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+ | + | <tool id="VAP" name="VAPPER" version="1.1.0"> | +
| + | <description>is a Variant Antigen Profiler that accurately quantifies the variant antigen diversity or presence in a Trypanosoma congolense or T.vivax isolate</description> | +
| + | <requirements> | +
| + | <requirement type="package" version="1.2.10">velvet</requirement> | +
| + | <requirement type="package" version="3.1b2">HMMER</requirement> | +
| + | <requirement type="package" version="2.2.6">bowtie2</requirement> | +
| + | <requirement type="package" version="1.6">samtools</requirement> | +
| + | <requirement type="package" version="2.2.1">cufflinks</requirement> | +
| + | <requirement type="package" version="2.7.1">blast</requirement> | +
| + | <requirement type="package" version="6.6.0.0">EMBOSS</requirement> | +
| + | <requirement type="package" version="0.8.0">seaborn</requirement> | +
| + | </requirements> | +
| + | + | +
| + | + | +
| + | <command interpreter="python" detect_errors="exit_code"> | +
| + | #if $TrypType.species == "Trypanosoma congolense": | +
| + | #if $TrypType.GT.analysis == "Genomic": | +
| + | #if $TrypType.GT.contigs.preassem == "Contig available": | +
| + | <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 --> | +
| + | Vap.py g_contigs $xname $P $TrypType.GT.contigs.contig $html_file $html_file.extra_files_path | +
| + | #else | +
| + | <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 --> | +
| + | Vap.py g_assemble $xname $P $TrypType.GT.contigs.kmers $TrypType.GT.contigs.inslen $TrypType.GT.contigs.covcut $TrypType.GT.contigs.forward $TrypType.GT.contigs.reverse $html_file $html_file.extra_files_path | +
| + | #end if | +
| + | #else | +
| + | <!-- name:2, pdfexport:3, strain:4, forward:5, reverse:6, html_file:7, html_resource:8 --> | +
| + | Vap.py transcipt $xname $P $TrypType.GT.strain $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path | +
| + | #end if | +
| + | #else | +
| + | #if $TrypType.GT.analysis == "Transcriptomic": | +
| + | Vap.py v_transcript $xname $P $TrypType.GT.vtreference $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path | +
| + | #else | +
| + | #if $TrypType.contigs.preassem == "Contig available": | +
| + | <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 --> | +
| + | Vap.py v_contigs $xname $P $TrypType.contigs.contig $html_file $html_file.extra_files_path | +
| + | #else | +
| + | <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 --> | +
| + | Vap.py v_assemble $xname $P $TrypType.contigs.kmers $TrypType.contigs.inslen 0 $TrypType.contigs.forward $TrypType.contigs.reverse $html_file $html_file.extra_files_path | +
| + | #end if | +
| + | #end if | +
| + | #end if | +
| + | + | +
| + | </command> | +
| + | + | +
| + | <inputs> | +
| + | <param name="xname" size = "30" type="text" value = "Test" label="Prefix Name" /> | +
| + | <conditional name = "TrypType"> | +
| + | <param name = "species" type = 'select' label="Select Species"> | +
| + | <option value = "Trypanosoma congolense" selected="true"></option> | +
| + | <option value = "Trypanosoma vivax"></option> | +
| + | </param> | +
| + | <when value = "Trypanosoma congolense"> | +
| + | <conditional name = "GT"> | +
| + | <param name="analysis" type = "select" label = "Genomic or Transcriptomic Analysis?"> | +
| + | <option value = "Genomic" selected = "true"></option> | +
| + | <option value = "Transcriptomic"></option> | +
| + | </param> | +
| + | <when value = "Genomic"> | +
| + | <conditional name = "contigs"> | +
| + | <param name = "preassem" type = "select" label = "Contig file available?"> | +
| + | <option value = "Full assembly" selected = "true"></option> | +
| + | <option value = "Contig available"></option> | +
| + | </param> | +
| + | <when value = "Full assembly"> | +
| + | <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param> | +
| + | <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param> | +
| + | <param name = "covcut" type="integer" value="5" min="1" max="999" label = "Coverage cut off"></param> | +
| + | <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> | +
| + | <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> | +
| + | </when> | +
| + | <when value = "Contig available"> | +
| + | <param name="contig" type="data" format="fasta" label="Contig file"/> | +
| + | </when> | +
| + | </conditional> | +
| + | </when> | +
| + | <when value = "Transcriptomic"> | +
| + | <param name = "strain" type="select" label = "Select Reference Strain"> | +
| + | <option value = "Tc148"></option> | +
| + | <option value = "IL3000"></option> | +
| + | </param> | +
| + | <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> | +
| + | <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> | +
| + | </when> | +
| + | </conditional> | +
| + | </when> | +
| + | <when value="Trypanosoma vivax"> | +
| + | <conditional name = "GT"> | +
| + | <param name="analysis" type = "select" label = "Genomic or Transcriptomic Analysis?"> | +
| + | <option value = "Genomic" selected = "true"></option> | +
| + | <option value = "Transcriptomic"></option> | +
| + | </param> | +
| + | <when value = "Genomic"> | +
| + | <conditional name = "contigs"> | +
| + | <param name = "preassem" type = "select" label = "Contig file available?"> | +
| + | <option value = "Full assembly" selected = "true"></option> | +
| + | <option value = "Contig available"></option> | +
| + | </param> | +
| + | <when value = "Full assembly"> | +
| + | <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param> | +
| + | <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param> | +
| + | <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> | +
| + | <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> | +
| + | </when> | +
| + | <when value = "Contig available"> | +
| + | <param name="contig" type="data" format="fasta" label="Contig file"/> | +
| + | </when> | +
| + | </conditional> | +
| + | </when> | +
| + | <when value = "Transcriptomic"> | +
| + | <param name = "vtreference" type="data" format="fasta" label = "Reference File"/> | +
| + | <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> | +
| + | <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> | +
| + | </when> | +
| + | </conditional> | +
| + | </when> | +
| + | </conditional> | +
| + | + | +
| + | <param name="P" type="boolean" truevalue='PDF_Yes' falsevalue='PDF_No' label="Export PDF of figures" /> | +
| + | </inputs> | +
| + | + | +
| + | <outputs> | +
| + | <data format="html" name = "html_file" label = "${xname.value}_html"/> | +
| + | </outputs> | +
| + | <tests> | +
| + | <test> | +
| + | <param name = "xname" value = "Test"/> | +
| + | <conditional name = "TrypType"> | +
| + | <param name = "species" value = "Trypanosoma congolense"/> | +
| + | </conditional> | +
| + | <conditional name = "GT"> | +
| + | <param name = "analysis" value = "Genomic"/> | +
| + | </conditional> | +
| + | <conditional name = "contigs"> | +
| + | <param name = "preassem" value = "Contig available"/> | +
| + | <param name="contig" value = "Test.fa"/> | +
| + | </conditional> | +
| + | <param name = "P" value = 'PDF_No'/> | +
| + | <output name = "html_file" file = 'Test_html' ftype = 'html'/> | +
| + | </test> | +
| + | </tests> | +
| + | </tool> | +
| + | + | +