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annotate seq2hla.xml @ 2:62423040f17e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:35:37 +0000
parents 1db16e5fde32
children 2e2130c69672
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1 <tool id="seq2hla" name="seq2HLA" version="2.2.0+galaxy1">
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2 <description>HLA genotype and expression from RNA-seq</description>
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3 <xrefs>
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4 <xref type="bio.tools">seq2hla</xref>
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5 </xrefs>
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6 <requirements>
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7 <!-- needed because of some non POSIX compliant wc usage -->
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8 <requirement type="package" version="8.31">coreutils</requirement>
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9 <requirement type="package" version="2.2">seq2hla</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 seq2HLA --runName='$run_name' -1 '$fastq_input1' -2 '$fastq_input2'
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13 #if str($trim) != '':
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14 --trim3=$trim
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15 #end if
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16 -p \${GALAXY_SLOTS:-1} >> '$seq2hla_log'
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17 && cp -p '${run_name}-ClassI.HLAgenotype2digits' '${c1_genotype2digits}'
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18 && cp -p '${run_name}-ClassI.HLAgenotype4digits' '${c1_genotype4digits}'
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19 && echo '#Locus_RPKM' | cat - '${run_name}-ClassI.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c1_expression}'
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20 && cp -p '${run_name}-ClassII.HLAgenotype4digits' '${c2_genotype4digits}'
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21 && echo '#Locus_RPKM' | cat - '${run_name}-ClassII.expression' | sed 's/^\(.*\): \([0-9.]*\).*$/\1_\2/' | tr '_' '\t' > '${c2_expression}'
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22 && cp -p '${run_name}.ambiguity' '${ambiguity}'
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23 ]]></command>
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24 <inputs>
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25 <param name="run_name" type="text" value="sample1" label="Name prefix for this analysis">
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26 <validator type="regex" message="Use letters,digits,_.-">^[A-Za-z0-9_\-+.]+$</validator>
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27 </param>
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28 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
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29 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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30 <param name="trim" type="integer" value="" min="0" optional="true" label="Trim bases from 3 prime"
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31 help="trim this many bases from the low-quality end of each read" />
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32 </inputs>
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33 <outputs>
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34 <data format="txt" name="seq2hla_log" label="${tool.name} on ${on_string}: ${run_name} logfile"/>
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35 <data format="tabular" name="c1_genotype2digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype2digits"/>
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36 <data format="tabular" name="c1_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassI.HLAgenotype4digits"/>
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37 <data format="tabular" name="c2_genotype4digits" label="${tool.name} on ${on_string}: ${run_name}-ClassII.HLAgenotype4digits"/>
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38 <data format="tabular" name="c1_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassI.expression"/>
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39 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/>
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40 <data format="tabular" name="c2_expression" label="${tool.name} on ${on_string}: ${run_name}-ClassII.expression"/>
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41 <data format="txt" name="ambiguity" label="${tool.name} on ${on_string}: ${run_name}.ambiguity"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="run_name" value="test"/>
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46 <param name="fastq_input1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
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47 <param name="fastq_input2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
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48 <output name="c1_genotype4digits">
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49 <assert_contents>
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50 <has_text text="A*24:02" />
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51 </assert_contents>
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52 </output>
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53 </test>
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54 </tests>
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55 <help><![CDATA[
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56
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57 **seq2HLA** *HLA typing from RNA-Seq sequence reads*
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58
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59 Release: 2.2
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60
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61 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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62 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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63 a p-value for each call, and the expression of each class
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64
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65 **Inputs**
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66
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67 Paired read fastq files with illumina style IDs.
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68
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69
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70 **Outputs**
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71
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72 1. <prefix>-ClassI.HLAgenotype2digits => 2 digit result of Class I
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73 2. <prefix>-ClassII.HLAgenotype2digits => 2 digit result of Class II
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74 3. <prefix>-ClassI.HLAgenotype4digits => 4 digit result of Class I
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75 4. <prefix>-ClassII.HLAgenotype4digits => 4 digit result of Class II
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76 5. <prefix>.ambiguity => reports typing ambuigities (more than one solution for an allele possible)
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77 6. <prefix>-ClassI.expression => expression of Class I alleles
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78 7. <prefix>-ClassII.expression => expression of Class II alleles
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79
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80
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81 ClassI.HLAgenotype4digits
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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82
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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83 ======= ======== =========== ======== ============
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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84 #Locus Allele 1 Confidence Allele 2 Confidence
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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85 ======= ======== =========== ======== ============
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
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86 A A*03:01 0.000510333 A*02:01' 0.0005975604
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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87 B B*50:01 0.001271273 B*58:02 3.52561e-05
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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88 C C*04:01 0.06362723 C*06:02 0.04725865
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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89 ======= ======== =========== ======== ============
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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90
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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91
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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92 ClassI.expression
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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93
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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94 ======= ======
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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95 #Locus RPKM
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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96 ======= ======
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
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97 A 89.59
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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98 B 139.66
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
iuc
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99 C 184.42
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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100 ======= ======
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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101
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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102
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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103 .. _seq2HLA: https://bitbucket.org/sebastian_boegel/seq2hla
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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104
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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105 ]]></help>
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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106 <citations>
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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107 <citation type="doi">10.1186/gm403</citation>
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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108 </citations>
00b89af60f18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit 96f219ed86ce674def72c73393d3c29c87cb56e5"
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109 </tool>