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annotate tools/cgatools17/testvariants_v17.xml @ 1:3a2e0f376f26 draft

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Minor change to tv2vcf.xml to allow for workflow automation
author dgdekoning
date Wed, 21 Oct 2015 10:09:15 -0400
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1 <tool id="cg_testvariants" name="TestVariants" version="1.7.1">
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2
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3 <description>Test for the presence of variants</description>
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4
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5 <requirements>
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6 <requirement type="package" version="1">cgatools17</requirement>
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7 </requirements>
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8
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9 <command> <!--run executable-->
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10 cgatools | head -1;
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11 cgatools testvariants
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12 --beta
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13 --reference ${crr.fields.crr_path}
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14 --output $output
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15 --input $listing
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16 --variants
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17 #for $v in $file_types.varfiles <!--get each var/mastervar file-->
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18 ${v.input}
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19 #end for
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20 </command>
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21
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22 <inputs>
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23 <!--form field to select crr file-->
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24 <param name="crr" type="select" label="Reference Build">
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25 <options from_data_table="cg_anno_files" />
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26 </param>
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27
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28 <!--form fields to select variant list-->
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29 <param name="listing" type="data" format="tabular" label="Select variant list"/>
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30
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31 <!--conditional to select input file type-->
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32 <conditional name="file_types">
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33 <param name="file_type" type="select" label="Select the input file type">
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34 <option value="var" selected="true">var files</option>
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35 <option value="mastervar">mastervar files</option>
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36 </param>
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37 <when value="var">
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38 <repeat name="varfiles" title="Variant files">
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39 <param name="input" type="data" format="cg_var" label="Dataset"/>
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40 </repeat>
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41 </when>
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42 <when value="mastervar">
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43 <repeat name="varfiles" title="Variant files">
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44 <param name="input" type="data" format="cg_mastervar" label="Dataset"/>
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45 </repeat>
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46 </when>
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47 </conditional>
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48
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49 <!-- prefix for output file so you dont have to manually rename history items -->
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50 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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51 </inputs>
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52
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53
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54 <outputs>
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55 <data format="tabular" name="output" label="$fname ${tool.name} on ${on_string}"/>
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56 </outputs>
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57
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58 <help>
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59 **What it does**
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60
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61 This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants.
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62
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63 **cgatools 1.7.1 Documentation**
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64
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65 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
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66
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67 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
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68
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69 **Command line reference**::
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70
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71 COMMAND NAME
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72 testvariants - Tests variant files for presence of variants.
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73
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74 DESCRIPTION
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75 Tests variant files for presence of variants. The output is a tab-delimited
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76 file consisting of the columns of the input variants file, plus a column
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77 for each assembly results file that contains a character code for each
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78 allele. The character codes have meaning as follows:
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79
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80 0 This allele of this genome is consistent with the reference at this
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81 locus but inconsistent with the variant.
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82 1 This allele of this genome has the input variant at this locus.
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83 N This allele of this genome has no-calls but is consistent with the
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84 input variant.
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85
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86 OPTIONS
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87 -h [ --help ]
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88 Print this help message.
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89
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90 --beta
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91 This is a beta command. To run this command, you must pass the --beta
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92 flag.
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93
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94 --reference arg
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95 The reference crr file.
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96
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97 --input arg (=STDIN)
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98 The input variants to test for.
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99
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100 --output arg (=STDOUT)
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101 The output file (may be omitted for stdout).
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102
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103 --variants arg
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104 The input variant files (may be passed in as arguments at the end of
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105 the command).
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106
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107 SUPPORTED FORMAT_VERSION
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108 0.3 or later
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109 </help>
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110 </tool>