annotate VCF_to_VariantDB.xml @ 3:f2525e35b8e9 draft

typo in macros file
author geert-vandeweyer
date Wed, 19 Feb 2014 06:47:41 -0500
parents d03a63a57e82
children 7ebc71784e9f
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1 <tool id="VCF_to_DB_rev" name="VCF to VariantDB" version="0.1.2">
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2 <description></description>
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3 <expand macro="requirements" />
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4 <macros>
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5 <import>VCF_to_VariantDB_macros.xml</import>
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6 </macros>
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7 <command interpreter="perl">
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8 VCF_to_DB_reverse.pl
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9 -H '@URL@'
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10 -R $__root_dir__
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11 ## input file
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12 -v $input1
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13 -V $__app__.security.encode_id( '%s' % $input1.id )
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14 ## user email, for identification in DataBase
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15 -u $__user_email__
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16
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17 ## OUTPUT FILE
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18 -o $output1
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19
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20 ## SAMPLE GENDER
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21 #if $samplegender != "undef":
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22 -g $samplegender
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23 #end if
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24
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25 ## SAMPLE NAME
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26 #if $namefromselect.namesource == "typed" :
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27 #if $namefromselect.typedname != "":
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28 -n "${namefromselect.typedname}"
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29 #end if
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30 #elif $namefromselect.namesource == "other":
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31 -n "${namefromselect.namefile.display_name}"
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32 #elif $namefromselect.namesource == "vcf":
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33 -n "${input1.display_name}"
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34 #end if
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35
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36 ## DATA FILES
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37 #if $sendData.store == "true":
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38 -b $bamfile
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39 -B ${bamfile.metadata.bam_index}
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40 -c $__app__.security.encode_id( '%s' % $bamfile.id )
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41 #end if
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42
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43 ## The server to send results to
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44 -S $server
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45
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46
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47 </command>
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48 <requirements>
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49 <requirement type="package">tabix</requirement>
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50 </requirements>
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51 <inputs>
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52 <param name="input1" type="data" format="vcf" label="VCF file" help="Unified Genotyper VCF File" />
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53 <conditional name="sendData">
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54 <param name="store" type="select" label="Store VCF and BAM Files:" help="This option allows you to send the BAM and VCF files to our storage server for dynamic loading into IGV. If you store them there, please delete them here." >
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55 <option value="false">No</option>
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56 <option value="true">Yes</option>
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57 </param>
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58 <when value="true">
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59 <param name="bamfile" type="data" format="bam" label="BAM File." />
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60 </when>
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61 </conditional>
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62
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63 <conditional name="namefromselect">
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64 <param name="namesource" type="select" label="Provide a Sample Name :" help="If no name is specified, a new sample will be created, and you will be notified of the name" >
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65 <option value="typed">Type the samplename</option>
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66 <option value="vcf">Use the VCF File name</option>
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67 <option value="other">Select a file to base the name on</option>
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68 </param>
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69 <when value="typed">
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70 <param name="typedname" type="text" size="25" label="Sample Name." />
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71 </when>
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72 <when value="other">
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73 <param name="namefile" type="data" format="sam,bam,fastq,fasta,bed,fastqsanger,fastqillumina,txt,vcf" label="Select a file from the history to base the sample name upon" />
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74 </when>
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75 </conditional>
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76 <param name="samplegender" type="select" label="Sample Gender: " help="This can be set from the database frontend as well.">
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77 <option value="undef">Unspecified</option>
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78 <option value="Male">Male</option>
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79 <option value="Female">Female</option>
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80 </param>
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81 <param name="server" type="select" label="VariantDB-Server: " help="Specify the VariantDB server you wish to send the data to. You MUST have a valid account on the target server, identical to your account here.">
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82 <option value="http://143.169.238.104/variantdb/">Main Server @ University of Antwerp</option>
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83 </param>
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84 </inputs>
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85 <outputs>
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86 <data format="txt" name="output1" label="${tool.name} on ${on_string}: Result"/>
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87 </outputs>
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88 <help>
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89
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90 **What it does**
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91
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92 This tools sends the results from the GATK unified genotyper to a VariantDB server. From there, variants can be compared between samples, filtered on various annotations etc. To add servers, specify them in the tool configuration XML file.
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93
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94 ------
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95
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96
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97 **Input file**
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98
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99 VCF file from the GATK Unified Genotyper.
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100
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101 ------
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102
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103 **Outputs**
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104
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105 Text file with some results from the vcf-parser.
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106
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107 </help>
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108 </tool>
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109
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110