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comparison hla_dq.xml @ 0:10a407fb5072 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
author erasmus-medical-center
date Wed, 30 May 2018 07:50:21 -0400
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children 4fc47a3ff9e8
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1 <tool id="hla_dq" name="HLA-DQ typing" version="1.0">
2 <description> Determine possible associated types given BLAST IMGT/HLA annotation</description>
3 <command detect_errors="exit_code"><![CDATA[
4 python '$__tool_directory__/hla_dq.py'
5 #for $i in $filesA:
6 -A '$i.A'
7 #end for
8 #for $i in $filesB:
9 -B '$i.B'
10 #end for
11 #if $column and $column is not None:
12 --column $column
13 #end if
14 ]]></command>
15 <inputs>
16 <!-- use repeats cuz order matters -->
17 <repeat name="filesA" title="BLAST results A gene sequences" min="1">
18 <param argument="-A" label="BLAST IMGT/HLA hits A gene" type="data" format="tabular"/>
19 </repeat>
20 <repeat name="filesB" title="BLAST results B gene sequences" min="1">
21 <param argument="-B" label="BLAST IMGT/HLA hits B gene" type="data" format="tabular"/>
22 </repeat>
23 <param argument="--column" label="Column number containing the BLAST IMGT/HLA genotype annotation" type="integer" value="5" min="1" help="Example annotation: HLA:HLA11066 DQA1*01:05:02 768 bp"/>
24 </inputs>
25 <outputs>
26 <data name="serotype_table" format="tabular" from_work_dir="results.tsv" label="${tool.name} on ${on_string}: Serotype table"/>
27 </outputs>
28 <tests>
29 <test><!-- test with real data -->
30 <repeat name="filesA">
31 <param name="A" value="sideA1.blast.tsv"/>
32 </repeat>
33 <repeat name="filesA">
34 <param name="A" value="sideA2.blast.tsv"/>
35 </repeat>
36 <repeat name="filesB">
37 <param name="B" value="sideB1.blast.tsv"/>
38 </repeat>
39 <repeat name="filesB">
40 <param name="B" value="sideB2.blast.tsv"/>
41 </repeat>
42 <output name="serotype_table" file="test1_results.tsv"/>
43 </test>
44 <test><!-- test three files each and data leading to serotypes -->
45 <repeat name="filesA">
46 <param name="A" value="sideA1.blast.tsv"/>
47 </repeat>
48 <repeat name="filesA">
49 <param name="A" value="sideA2.blast.tsv"/>
50 </repeat>
51 <repeat name="filesA">
52 <param name="A" value="all_sideA3.blast.tsv"/>
53 </repeat>
54 <repeat name="filesB">
55 <param name="B" value="sideB1.blast.tsv"/>
56 </repeat>
57 <repeat name="filesB">
58 <param name="B" value="sideB2.blast.tsv"/>
59 </repeat>
60 <repeat name="filesB">
61 <param name="B" value="all_sideB3.blast.tsv"/>
62 </repeat>
63 <output name="serotype_table" file="test2_results.tsv"/>
64 </test>
65 </tests>
66
67 <help><![CDATA[
68
69 Given files annotated with BLAST and IMGT/HLA database for HLA-A and HLA-B gene (one or more files each), determine possible associated serotypes.
70
71 ===== ===== =====
72 DQA1 DQB1 type
73 ===== ===== =====
74 02:01 02:02 DQ2.2
75 03:03 02:02 DQ2.3
76 05:01 02:01 DQ2.3
77 03:01 03:02 DQ8
78 03:02 03:02 DQ8
79 03:03 03:02 DQ8
80 ===== ===== =====
81
82 Example result table:
83
84 ==== ==== =========
85 type A1 A2
86 ==== ==== =========
87 B1 DQ8 None
88 B2 None DQ2.2;DQ8
89 ==== ==== =========
90
91 Where A1, A2 correspond to two annotated input files given for gene A, each representing possible allele sequence
92
93 ]]></help>
94 </tool>