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annotate gatk.xml @ 0:b80ff7f43ad1 draft default tip

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planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
author avowinkel
date Thu, 24 Sep 2015 12:10:01 -0400
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b80ff7f43ad1 planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="gatk" name="GATK" version="@VERSION@.d9">
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3 <description>tool collection Version @VERSION@</description>
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4 <macros>
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5 <import>gatk_macros.xml</import>
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6 <import>realigner_target_creator.xml</import>
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7 <import>indel_realigner.xml</import>
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8 <import>base_recalibrator.xml</import>
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9 <import>analyze_covariates.xml</import>
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10 <import>print_reads.xml</import>
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11 <import>haplotype_caller.xml</import>
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12 <import>genotype_gvcfs.xml</import>
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13 <import>combine_gvcfs.xml</import>
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14 <import>combine_variants.xml</import>
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15 </macros>
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16 <expand macro="requirements"/>
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17 <stdio>
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18 <regex match="^INFO" level="log"/>
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19 <regex match="^WARN" level="warning"/>
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20 <regex match="Using .* implementation of PairHMM" level="warning"/>
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21 <regex match="There is insufficient memory for the Java Runtime Environment to continue" level="fatal"/>
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22 <regex match="^##### ERROR" level="fatal"/>
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23 <exit_code range="1:" level="fatal"/>
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24 </stdio>
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25 <command><![CDATA[
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26 ############################
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27 ## import analysis specific preprocessings by using cheetahs internal searchList
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28 ## if not defined, ignore
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29 ############################
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30 #if $analysis_type.analysis_type_selector + "Preprocessing" in vars()['SL'][2]
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31 #set $analysisPreprocessing = vars()['SL'][2][$analysis_type.analysis_type_selector + "Preprocessing"]
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32 #include source=$analysisPreprocessing
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33 #end if
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34
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35 ############################
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36 ## GATK tool unspecific options
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37 ############################
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38 @GATK_EXEC@
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39
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40 --analysis_type ${analysis_type.analysis_type_selector}
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41 --reference_sequence ${ref_file.fields.path}
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42
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43 --log_to_file ${output_log}
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44
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45 #if $cond_intervals.cond_intervals_enabled
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46 #for $interval in $cond_intervals.intervals:
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47 --intervals ${interval.L}
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48 #end for
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49 #end if
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50
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51 #if $cond_BQSR.cond_BQSR_enabled
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52 --BQSR $cond_BQSR.BQSR
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53 #end if
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54
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55 ############################
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56 ## import analysis specific options by using cheetahs internal searchList
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57 ## if not defined throw raw python error until better idea
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58 ############################
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59 #if $analysis_type.analysis_type_selector + "Options" in vars()['SL'][2]
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60 #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"]
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61 #include source=$analysisOptions
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62 #else
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63 #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"]
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64 #end if
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65
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66 ############################
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67 ## only put ERROR or FATAL log messages into stderr
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68 ## but keep full log for printing into log file
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69 ############################
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70 2>&1 | awk '\$1 != "INFO" && \$1 != "WARN"' >&2
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71 ]]></command>
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72 <inputs>
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73 <param name="ref_file" type="select" label="Using reference genome" help="-R,‑‑reference_sequence &amp;lt;reference_sequence&amp;gt;">
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74 <options from_data_table="picard_indexes"/>
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75 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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76 </param>
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77 <conditional name="cond_intervals">
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78 <param name="cond_intervals_enabled" type="boolean" label="Select interval subset to operate on?"/>
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79 <when value="true">
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80 <repeat name="intervals" title="genomic interval over which to operate" help="-L,‑‑intervals &amp;lt;intervals&amp;gt;">
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81 <param name="L" type="text" value=""/>
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82 </repeat>
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83 </when>
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84 <when value="false"/>
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85 </conditional>
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86 <conditional name="cond_BQSR">
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87 <param name="cond_BQSR_enabled" type="boolean" label="Select covariates for on-the-fly recalibration?"/>
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88 <when value="true">
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89 <param name="BQSR" type="data" format="tabular" label="Input covariates table file for on-the-fly base quality score recalibration" help="-BQSR,‑‑BQSR &amp;lt;BQSR&amp;gt; intended primarily for use with BaseRecalibrator and PrintReads"/>
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90 </when>
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91 <when value="false"/>
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92 </conditional>
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93 <conditional name="cond_threads">
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94 <param name="cond_threads_enabled" type="boolean" label="Set computational options (cpu, mem)?"/>
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95 <when value="true">
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96 <param name="nt" type="integer" value="1" label="Number of data threads to allocate to this analysis" help="make sure, the option is available for the chosen tool"/>
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97 <param name="nct" type="integer" value="1" label="Number of CPU threads to allocate per data thread" help="make sure, the option is available for the chosen tool"/>
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98 <param name="mem" type="integer" value="0" label="Overwrite Memory in MB (0 = don't overwrite)" help="Overwrites all other defaults and might lead to crash the run. States mem per data thread"/>
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99 </when>
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100 <when value="false"/>
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101 </conditional>
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102 <conditional name="analysis_type">
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103 <param name="analysis_type_selector" type="select" label="Analysis Type">
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104 <option value="RealignerTargetCreator">RealignerTargetCreator</option>
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105 <option value="IndelRealigner">IndelRealigner</option>
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106 <option value="BaseRecalibrator">BaseRecalibrator</option>
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107 <option value="AnalyzeCovariates">AnalyzeCovariates</option>
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108 <option value="PrintReads">PrintReads</option>
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109 <option value="HaplotypeCaller">HaplotypeCaller</option>
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110 <option value="GenotypeGVCFs">GenotypeGVCFs</option>
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111 <option value="CombineGVCFs">CombineGVCFs</option>
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112 <option value="CombineVariants">CombineVariants</option>
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113 </param>
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114 <when value="RealignerTargetCreator">
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115 <expand macro="RealignerTargetCreatorParameters" tag="rtc"/>
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116 </when>
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117 <when value="IndelRealigner">
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118 <expand macro="IndelRealignerParameters" tag="ir"/>
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119 </when>
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120 <when value="BaseRecalibrator">
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121 <expand macro="BaseRecalibratorParameters" tag="br"/>
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122 </when>
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123 <when value="AnalyzeCovariates">
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124 <expand macro="AnalyzeCovariatesParameters" tag="ac"/>
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125 </when>
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126 <when value="PrintReads">
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127 <expand macro="PrintReadsParameters" tag="pr"/>
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128 </when>
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129 <when value="HaplotypeCaller">
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130 <expand macro="HaplotypeCallerParameters" tag="hc"/>
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131 </when>
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132 <when value="GenotypeGVCFs">
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133 <expand macro="GenotypeGVCFsParameters" tag="gg"/>
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134 </when>
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135 <when value="CombineGVCFs">
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136 <expand macro="CombineGVCFsParameters" tag="cg"/>
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137 </when>
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138 <when value="CombineVariants">
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139 <expand macro="CombineVariantsParameters" tag="cv"/>
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140 </when>
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141 </conditional>
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142 </inputs>
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143 <outputs>
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144 <expand macro="RealignerTargetCreatorOutput" tag="rtc">
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145 <filter>analysis_type['analysis_type_selector'] == 'RealignerTargetCreator'</filter>
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146 </expand>
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147 <expand macro="IndelRealignerOutput" tag="ir">
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148 <filter>analysis_type['analysis_type_selector'] == 'IndelRealigner'</filter>
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149 </expand>
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150 <expand macro="BaseRecalibratorOutput" tag="br">
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151 <filter>analysis_type['analysis_type_selector'] == 'BaseRecalibrator'</filter>
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152 </expand>
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153 <expand macro="AnalyzeCovariatesOutput" tag="ac">
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154 <filter>analysis_type['analysis_type_selector'] == 'AnalyzeCovariates'</filter>
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155 </expand>
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156 <expand macro="PrintReadsOutput" tag="pr">
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157 <filter>analysis_type['analysis_type_selector'] == 'PrintReads'</filter>
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158 </expand>
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159 <expand macro="HaplotypeCallerOutput" tag="hc">
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160 <filter>analysis_type['analysis_type_selector'] == 'HaplotypeCaller'</filter>
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161 </expand>
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162 <expand macro="GenotypeGVCFsOutput" tag="gg">
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163 <filter>analysis_type['analysis_type_selector'] == 'GenotypeGVCFs'</filter>
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164 </expand>
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165 <expand macro="CombineGVCFsOutput" tag="cg">
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166 <filter>analysis_type['analysis_type_selector'] == 'CombineGVCFs'</filter>
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167 </expand>
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168 <expand macro="CombineVariantsOutput" tag="cv">
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169 <filter>analysis_type['analysis_type_selector'] == 'CombineVariants'</filter>
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170 </expand>
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171 <data format="txt" name="output_log" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (log)"/>
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172 </outputs>
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173 <expand macro="macro_tests"/>
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174 <citations>
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175 <citation type="doi">10.1101/gr.107524.110</citation>
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176 <citation type="doi">10.1038/ng.806</citation>
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177 <citation type="doi">10.1002/0471250953.bi1110s43</citation>
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178 </citations>
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179 </tool>