Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate tools/cgatools17/snpdiff_v17.xml @ 14:59a2f9ad76dd draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 4df562cd801221f33652de8b8b4dbbf41deea8ea-dirty
author yhoogstrate
date Tue, 17 Nov 2015 04:43:00 -0500
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1
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1 <tool id="cg_snpdiff" name="SNPDiff" version="1.7.1">
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2
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3 <description>compares snp calls to a Complete Genomics variant file.</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>
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10 cgatools | head -1;
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11 cgatools snpdiff
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12 --reference ${crr.fields.crr_path}
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13 --variants $varfile
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14 --genotypes $genotype
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15 --output-prefix cg_
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16 --reports `echo ${report1} ${report2} ${report3} | sed 's/ */,/g'`
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17 </command>
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18
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19 <inputs>
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20 <param name="crr" type="select" label="Reference build">
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21 <options from_data_table="cg_anno_files" />
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22 </param>
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23 <param name="varfile" type="data" format="cg_var" label="Var file"/>
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24
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25 <param name="genotype" type="data" format="tabular" label="Genotypes file with SNP calls" help="The genotypes file is a tab-delimited file with at least the following columns (additional columns may be given): Chromosome (Required), Offset0Based (Required), GenotypesStrand (Optional), Genotypes (Optional)"/>
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26
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27 <param name="report1" type="select" label="Create report Output">
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28 <option value="">no</option>
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29 <option value="Output">yes</option>
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30 </param>
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31 <param name="report2" type="select" label="Create report Verbose">
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32 <option value="">no</option>
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33 <option value="Verbose">yes</option>
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34 </param>
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35 <param name="report3" type="select" label="Create report Stats">
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36 <option value="">no</option>
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37 <option value="Stats">yes</option>
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38 </param>
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39 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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40 </inputs>
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41
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42 <outputs>
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43 <data format="tabular" name="output1" from_work_dir="cg_Output.tsv" label="$fname ${tool.name} on ${on_string}: Output">
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44 <filter>(report1 == 'Output')</filter>
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45 </data>
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46 <data format="tabular" name="output2" from_work_dir="cg_Verbose.tsv" label="$fname ${tool.name} on ${on_string}: Verbose">
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47 <filter>(report2 == 'Verbose')</filter>
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48 </data>
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49 <data format="tabular" name="output3" from_work_dir="cg_Stats.tsv" label="$fname ${tool.name} on ${on_string}: Stats">
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50 <filter>(report3 == 'Stats')</filter>
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51 </data>
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52 </outputs>
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53 <help>
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54 **What it does**
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55
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56 This tool ompares snp calls to a Complete Genomics variant file.
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57
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58 **cgatools 1.7.1 Documentation**
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59
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60 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
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61
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62 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
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63
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64 **Command line reference**::
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65
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66 COMMAND NAME
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67 snpdiff - Compares snp calls to a Complete Genomics variant file.
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68
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69 DESCRIPTION
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70 Compares the snp calls in the "genotypes" file to the calls in a Complete
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71 Genomics variant file. The genotypes file is a tab-delimited file with at
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72 least the following columns (additional columns may be given):
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73
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74 Chromosome (Required) The name of the chromosome.
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75 Offset0Based (Required) The 0-based offset in the chromosome.
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76 GenotypesStrand (Optional) The strand of the calls in the Genotypes
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77 column (+ or -, defaults to +).
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78 Genotypes (Optional) The calls, one per allele. The following
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79 calls are recognized:
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80 A,C,G,T A called base.
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81 N A no-call.
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82 - A deleted base.
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83 . A non-snp variation.
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84
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85 The output is a tab-delimited file consisting of the columns of the
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86 original genotypes file, plus the following additional columns:
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87
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88 Reference The reference base at the given position.
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89 VariantFile The calls made by the variant file, one per allele.
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90 The character codes are the same as is described for
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91 the Genotypes column.
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92 DiscordantAlleles (Only if Genotypes is present) The number of
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93 Genotypes alleles that are discordant with calls in
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94 the VariantFile. If the VariantFile is described as
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95 haploid at the given position but the Genotypes is
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96 diploid, then each genotype allele is compared
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97 against the haploid call of the VariantFile.
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98 NoCallAlleles (Only if Genotypes is present) The number of
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99 Genotypes alleles that were no-called by the
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100 VariantFile. If the VariantFile is described as
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101 haploid at the given position but the Genotypes is
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102 diploid, then a VariantFile no-call is counted twice.
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103
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104 The verbose output is a tab-delimited file consisting of the columns of the
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105 original genotypes file, plus the following additional columns:
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106
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107 Reference The reference base at the given position.
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108 VariantFile The call made by the variant file for one allele (there is
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109 a line in this file for each allele). The character codes
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110 are the same as is described for the Genotypes column.
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111 [CALLS] The rest of the columns are pasted in from the VariantFile,
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112 describing the variant file line used to make the call.
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113
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114 The stats output is a comma-separated file with several tables describing
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115 the results of the snp comparison, for each diploid genotype. The tables
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116 all describe the comparison result (column headers) versus the genotype
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117 classification (row labels) in different ways. The "Locus classification"
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118 tables have the most detailed match classifications, while the "Locus
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119 concordance" tables roll these match classifications up into "discordance"
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120 and "no-call". A locus is considered discordant if it is discordant for
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121 either allele. A locus is considered no-call if it is concordant for both
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122 alleles but has a no-call on either allele. The "Allele concordance"
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123 describes the comparison result on a per-allele basis.
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124
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125 OPTIONS
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126 -h [ --help ]
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127 Print this help message.
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128
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129 --reference arg
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130 The input crr file.
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131
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132 --variants arg
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133 The input variant file.
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134
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135 --genotypes arg
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136 The input genotypes file.
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137
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138 --output-prefix arg
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139 The path prefix for all output reports.
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140
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141 --reports arg (=Output,Verbose,Stats)
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142 Comma-separated list of reports to generate. A report is one of:
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143 Output The output genotypes file.
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144 Verbose The verbose output file.
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145 Stats The stats output file.
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146
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147 SUPPORTED FORMAT_VERSION
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148 0.3 or later
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149 </help>
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150 </tool>