Mercurial > repos > johnheap > vapper
comparison VAP.xml @ 0:36cb22bd911d draft
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
author | johnheap |
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date | Wed, 04 Jul 2018 16:39:13 -0400 |
parents | |
children | 199e5afe498d |
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-1:000000000000 | 0:36cb22bd911d |
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1 <tool id="VAP" name="VAP" version="0.0.5"> | |
2 <description>is a Variant Antigen Profiler that accurately quantifies the variant antigen diversity or presence in a Trypanosoma congolense or T.vivax isolate</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.2.10">velvet</requirement> | |
5 <requirement type="package" version="3.1b2">HMMER</requirement> | |
6 <requirement type="package" version="2.2.6">bowtie2</requirement> | |
7 <requirement type="package" version="1.6">samtools</requirement> | |
8 <requirement type="package" version="2.2.1">cufflinks</requirement> | |
9 <requirement type="package" version="2.7.1">blast</requirement> | |
10 </requirements> | |
11 | |
12 | |
13 <command interpreter="python" detect_errors="exit_code"> | |
14 #if $TrypType.species == "Trypanosoma congolense": | |
15 #if $TrypType.GT.analysis == "Genomic": | |
16 #if $TrypType.GT.contigs.preassem == "Contig available": | |
17 <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 --> | |
18 Vap.py g_contigs $xname $P $TrypType.GT.contigs.contig $html_file $html_file.extra_files_path | |
19 #else | |
20 <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 --> | |
21 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 | |
22 #end if | |
23 #else | |
24 <!-- name:2, pdfexport:3, strain:4, forward:5, reverse:6, html_file:7, html_resource:8 --> | |
25 Vap.py transcipt $xname $P $TrypType.GT.strain $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path | |
26 #end if | |
27 #else | |
28 #if $TrypType.contigs.preassem == "Contig available": | |
29 <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 --> | |
30 Vap.py v_contigs $xname $P $TrypType.contigs.contig $html_file $html_file.extra_files_path | |
31 #else | |
32 <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 --> | |
33 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 | |
34 #end if | |
35 #end if | |
36 | |
37 </command> | |
38 | |
39 <inputs> | |
40 <param name="xname" size = "30" type="text" value = "Test" label="Prefix Name" /> | |
41 <conditional name = "TrypType"> | |
42 <param name = "species" type = 'select' label="Select Species"> | |
43 <option value = "Trypanosoma congolense" selected="true"></option> | |
44 <option value = "Trypanosoma vivax"></option> | |
45 </param> | |
46 <when value = "Trypanosoma congolense"> | |
47 <conditional name = "GT"> | |
48 <param name="analysis" type = "select" label = "Genomic or Transcriptomic Analysis?"> | |
49 <option value = "Genomic" selected = "true"></option> | |
50 <option value = "Transcriptomic"></option> | |
51 </param> | |
52 <when value = "Genomic"> | |
53 <conditional name = "contigs"> | |
54 <param name = "preassem" type = "select" label = "Contig file available?"> | |
55 <option value = "Full assembly" selected = "true"></option> | |
56 <option value = "Contig available"></option> | |
57 </param> | |
58 <when value = "Full assembly"> | |
59 <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param> | |
60 <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param> | |
61 <param name = "covcut" type="integer" value="5" min="1" max="999" label = "Coverage cut off"></param> | |
62 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> | |
63 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> | |
64 </when> | |
65 <when value = "Contig available"> | |
66 <param name="contig" type="data" format="fasta" label="Contig file"/> | |
67 </when> | |
68 </conditional> | |
69 </when> | |
70 <when value = "Transcriptomic"> | |
71 <param name = "strain" type="select" label = "Select Reference Strain"> | |
72 <option value = "Tc148"></option> | |
73 <option value = "IL3000"></option> | |
74 </param> | |
75 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> | |
76 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> | |
77 </when> | |
78 </conditional> | |
79 </when> | |
80 <when value="Trypanosoma vivax"> | |
81 <conditional name = "contigs"> | |
82 <param name = "preassem" type = "select" label = "Contig file available?"> | |
83 <option value = "Full assembly" selected = "true"></option> | |
84 <option value = "Contig available"></option> | |
85 </param> | |
86 <when value = "Full assembly"> | |
87 <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param> | |
88 <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param> | |
89 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> | |
90 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> | |
91 </when> | |
92 <when value = "Contig available"> | |
93 <param name="contig" type="data" format="fasta" label="Contig file"/> | |
94 </when> | |
95 </conditional> | |
96 </when> | |
97 </conditional> | |
98 | |
99 <param name="P" type="boolean" truevalue='PDF_Yes' falsevalue='PDF_No' label="Export PDF of figures" /> | |
100 </inputs> | |
101 | |
102 <outputs> | |
103 <data format="html" name = "html_file" label = "${xname.value}_html"/> | |
104 </outputs> | |
105 <tests> | |
106 <test> | |
107 <param name = "xname" value = "Test"/> | |
108 <conditional name = "TrypType"> | |
109 <param name = "species" value = "Trypanosoma congolense"/> | |
110 </conditional> | |
111 <conditional name = "GT"> | |
112 <param name = "analysis" value = "Genomic"/> | |
113 </conditional> | |
114 <conditional name = "contigs"> | |
115 <param name = "preassem" value = "Contig available"/> | |
116 <param name="contig" value = "Test.fa"/> | |
117 </conditional> | |
118 <param name = "P" value = 'PDF_No'/> | |
119 <output name = "html_file" file = 'Test_html' ftype = 'html'/> | |
120 </test> | |
121 </tests> | |
122 </tool> | |
123 |