Mercurial > repos > johnheap > vapper_galaxy
changeset 8:04b8c470736b draft
Uploaded
| author | johnheap |
|---|---|
| date | Wed, 04 Jul 2018 11:33:47 -0400 |
| parents | 08b35d28e826 |
| children | dce3c5509b96 |
| files | VAP.xml |
| diffstat | 1 files changed, 123 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VAP.xml Wed Jul 04 11:33:47 2018 -0400 @@ -0,0 +1,123 @@ +<tool id="VAPPER" name="VAPPER" version="1.0.0"> + <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> + </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.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 + + </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 = "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> + </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> +