Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate tools/cgatools17/testvariants_v17.xml @ 14:59a2f9ad76dd draft

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author yhoogstrate
date Tue, 17 Nov 2015 04:43:00 -0500
parents ff641b41735f
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1 <tool id="cg_testvariants" name="TestVariants" version="1.7.1.b">
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2 <description>Test for the presence of variants</description>
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4 <requirements>
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5 <requirement type="package" version="1">cgatools17</requirement>
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6 </requirements>
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8 <version_command>cgatools | head -1</version_command>
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10 <command>
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11 cgatools testvariants
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12 --beta
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13 --reference
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14
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15 #if $reference_gene_sets_source.source_select == "indexed_filtered"
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16 ${reference_gene_sets_source.crr.fields.crr_path}
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17 #else if $reference_gene_sets_source.source_select == "history"
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18 ${reference_gene_sets_source.crr}
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19 #end if
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21 --output $output
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22 --input $listing
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23 --variants
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24 #for $v in $file_types.varfiles <!--get each var/mastervar file-->
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25 ${v.input}
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26 #end for
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27 </command>
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29 <inputs>
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30 <!--form field to select crr file-->
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31
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32 <conditional name="reference_gene_sets_source">
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33 <param name="source_select" type="select" label="GFF/GTF Source">
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34 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
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35 <option value="history">Use reference from the history</option>
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36 </param>
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37 <when value="indexed_filtered">
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38 <param name="crr" type="select" label="Reference Build">
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39 <options from_data_table="cg_anno_files" />
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40 </param>
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41 </when>
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42 <when value="history">
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43 <param name="crr" format="crr" type="data" label="Reference build" help="In crr format (you can use fasta2crr for conversion)" />
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44 </when>
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45 </conditional>
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46
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47 <!--form fields to select variant list-->
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48 <param name="listing" type="data" format="tabular" label="Select variant list"/>
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49
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50 <!--conditional to select input file type-->
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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">
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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">
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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 <!-- prefix for output file so you dont have to manually rename history items -->
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69 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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70 </inputs>
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71
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72
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73 <outputs>
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74 <data format="tabular" name="output" label="$fname ${tool.name} on ${on_string}"/>
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75 </outputs>
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76
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77 <help>
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78 **What it does**
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79
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80 This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants.
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81
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82 **cgatools 1.7.1 Documentation**
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83
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84 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
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85
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86 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
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87
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88 **Command line reference**::
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89
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90 COMMAND NAME
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91 testvariants - Tests variant files for presence of variants.
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92
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93 DESCRIPTION
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94 Tests variant files for presence of variants. The output is a tab-delimited
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95 file consisting of the columns of the input variants file, plus a column
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96 for each assembly results file that contains a character code for each
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97 allele. The character codes have meaning as follows:
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98
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99 0 This allele of this genome is consistent with the reference at this
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100 locus but inconsistent with the variant.
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101 1 This allele of this genome has the input variant at this locus.
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102 N This allele of this genome has no-calls but is consistent with the
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103 input variant.
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104
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105 OPTIONS
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106 -h [ --help ]
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107 Print this help message.
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108
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109 --beta
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110 This is a beta command. To run this command, you must pass the --beta
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111 flag.
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112
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113 --reference arg
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114 The reference crr file.
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115
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116 --input arg (=STDIN)
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117 The input variants to test for.
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118
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119 --output arg (=STDOUT)
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120 The output file (may be omitted for stdout).
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121
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122 --variants arg
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123 The input variant files (may be passed in as arguments at the end of
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124 the command).
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125
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126 SUPPORTED FORMAT_VERSION
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127 0.3 or later
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128 </help>
1
3a2e0f376f26 Minor change to tv2vcf.xml to allow for workflow automation
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129 </tool>