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1 <tool id="gatk_realigner_target_creator" name="Realigner Target Creator" version="0.0.4">
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2 <description>for use in local realignment</description>
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3 <requirements>
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4 <requirement type="package" version="1.4">gatk</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 </requirements>
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7 <macros>
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8 <import>gatk_macros.xml</import>
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9 </macros>
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10 <command interpreter="python">gatk_wrapper.py
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11 --max_jvm_heap_fraction "1"
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12 --stdout "${output_log}"
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13 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
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14 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
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15 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
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16 #end if
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17 -p 'java
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18 -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar"
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19 -T "RealignerTargetCreator"
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20 -o "${output_interval}"
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21 -et "NO_ET" ##ET no phone home
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22 --num_threads \${GALAXY_SLOTS:-4}
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23 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
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24 #if $reference_source.reference_source_selector != "history":
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25 -R "${reference_source.ref_file.fields.path}"
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26 #end if
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27 '
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28 #set $rod_binding_names = dict()
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29 #for $rod_binding in $rod_bind:
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30 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
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31 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
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32 #else
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33 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
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34 #end if
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35 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
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36 -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
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37 #end for
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38
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39 #include source=$standard_gatk_options#
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40 ##start analysis specific options
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41 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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42 -p '
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43 --minReadsAtLocus "${analysis_param_type.minReadsAtLocus}"
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44 --windowSize "${analysis_param_type.windowSize}"
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45 --mismatchFraction "${analysis_param_type.mismatchFraction}"
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46 --maxIntervalSize "${analysis_param_type.maxIntervalSize}"
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47 '
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48 #end if
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49 </command>
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50 <inputs>
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51 <conditional name="reference_source">
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52 <expand macro="reference_source_selector_param" />
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53 <when value="cached">
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54 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;">
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55 <validator type="unspecified_build" />
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56 <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
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57 </param>
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58 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;" >
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59 <options from_data_table="gatk_picard_indexes">
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60 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
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61 </options>
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62 <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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63 </param>
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64 </when>
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65 <when value="history">
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66 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" />
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67 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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68 <options>
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69 <filter type="data_meta" key="dbkey" ref="input_bam" />
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70 </options>
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71 </param>
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72 </when>
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73 </conditional>
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74
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75 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-known,--known &lt;known&gt;">
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76 <conditional name="rod_bind_type">
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77 <param name="rod_bind_type_selector" type="select" label="Binding Type">
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78 <option value="dbsnp" selected="True">dbSNP</option>
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79 <option value="snps">SNPs</option>
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80 <option value="indels">INDELs</option>
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81 <option value="custom">Custom</option>
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82 </param>
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83 <when value="dbsnp">
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84 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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85 </when>
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86 <when value="snps">
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87 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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88 </when>
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89 <when value="indels">
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90 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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91 </when>
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92 <when value="custom">
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93 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
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94 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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95 </when>
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96 </conditional>
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97 </repeat>
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98
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99 <expand macro="gatk_param_type_conditional" />
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100
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101 <expand macro="analysis_type_conditional">
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102 <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" help="-window,--windowSize &lt;windowSize&gt;" />
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103 <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to <= 0 or > 1 (-mismatch,--mismatchFraction &lt;mismatchFraction&gt;)"/>
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104 <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" help="-minReads,--minReadsAtLocus &lt;minReadsAtLocus&gt;" />
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105 <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &lt;maxIntervalSize&gt;" />
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106 </expand>
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107 </inputs>
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108 <outputs>
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109 <data format="gatk_interval" name="output_interval" label="${tool.name} on ${on_string} (GATK intervals)" />
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110 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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111 </outputs>
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112 <tests>
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113 <test>
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114 <param name="reference_source_selector" value="history" />
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115 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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116 <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" />
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117 <param name="rod_bind_type_selector" value="dbsnp" />
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118 <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
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119 <param name="gatk_param_type_selector" value="basic" />
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120 <param name="analysis_param_type_selector" value="advanced" />
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121 <param name="windowSize" value="10" />
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122 <param name="mismatchFraction" value="0.15" />
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123 <param name="minReadsAtLocus" value="4" />
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124 <param name="maxIntervalSize" value="500" />
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125 <output name="output_interval" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" />
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126 <output name="output_log" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains" compare="contains"/>
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127 </test>
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128 </tests>
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129 <help>
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130 **What it does**
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131
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132 Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string.
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133
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134 For more information on local realignment around indels using the GATK, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels>`_.
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135
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136 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_.
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137
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138 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_.
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139
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140 ------
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141
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142 **Inputs**
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143
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144 GenomeAnalysisTK: RealignerTargetCreator accepts an aligned BAM input file.
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145
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146
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147 **Outputs**
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148
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149 The output is in GATK Interval format.
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150
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151
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152 Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats.
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153
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154 -------
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155
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156 **Settings**::
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157
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158 windowSize window size for calculating entropy or SNP clusters
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159 mismatchFraction fraction of base qualities needing to mismatch for a position to have high entropy; to disable set to <= 0 or > 1
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160 minReadsAtLocus minimum reads at a locus to enable using the entropy calculation
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161 maxIntervalSize maximum interval size
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162
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163 @CITATION_SECTION@
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164 </help>
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165 </tool>
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