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comparison seq2hla.xml @ 0:262d5334c786 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/seq2hla commit fb1e8b800e7dcd411c7281d1ed05e192fba14fcc-dirty
author jjohnson
date Thu, 22 Dec 2016 09:15:31 -0500
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1 <tool id="seq2hla" name="seq2HLA" version="0.1.0">
2 <description>HLA genotype and expression from RNA-seq</description>
3 <requirements>
4 <requirement type="package" version="2.2">seq2HLA</requirement>
5 <requirement type="package" version="1.0.0">bowtie</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" />
9 </stdio>
10 <command><![CDATA[
11 seq2HLA --runName="$run_name" -1 "$fastq_input1" -2 "$fastq_input2"
12 #if str($trim) != '':
13 --trim3=$trim
14 #end if
15 -p \${GALAXY_SLOTS:-1} >> "$seq2hla_log"
16 && cp -p "${run_name}-ClassI.HLAgenotype2digits" "${c1_genotype2digits}"
17 && cp -p "${run_name}-ClassI.HLAgenotype4digits" "${c1_genotype4digits}"
18 && echo "#Locus_RPKM" | cat - "${run_name}-ClassI.expression" | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > "${c1_expression}"
19 && cp -p "${run_name}-ClassII.HLAgenotype4digits" "${c2_genotype4digits}"
20 && echo "#Locus_RPKM" | cat - "${run_name}-ClassII.expression" | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > "${c2_expression}"
21 && cp -p "${run_name}.ambiguity" "${ambiguity}"
22 ]]></command>
23 <inputs>
24 <param name="run_name" type="text" value="sample1" label="Name prefix for this analysis">
25 <validator type="regex" message="Use letters,digits,_.-">^[A-Za-z0-9_\-+.]+$</validator>
26 </param>
27 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
28 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
29 <param name="trim" type="integer" value="" min="0" optional="true" label="Trim bases from 3 prime"
30 help="trim this many bases from the low-quality end of each read" />
31 </inputs>
32 <outputs>
33 <data format="txt" name="seq2hla_log" label="${tool.name} on ${on_string}: ${run_name} logfile"/>
34 <data format="tabular" name="c1_genotype2digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype2digits"/>
35 <data format="tabular" name="c1_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype4digits"/>
36 <data format="tabular" name="c2_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassII.HLAgenotype4digits"/>
37 <data format="tabular" name="c1_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassI.expression"/>
38 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/>
39 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/>
40 <data format="txt" name="ambiguity" label="${tool.name} on ${on_string}: ${run_name}.ambiguity"/>
41 </outputs>
42 <tests>
43 <test>
44 <param name="run_name" value="test"/>
45 <param name="fastq_input1" ftype="fastqsanger" value="reads1.fastq"/>
46 <param name="fastq_input2" ftype="fastqsanger" value="reads2.fastq"/>
47 <output name="c1_genotype4digits">
48 <assert_contents>
49 <has_text text="A*24:02" />
50 </assert_contents>
51 </output>
52 </test>
53 </tests>
54 <help><![CDATA[
55 **seq2HLA** *HLA typing from RNA-Seq sequence reads*
56
57 Release: 2.2
58
59 seq2HLA_ is an in-silico method, written in python and R, which takes standard RNA-Seq sequence reads in fastq format
60 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),
61 a p-value for each call, and the expression of each class
62
63 **Inputs**
64
65 Paired read fastq files with illumina style IDs.
66
67
68 **Outputs**
69
70 1. <prefix>-ClassI.HLAgenotype2digits => 2 digit result of Class I
71 2. <prefix>-ClassII.HLAgenotype2digits => 2 digit result of Class II
72 3. <prefix>-ClassI.HLAgenotype4digits => 4 digit result of Class I
73 4. <prefix>-ClassII.HLAgenotype4digits => 4 digit result of Class II
74 5. <prefix>.ambiguity => reports typing ambuigities (more than one solution for an allele possible)
75 6. <prefix>-ClassI.expression => expression of Class I alleles
76 7. <prefix>-ClassII.expression => expression of Class II alleles
77
78
79 ClassI.HLAgenotype4digits
80
81 ======= ======== =========== ======== ============
82 #Locus Allele 1 Confidence Allele 2 Confidence
83 ======= ======== =========== ======== ============
84 A A*03:01 0.000510333 A*02:01' 0.0005975604
85 B B*50:01 0.001271273 B*58:02 3.52561e-05
86 C C*04:01 0.06362723 C*06:02 0.04725865
87 ======= ======== =========== ======== ============
88
89
90 ClassI.expression
91
92 ======= ======
93 #Locus RPKM
94 ======= ======
95 A 89.59
96 B 139.66
97 C 184.42
98 ======= ======
99
100
101 .. _seq2HLA: https://bitbucket.org/sebastian_boegel/seq2hla
102
103 ]]></help>
104 <citations>
105 <citation type="doi">10.1186/gm403</citation>
106 </citations>
107 </tool>