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annotate 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
parents
children 5a7cd6c39085
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52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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1 <tool id="seq2hla" name="seq2HLA" version="2.2.0">
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2 <description>HLA genotype and expression from RNA-seq</description>
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3 <requirements>
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4 <!-- needed because of some non POSIX compliant wc usage -->
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5 <requirement type="package" version="8.31">coreutils</requirement>
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6 <requirement type="package" version="2.2">seq2hla</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 seq2HLA --runName='$run_name' -1 '$fastq_input1' -2 '$fastq_input2'
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10 #if str($trim) != '':
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11 --trim3=$trim
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12 #end if
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13 -p \${GALAXY_SLOTS:-1} >> '$seq2hla_log'
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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14 && cp -p '${run_name}-ClassI.HLAgenotype2digits' '${c1_genotype2digits}'
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15 && cp -p '${run_name}-ClassI.HLAgenotype4digits' '${c1_genotype4digits}'
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16 && echo '#Locus_RPKM' | cat - '${run_name}-ClassI.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c1_expression}'
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17 && cp -p '${run_name}-ClassII.HLAgenotype4digits' '${c2_genotype4digits}'
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18 && echo '#Locus_RPKM' | cat - '${run_name}-ClassII.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c2_expression}'
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19 && cp -p '${run_name}.ambiguity' '${ambiguity}'
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20 ]]></command>
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21 <inputs>
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22 <param name="run_name" type="text" value="sample1" label="Name prefix for this analysis">
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23 <validator type="regex" message="Use letters,digits,_.-">^[A-Za-z0-9_\-+.]+$</validator>
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24 </param>
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25 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
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26 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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27 <param name="trim" type="integer" value="" min="0" optional="true" label="Trim bases from 3 prime"
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28 help="trim this many bases from the low-quality end of each read" />
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29 </inputs>
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30 <outputs>
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31 <data format="txt" name="seq2hla_log" label="${tool.name} on ${on_string}: ${run_name} logfile"/>
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32 <data format="tabular" name="c1_genotype2digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype2digits"/>
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33 <data format="tabular" name="c1_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype4digits"/>
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34 <data format="tabular" name="c2_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassII.HLAgenotype4digits"/>
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35 <data format="tabular" name="c1_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassI.expression"/>
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36 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/>
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37 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/>
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38 <data format="txt" name="ambiguity" label="${tool.name} on ${on_string}: ${run_name}.ambiguity"/>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="run_name" value="test"/>
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43 <param name="fastq_input1" ftype="fastqsanger" value="reads1.fastq"/>
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44 <param name="fastq_input2" ftype="fastqsanger" value="reads2.fastq"/>
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45 <output name="c1_genotype4digits">
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46 <assert_contents>
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47 <has_text text="A*24:02" />
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48 </assert_contents>
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49 </output>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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53
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54 **seq2HLA** *HLA typing from RNA-Seq sequence reads*
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55
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56 Release: 2.2
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57
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58 seq2HLA_ is an in-silico method, written in python and R, which takes standard RNA-Seq sequence reads in fastq format
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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),
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60 a p-value for each call, and the expression of each class
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61
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62 **Inputs**
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63
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64 Paired read fastq files with illumina style IDs.
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65
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66
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67 **Outputs**
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68
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69 1. <prefix>-ClassI.HLAgenotype2digits => 2 digit result of Class I
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70 2. <prefix>-ClassII.HLAgenotype2digits => 2 digit result of Class II
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71 3. <prefix>-ClassI.HLAgenotype4digits => 4 digit result of Class I
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72 4. <prefix>-ClassII.HLAgenotype4digits => 4 digit result of Class II
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73 5. <prefix>.ambiguity => reports typing ambuigities (more than one solution for an allele possible)
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74 6. <prefix>-ClassI.expression => expression of Class I alleles
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75 7. <prefix>-ClassII.expression => expression of Class II alleles
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76
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78 ClassI.HLAgenotype4digits
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79
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80 ======= ======== =========== ======== ============
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81 #Locus Allele 1 Confidence Allele 2 Confidence
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82 ======= ======== =========== ======== ============
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
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83 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"
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84 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
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85 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"
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86 ======= ======== =========== ======== ============
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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87
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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88
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
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89 ClassI.expression
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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90
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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91 ======= ======
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
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92 #Locus RPKM
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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93 ======= ======
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
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94 A 89.59
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
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95 B 139.66
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
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96 C 184.42
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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97 ======= ======
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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98
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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99
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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100 .. _seq2HLA: https://bitbucket.org/sebastian_boegel/seq2hla
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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101
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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102 ]]></help>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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103 <citations>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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104 <citation type="doi">10.1186/gm403</citation>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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105 </citations>
52bba1cd3823 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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106 </tool>