_line line="rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
+                    <has_line line="763031&#009;Rv0667&#009;c.3225T>C&#009;1.000" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[