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1 <tool id="cga_listvariant" name="listvariants" version="0.0.1">
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2
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3 <description>lists all called variants</description> <!--adds description in toolbar-->
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4
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5 <command> <!--run executable-->
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6 cgatools listvariants
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7 --beta
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8 --reference ${crr.fields.path}
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9 --output $output
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10 --variants
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11 #for $v in $varfiles <!--get each var file-->
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12 ${v.input}
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13 #end for
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14 #if $include_list.listing == "yes" <!--only added when yes-->
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15 --variant-listing $include_list.list
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16 #end if
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17 $longvar
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18 </command>
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19
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20 <inputs>
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21 <!--form field to select crr file-->
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22 <param name="crr" type="select" label="Genome build">
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23 <options from_data_table="cgatools" />
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24 </param>
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25
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26 <!--form field to select long variants option-->
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27 <param name="longvar" type="select" label="List long variants?">
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28 <option value="" selected="true">no</option>
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29 <option value="--list-long-variants">yes</option>
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30 </param>
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31
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32 <!--form fields to include existing variant list-->
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33 <conditional name="include_list">
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34 <param name="listing" type="select" label="Include variant listing?">
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35 <option value="no" selected="true">no</option>
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36 <option value="yes">yes</option>
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37 </param>
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38 <when value="yes">
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39 <param name="list" type="data" format="tabular" label="Variant listing"/>
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40 </when>
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41 </conditional>
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42
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43 <!--form field to select all variant files-->
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44 <repeat name="varfiles" title="Var file">
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45 <param name="input" type="data" format="tabular" label="Dataset">
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46 <validator type="unspecified_build" />
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47 <validator type="dataset_metadata_in_file" filename="cgatools.loc"
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48 metadata_name="dbkey" metadata_column="0"
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49 message="cgatools is not currently available for this build."/>
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50 </param>
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51 </repeat>
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52 </inputs>
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53
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54 <outputs>
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55 <data format="tabular" name="output" />
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56 </outputs>
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57
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58 <help>
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59
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60 **What it does**
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61
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62 This tool uses the cgatools listvariants to list all called variants present in the var or mastervar files.
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63
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64 cgatools: http://sourceforge.net/projects/cgatools/files/
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65
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66 -----
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67
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68 **cgatools Manual**::
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69
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70 COMMAND NAME
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71 listvariants - Lists the variants present in a variant file.
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72
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73 DESCRIPTION
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74 Lists all called variants present in the specified variant files, in a
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75 format suitable for processing by the testvariants command. The output is a
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76 tab-delimited file consisting of the following columns:
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77
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78 variantId Sequential id assigned to each variant.
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79 chromosome The chromosome of the variant.
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80 begin 0-based reference offset of the beginning of the variant.
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81 end 0-based reference offset of the end of the variant.
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82 varType The varType as extracted from the variant file.
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83 reference The reference sequence.
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84 alleleSeq The variant allele sequence as extracted from the variant
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85 file.
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86 xRef The xRef as extrated from the variant file.
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87
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88 OPTIONS
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89 -h [ --help ]
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90 Print this help message.
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91
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92 --beta
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93 This is a beta command. To run this command, you must pass the --beta
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94 flag.
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95
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96 --reference arg
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97 The reference crr file.
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98
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99 --output arg (=STDOUT)
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100 The output file (may be omitted for stdout).
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101
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102 --variants arg
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103 The input variant files (may be positional args).
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104
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105 --variant-listing arg
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106 The output of another listvariants run, to be merged in to produce the
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107 output of this run.
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108
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109 --list-long-variants
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110 In addition to listing short variants, list longer variants as well
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111 (10's of bases) by concatenating nearby calls.
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112
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113
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114
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115 SUPPORTED FORMAT_VERSION
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116 0.3 or later
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117 </help>
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118 </tool>
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