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comparison seq2hla.xml @ 0:52bba1cd3823 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
author iuc
date Thu, 20 Feb 2020 18:27:07 -0500
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children 5a7cd6c39085
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1 <tool id="seq2hla" name="seq2HLA" version="2.2.0">
2 <description>HLA genotype and expression from RNA-seq</description>
3 <requirements>
4 <!-- needed because of some non POSIX compliant wc usage -->
5 <requirement type="package" version="8.31">coreutils</requirement>
6 <requirement type="package" version="2.2">seq2hla</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 seq2HLA --runName='$run_name' -1 '$fastq_input1' -2 '$fastq_input2'
10 #if str($trim) != '':
11 --trim3=$trim
12 #end if
13 -p \${GALAXY_SLOTS:-1} >> '$seq2hla_log'
14 && cp -p '${run_name}-ClassI.HLAgenotype2digits' '${c1_genotype2digits}'
15 && cp -p '${run_name}-ClassI.HLAgenotype4digits' '${c1_genotype4digits}'
16 && echo '#Locus_RPKM' | cat - '${run_name}-ClassI.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c1_expression}'
17 && cp -p '${run_name}-ClassII.HLAgenotype4digits' '${c2_genotype4digits}'
18 && echo '#Locus_RPKM' | cat - '${run_name}-ClassII.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c2_expression}'
19 && cp -p '${run_name}.ambiguity' '${ambiguity}'
20 ]]></command>
21 <inputs>
22 <param name="run_name" type="text" value="sample1" label="Name prefix for this analysis">
23 <validator type="regex" message="Use letters,digits,_.-">^[A-Za-z0-9_\-+.]+$</validator>
24 </param>
25 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
26 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
27 <param name="trim" type="integer" value="" min="0" optional="true" label="Trim bases from 3 prime"
28 help="trim this many bases from the low-quality end of each read" />
29 </inputs>
30 <outputs>
31 <data format="txt" name="seq2hla_log" label="${tool.name} on ${on_string}: ${run_name} logfile"/>
32 <data format="tabular" name="c1_genotype2digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype2digits"/>
33 <data format="tabular" name="c1_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype4digits"/>
34 <data format="tabular" name="c2_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassII.HLAgenotype4digits"/>
35 <data format="tabular" name="c1_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassI.expression"/>
36 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/>
37 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/>
38 <data format="txt" name="ambiguity" label="${tool.name} on ${on_string}: ${run_name}.ambiguity"/>
39 </outputs>
40 <tests>
41 <test>
42 <param name="run_name" value="test"/>
43 <param name="fastq_input1" ftype="fastqsanger" value="reads1.fastq"/>
44 <param name="fastq_input2" ftype="fastqsanger" value="reads2.fastq"/>
45 <output name="c1_genotype4digits">
46 <assert_contents>
47 <has_text text="A*24:02" />
48 </assert_contents>
49 </output>
50 </test>
51 </tests>
52 <help><![CDATA[
53
54 **seq2HLA** *HLA typing from RNA-Seq sequence reads*
55
56 Release: 2.2
57
58 seq2HLA_ is an in-silico method, written in python and R, which takes standard RNA-Seq sequence reads in fastq format
59 as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution),
60 a p-value for each call, and the expression of each class
61
62 **Inputs**
63
64 Paired read fastq files with illumina style IDs.
65
66
67 **Outputs**
68
69 1. <prefix>-ClassI.HLAgenotype2digits => 2 digit result of Class I
70 2. <prefix>-ClassII.HLAgenotype2digits => 2 digit result of Class II
71 3. <prefix>-ClassI.HLAgenotype4digits => 4 digit result of Class I
72 4. <prefix>-ClassII.HLAgenotype4digits => 4 digit result of Class II
73 5. <prefix>.ambiguity => reports typing ambuigities (more than one solution for an allele possible)
74 6. <prefix>-ClassI.expression => expression of Class I alleles
75 7. <prefix>-ClassII.expression => expression of Class II alleles
76
77
78 ClassI.HLAgenotype4digits
79
80 ======= ======== =========== ======== ============
81 #Locus Allele 1 Confidence Allele 2 Confidence
82 ======= ======== =========== ======== ============
83 A A*03:01 0.000510333 A*02:01' 0.0005975604
84 B B*50:01 0.001271273 B*58:02 3.52561e-05
85 C C*04:01 0.06362723 C*06:02 0.04725865
86 ======= ======== =========== ======== ============
87
88
89 ClassI.expression
90
91 ======= ======
92 #Locus RPKM
93 ======= ======
94 A 89.59
95 B 139.66
96 C 184.42
97 ======= ======
98
99
100 .. _seq2HLA: https://bitbucket.org/sebastian_boegel/seq2hla
101
102 ]]></help>
103 <citations>
104 <citation type="doi">10.1186/gm403</citation>
105 </citations>
106 </tool>