# HG changeset patch # User johnheap # Date 1559591770 14400 # Node ID 7d1f86b4718d2ab2eb32d5189ce8f34380a1021c # Parent 8c210b4ad003438e28facf8ba2432c230c59f432 Uploaded diff -r 8c210b4ad003 -r 7d1f86b4718d VAP.xml --- a/VAP.xml Mon Jun 03 14:29:04 2019 -0400 +++ b/VAP.xml Mon Jun 03 15:56:10 2019 -0400 @@ -1,1412 +1,142 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - VAPPER-Galaxy/VAP.xml at master · johnheap/VAPPER-Galaxy · GitHub - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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+ + is a Variant Antigen Profiler that accurately quantifies the variant antigen diversity or presence in a Trypanosoma congolense or T.vivax isolate + + velvet + HMMER + bowtie2 + samtools + cufflinks + blast + EMBOSS + seaborn + -
+ + #if $TrypType.species == "Trypanosoma congolense": + #if $TrypType.GT.analysis == "Genomic": + #if $TrypType.GT.contigs.preassem == "Contig available": + + Vap.py g_contigs $xname $P $TrypType.GT.contigs.contig $html_file $html_file.extra_files_path + #else + + 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 + + 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": + + Vap.py v_contigs $xname $P $TrypType.contigs.contig $html_file $html_file.extra_files_path + #else + + 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 - - -
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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>
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<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
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</command>
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<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>
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<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>
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