Mercurial > repos > iuc > seq2hla

annotate seq2hla.xml @ 2:86d0ce0560a1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
author iuc
date Tue, 07 Mar 2023 13:10:18 +0000
parents 5a7cd6c39085
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
1 <tool id="seq2hla" name="seq2HLA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
2 <description>HLA genotype and expression from RNA-seq</description>
2
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
3 <macros>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
4 <token name="@TOOL_VERSION@">2.3</token>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
5 <token name="@VERSION_SUFFIX@">0</token>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
6 </macros>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
7 <xrefs>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
8 <xref type="bio.tools">seq2hla</xref>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
9 </xrefs>
0
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
10 <requirements>
2
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
11 <requirement type="package" version="@TOOL_VERSION@">seq2hla</requirement>
0
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
12 </requirements>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
13 <command detect_errors="exit_code"><![CDATA[
2
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
14 seq2HLA --runName='$run_name'
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
15 #if str( $fastq_input.fastq_input_selector ) == "paired":
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
16 -1 '${fastq_input.fastq_input1}'
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
17 -2 '${fastq_input.fastq_input2}'
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
18 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
19 -1 '${fastq_input.fastq_input1.forward}'
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
20 -2 '${fastq_input.fastq_input1.reverse}'
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
21 #end if
0
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
22 #if str($trim) != '':
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
23 --trim3=$trim
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
24 #end if
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
25 -p \${GALAXY_SLOTS:-1} >> '$seq2hla_log'
2
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
26 && cp -p '${run_name}-ClassI-class.HLAgenotype2digits' '${c1_genotype2digits}'
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
27 && cp -p '${run_name}-ClassI-class.HLAgenotype4digits' '${c1_genotype4digits}'
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
28 && echo '#Locus_RPKM' | cat - '${run_name}-ClassI-class.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c1_expression}'
0
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
29 && cp -p '${run_name}-ClassII.HLAgenotype4digits' '${c2_genotype4digits}'
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
30 && echo '#Locus_RPKM' | cat - '${run_name}-ClassII.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c2_expression}'
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
31 && cp -p '${run_name}.ambiguity' '${ambiguity}'
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
32 ]]></command>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
33 <inputs>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
34 <param name="run_name" type="text" value="sample1" label="Name prefix for this analysis">
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
35 <validator type="regex" message="Use letters,digits,_.-">^[A-Za-z0-9_\-+.]+$</validator>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
36 </param>
2
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
37 <conditional name="fastq_input">
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
38 <param name="fastq_input_selector" type="select" label="Paired-end reads" help="Select between paired and paired-collection data">
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
39 <option value="paired">Paired</option>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
40 <option value="paired_collection">Paired Collection</option>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
41 </param>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
42 <when value="paired">
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
43 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
44 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
45 </when>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
46 <when value="paired_collection">
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
47 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a collection of paired-end reads"/>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
48 </when>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
49 </conditional>
0
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
50 <param name="trim" type="integer" value="" min="0" optional="true" label="Trim bases from 3 prime"
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
51 help="trim this many bases from the low-quality end of each read" />
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
52 </inputs>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
53 <outputs>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
54 <data format="txt" name="seq2hla_log" label="${tool.name} on ${on_string}: ${run_name} logfile"/>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
55 <data format="tabular" name="c1_genotype2digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype2digits"/>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
56 <data format="tabular" name="c1_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype4digits"/>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
57 <data format="tabular" name="c2_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassII.HLAgenotype4digits"/>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
58 <data format="tabular" name="c1_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassI.expression"/>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
59 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
60 <data format="txt" name="ambiguity" label="${tool.name} on ${on_string}: ${run_name}.ambiguity"/>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
61 </outputs>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
62 <tests>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
63 <test>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
64 <param name="run_name" value="test"/>
2
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
65 <conditional name="fastq_input">
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
66 <param name="fastq_input_selector" value="paired"/>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
67 <param name="fastq_input1" ftype="fastqsanger" value="reads1.fastq"/>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
68 <param name="fastq_input2" ftype="fastqsanger" value="reads2.fastq"/>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
69 </conditional>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
70 <output name="c1_genotype4digits">
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
71 <assert_contents>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
72 <has_text text="A*24:02" />
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
73 </assert_contents>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
74 </output>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
75 </test>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
76 <test>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
77 <param name="run_name" value="test_collection"/>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
78 <conditional name="fastq_input">
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
79 <param name="fastq_input_selector" value="paired_collection"/>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
80 <param name="fastq_input1">
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
81 <collection type="paired">
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
82 <element name="forward" ftype="fastqsanger" value="reads1.fastq" />
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
83 <element name="reverse" ftype="fastqsanger" value="reads2.fastq" />
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
84 </collection>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
85 </param>
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
86 </conditional>
0
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
87 <output name="c1_genotype4digits">
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
88 <assert_contents>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
89 <has_text text="A*24:02" />
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
90 </assert_contents>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
91 </output>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
92 </test>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
93 </tests>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
94 <help><![CDATA[
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
95
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
96 **seq2HLA** *HLA typing from RNA-Seq sequence reads*
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
97
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
98 Release: 2.2
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
99
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
100 seq2HLA_ is an in-silico method, written in python and R, which takes standard RNA-Seq sequence reads in fastq format
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
101 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),
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
102 a p-value for each call, and the expression of each class
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
103
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
104 **Inputs**
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
105
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
106 Paired read fastq files with illumina style IDs.
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
107
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
108
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
109 **Outputs**
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
110
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
111 1. <prefix>-ClassI.HLAgenotype2digits => 2 digit result of Class I
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
112 2. <prefix>-ClassII.HLAgenotype2digits => 2 digit result of Class II
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
113 3. <prefix>-ClassI.HLAgenotype4digits => 4 digit result of Class I
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
114 4. <prefix>-ClassII.HLAgenotype4digits => 4 digit result of Class II
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
115 5. <prefix>.ambiguity => reports typing ambuigities (more than one solution for an allele possible)
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
116 6. <prefix>-ClassI.expression => expression of Class I alleles
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
117 7. <prefix>-ClassII.expression => expression of Class II alleles
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
118
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
119
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
120 ClassI.HLAgenotype4digits
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
121
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
122 ======= ======== =========== ======== ============
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
123 #Locus Allele 1 Confidence Allele 2 Confidence
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
124 ======= ======== =========== ======== ============
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
125 A A*03:01 0.000510333 A*02:01' 0.0005975604
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
126 B B*50:01 0.001271273 B*58:02 3.52561e-05
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
127 C C*04:01 0.06362723 C*06:02 0.04725865
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
128 ======= ======== =========== ======== ============
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
129
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
130
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
131 ClassI.expression
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
132
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
133 ======= ======
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
134 #Locus RPKM
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
135 ======= ======
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
136 A 89.59
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
137 B 139.66
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
138 C 184.42
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
139 ======= ======
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
140
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
141
2
86d0ce0560a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 3a6a342d9b5e0dd2774629079e315c8f33be7d29
iuc
parents: 1
diff changeset
142 .. _seq2HLA: https://github.com/TRON-Bioinformatics/seq2HLA
0
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
143
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
144 ]]></help>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
145 <citations>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
146 <citation type="doi">10.1186/gm403</citation>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
147 </citations>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
parents:
diff changeset
148 </tool>