Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate tools/cgatools17/listvariants_v17.xml @ 5:64017ce705b6 draft

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author yhoogstrate
date Wed, 11 Nov 2015 03:51:05 -0500
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1 <tool id="cg_listvariant" name="ListVariants" version="1.7.1">
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3 <description>Lists all variants present in CG var or masterVar file</description>
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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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9 <version_command>cgatools | head -1</version_command>
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11 <command> <!--run executable-->
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12 cgatools
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13 listvariants
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14 --beta
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16 #if $reference_gene_sets_source.source_select == "indexed_filtered"
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17 ${reference_gene_sets_source.crr.fields.crr_path}
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18 #else if $reference_gene_sets_source.source_select == "history"
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19 ${reference_gene_sets_source.crr}
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20 #end if
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22 --output $output
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23 #if $include_list.listing == "yes" <!--only added when yes-->
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24 --variant-listing $include_list.list
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25 #end if
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26 $longvar
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27 --variants
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28 #for $v in $file_types.varfiles <!--get each var/mastervar file-->
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29 ${v.input}
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30 #end for
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32 </command>
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34 <inputs>
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35 <!--form field to select crr file-->
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36 <conditional name="reference_gene_sets_source">
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37 <param name="source_select" type="select" label="GFF/GTF Source">
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38 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
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39 <option value="history">Use reference from the history</option>
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40 </param>
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41 <when value="indexed_filtered">
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42 <param name="crr" type="select" label="Reference Build">
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43 <options from_data_table="cg_anno_files" />
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44 </param>
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45 </when>
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46 <when value="history">
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47 <param name="crr" format="crr" type="data" label="Reference build" help="In crr format (you can use fasta2crr for conversion)" />
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48 </when>
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49 </conditional>
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50
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51 <conditional name="file_types">
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52 <param name="file_type" type="select" label="Select the input file type">
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53 <option value="var" selected="true">var files</option>
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54 <option value="mastervar">mastervar files</option>
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55 </param>
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56 <when value="var">
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57 <repeat name="varfiles" title="Variant files" min="1">
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58 <param name="input" type="data" format="cg_var" label="Dataset"/>
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59 </repeat>
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60 </when>
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61 <when value="mastervar">
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62 <repeat name="varfiles" title="Variant files" min="1">
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63 <param name="input" type="data" format="cg_mastervar" label="Dataset"/>
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64 </repeat>
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65 </when>
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66 </conditional>
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67
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68 <param name="longvar" type="select" label="List long variants?">
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69 <option value="" selected="true">no</option>
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70 <option value="--list-long-variants">yes</option>
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71 </param>
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72
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73 <conditional name="include_list">
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74 <param name="listing" type="select" label="Include variant listing?">
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75 <option value="no" selected="true">no</option>
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76 <option value="yes">yes</option>
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77 </param>
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78 <when value="yes">
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79 <param name="list" type="data" format="tabular" label="Variant listing"/>
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80 </when>
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81 </conditional>
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82 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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83 </inputs>
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84
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85 <outputs>
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86 <data format="tabular" name="output" label="$fname ${tool.name} on ${on_string}"/>
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87 </outputs>
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88
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89 <help>
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90 **What it does**
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91
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92 This tool uses the cgatools listvariants to list all called variants present in the var or mastervar files.
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93
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94 **cgatools 1.7.1 Documentation**
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95
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96 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
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97
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98 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
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99
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100 **Command line reference**::
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101
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102 COMMAND NAME
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103 listvariants - Lists the variants present in a variant file.
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104
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105 DESCRIPTION
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106 Lists all called variants present in the specified variant files, in a
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107 format suitable for processing by the testvariants command. The output is a
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108 tab-delimited file consisting of the following columns:
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109
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110 variantId Sequential id assigned to each variant.
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111 chromosome The chromosome of the variant.
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112 begin 0-based reference offset of the beginning of the variant.
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113 end 0-based reference offset of the end of the variant.
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114 varType The varType as extracted from the variant file.
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115 reference The reference sequence.
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116 alleleSeq The variant allele sequence as extracted from the variant
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117 file.
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118 xRef The xRef as extrated from the variant file.
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119
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120 OPTIONS
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121 -h [ --help ]
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122 Print this help message.
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123
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124 --beta
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125 This is a beta command. To run this command, you must pass the --beta
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126 flag.
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127
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128 --reference arg
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129 The reference crr file.
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130
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131 --output arg (=STDOUT)
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132 The output file (may be omitted for stdout).
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133
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134 --variants arg
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135 The input variant files (may be positional args).
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136
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137 --variant-listing arg
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138 The output of another listvariants run, to be merged in to produce the
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139 output of this run.
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140
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141 --list-long-variants
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142 In addition to listing short variants, list longer variants as well
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143 (10's of bases) by concatenating nearby calls.
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144
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145 SUPPORTED FORMAT_VERSION
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146 0.3 or later
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147 </help>
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148 </tool>