Mercurial > repos > johnheap > vapper
annotate VAP.xml @ 1:199e5afe498d draft
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
author | johnheap |
---|---|
date | Wed, 04 Jul 2018 16:56:54 -0400 |
parents | 36cb22bd911d |
children | 4432e4183ebd |
rev | line source |
---|---|
1
199e5afe498d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
0
diff
changeset
|
1 <tool id="VAPPER" name="VAPPER" version="1.0.0"> |
0
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
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> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
3 <requirements> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
4 <requirement type="package" version="1.2.10">velvet</requirement> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
5 <requirement type="package" version="3.1b2">HMMER</requirement> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
6 <requirement type="package" version="2.2.6">bowtie2</requirement> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
7 <requirement type="package" version="1.6">samtools</requirement> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
8 <requirement type="package" version="2.2.1">cufflinks</requirement> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
9 <requirement type="package" version="2.7.1">blast</requirement> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
10 </requirements> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
11 |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
12 |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
13 <command interpreter="python" detect_errors="exit_code"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
14 #if $TrypType.species == "Trypanosoma congolense": |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
15 #if $TrypType.GT.analysis == "Genomic": |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
16 #if $TrypType.GT.contigs.preassem == "Contig available": |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
17 <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 --> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
18 Vap.py g_contigs $xname $P $TrypType.GT.contigs.contig $html_file $html_file.extra_files_path |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
19 #else |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
20 <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 --> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
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 |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
22 #end if |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
23 #else |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
24 <!-- name:2, pdfexport:3, strain:4, forward:5, reverse:6, html_file:7, html_resource:8 --> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
25 Vap.py transcipt $xname $P $TrypType.GT.strain $TrypType.GT.forward $TrypType.GT.reverse $html_file $html_file.extra_files_path |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
26 #end if |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
27 #else |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
28 #if $TrypType.contigs.preassem == "Contig available": |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
29 <!-- name:2, pdfexport:3, contigs:4, html_file:5, html_resource:6 --> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
30 Vap.py v_contigs $xname $P $TrypType.contigs.contig $html_file $html_file.extra_files_path |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
31 #else |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
32 <!-- name = 2, pdfexport = 3, kmers = 4, inslen = 5, covcut = 6, forward = 7, reverse = 8, html_file = 9, html_resource = 10 --> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
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 |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
34 #end if |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
35 #end if |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
36 |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
37 </command> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
38 |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
39 <inputs> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
40 <param name="xname" size = "30" type="text" value = "Test" label="Prefix Name" /> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
41 <conditional name = "TrypType"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
42 <param name = "species" type = 'select' label="Select Species"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
43 <option value = "Trypanosoma congolense" selected="true"></option> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
44 <option value = "Trypanosoma vivax"></option> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
45 </param> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
46 <when value = "Trypanosoma congolense"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
47 <conditional name = "GT"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
48 <param name="analysis" type = "select" label = "Genomic or Transcriptomic Analysis?"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
49 <option value = "Genomic" selected = "true"></option> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
50 <option value = "Transcriptomic"></option> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
51 </param> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
52 <when value = "Genomic"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
53 <conditional name = "contigs"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
54 <param name = "preassem" type = "select" label = "Contig file available?"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
55 <option value = "Full assembly" selected = "true"></option> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
56 <option value = "Contig available"></option> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
57 </param> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
58 <when value = "Full assembly"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
59 <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
60 <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
61 <param name = "covcut" type="integer" value="5" min="1" max="999" label = "Coverage cut off"></param> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
62 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
63 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
64 </when> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
65 <when value = "Contig available"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
66 <param name="contig" type="data" format="fasta" label="Contig file"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
67 </when> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
68 </conditional> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
69 </when> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
70 <when value = "Transcriptomic"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
71 <param name = "strain" type="select" label = "Select Reference Strain"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
72 <option value = "Tc148"></option> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
73 <option value = "IL3000"></option> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
74 </param> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
75 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
76 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
77 </when> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
78 </conditional> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
79 </when> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
80 <when value="Trypanosoma vivax"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
81 <conditional name = "contigs"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
82 <param name = "preassem" type = "select" label = "Contig file available?"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
83 <option value = "Full assembly" selected = "true"></option> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
84 <option value = "Contig available"></option> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
85 </param> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
86 <when value = "Full assembly"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
87 <param name = "kmers" type="integer" value="65" min="31" max="99" label = "Specify kmers"></param> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
88 <param name = "inslen" type="integer" value="400" min="1" max="999" label = "Insert length"></param> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
89 <param name="forward" type="data" format="fastq" label="Forward NGS Read File"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
90 <param name="reverse" type="data" format="fastq" label="Reverse NGS Read File"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
91 </when> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
92 <when value = "Contig available"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
93 <param name="contig" type="data" format="fasta" label="Contig file"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
94 </when> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
95 </conditional> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
96 </when> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
97 </conditional> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
98 |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
99 <param name="P" type="boolean" truevalue='PDF_Yes' falsevalue='PDF_No' label="Export PDF of figures" /> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
100 </inputs> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
101 |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
102 <outputs> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
103 <data format="html" name = "html_file" label = "${xname.value}_html"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
104 </outputs> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
105 <tests> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
106 <test> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
107 <param name = "xname" value = "Test"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
108 <conditional name = "TrypType"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
109 <param name = "species" value = "Trypanosoma congolense"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
110 </conditional> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
111 <conditional name = "GT"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
112 <param name = "analysis" value = "Genomic"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
113 </conditional> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
114 <conditional name = "contigs"> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
115 <param name = "preassem" value = "Contig available"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
116 <param name="contig" value = "Test.fa"/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
117 </conditional> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
118 <param name = "P" value = 'PDF_No'/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
119 <output name = "html_file" file = 'Test_html' ftype = 'html'/> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
120 </test> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
121 </tests> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
122 </tool> |
36cb22bd911d
planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
johnheap
parents:
diff
changeset
|
123 |