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annotate gatk_macros.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 <macros>
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2
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package">gatk</requirement>
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6 <requirement type="set_environment">GATK_PATH</requirement>
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7 <requirement type="set_environment">GATK_SITE_OPTIONS</requirement>
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8 <requirement type="package" version="3.1.2.1">package_r_for_gatk_3_4_0</requirement>
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9 </requirements>
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10 </xml>
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11
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12 <xml name="version_command">
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13 <version_command><![CDATA[ @GATK_EXEC@ --help|grep '^The Genome' ]]></version_command>
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14 </xml>
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15
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16 <token name="@VERSION@">3.4-0</token>
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17 <token name="@OUTPUT_NAME_PREFIX@">${tool.name} - ${analysis_type.analysis_type_selector}</token>
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18 <token name="@GATK_EXEC@">
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19 <![CDATA[
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20 #if $cond_threads.cond_threads_enabled:
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21 #if int($cond_threads.nct) > 1:
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22 THREAD_STRING="-nct $cond_threads.nct" &&
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23 #end if
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24 #if int($cond_threads.nt) > 1:
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25 THREAD_STRING=$THREAD_STRING" -nt $cond_threads.nt" &&
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26 #end if
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27 #if int($cond_threads.mem) > 0:
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28 GATK_MEM=$cond_threads.mem &&
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29 #end if
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30 #end if
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31 java -Xmx\${GATK_MEM:-\${SLURM_MEM_PER_NODE:-4096}}M -jar "\$GATK_PATH/GenomeAnalysisTK.jar" \${THREAD_STRING:-}
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32 ]]>
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33 </token>
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34
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35 <xml name="macro_vcf_input" tokens="tag">
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36 <param name="input" type="data" format="vcf" multiple="true" label="Variant files (VCF format)" help="-V, &#8209;&#8209;variant">
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37 <validator type="unspecified_build" />
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38 <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." />
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39 </param>
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40 </xml>
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41 <token name="@token_vcf_input_pre@" tokens="tag">
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42 <![CDATA[
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43 ############################
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44 ## create links to gVCF input files with correct extensions
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45 ############################
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46 #for $i, $variant in enumerate($analysis_type.input):
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47 ln -s -f ${variant} variant_${i}.vcf &&
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48 #end for
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49 ]]>
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50 </token>
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51 <token name="@token_vcf_input@">
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52 <![CDATA[
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53 #for $i, $variant in enumerate($analysis_type.input):
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54 --variant variant_${i}.vcf
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55 #end for
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56 @token_reference_input@
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57 ]]>
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58 </token>
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59
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60
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61 <xml name="macro_gvcf_input" tokens="tag">
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62 <param name="input" type="data" format="vcf" multiple="true" label="Variant files (gVCF format)" help="-V, &#8209;&#8209;variant">
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63 <validator type="unspecified_build" />
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64 <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." />
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65 </param>
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66 </xml>
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67 <token name="@token_gvcf_input_pre@" tokens="tag">
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68 <![CDATA[
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69 ############################
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70 ## create links to gVCF input files with correct extensions
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71 ############################
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72 #for $i, $variant in enumerate($analysis_type.input):
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73 ln -s -f ${variant} variant_${i}.g.vcf &&
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74 #end for
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75 ]]>
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76 </token>
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77 <token name="@token_gvcf_input@">
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78 <![CDATA[
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79 #for $i, $variant in enumerate($analysis_type.input):
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80 --variant variant_${i}.g.vcf
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81 #end for
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82 @token_reference_input@
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83 ]]>
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84 </token>
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85
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86 <xml name="macro_bam_input">
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87 <conditional name="cond_bam_input">
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88 <param name="all_in_one" type="boolean" value="false" label="Input all BAM files in a single command" />
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89 <when value="true">
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90 <param name="input" type="data" format="bam" multiple="true" label="Input file containing sequence data (BAM)" help="-I, ‑‑input_file">
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91 <validator type="unspecified_build"/>
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92 <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build."/>
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93 </param>
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94 </when>
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95 <when value="false">
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96 <param name="input" type="data" format="bam" label="Input file containing sequence data (BAM)" help="-I, ‑‑input_file">
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97 <validator type="unspecified_build"/>
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98 <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build."/>
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99 </param>
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100 </when>
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101 </conditional>
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102 </xml>
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103 <token name="@token_bam_input_pre@">
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104 <![CDATA[
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105 ############################
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106 ## create links to bam input files with correct extensions
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107 ############################
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108 #if $analysis_type.cond_bam_input.all_in_one
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109 #for $i, $bam in enumerate($analysis_type.cond_bam_input.input):
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110 ln -s -f ${bam} input_${i}.bam &&
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111 ln -s -f ${bam.metadata.bam_index} input_${i}.bam.bai &&
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112 #end for
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113 #else
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114 ln -s -f ${analysis_type.cond_bam_input.input} input.bam &&
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115 ln -s -f ${analysis_type.cond_bam_input.input.metadata.bam_index} input.bam.bai &&
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116 #end if
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117 ]]>
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118 </token>
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119 <token name="@token_bam_input@">
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120 <![CDATA[
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121 #if $analysis_type.cond_bam_input.all_in_one
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122 #for $i, $bam in enumerate($analysis_type.cond_bam_input.input):
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123 --input_file input_${i}.bam
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124 #end for
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125 #else
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126 --input_file input.bam
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127 #end if
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128 @token_reference_input@
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129 ]]>
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130 </token>
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131
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132 <token name="@token_reference_input@">
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133 <![CDATA[
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134 ]]>
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135 </token>
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136 <xml name="macro_input" tokens="tag">
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137 <yield />
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138 </xml>
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139
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140 <xml name="macro_optional_parameters">
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141 <conditional name="optional_parameters">
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142 <param name="optional_parameters_enabled" type="boolean" label="Configure Optional Parameters" />
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143 <when value="true">
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144 <yield />
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145 </when>
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146 <when value="false" />
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147 </conditional>
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148 </xml>
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149
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150 <xml name="macro_advanced_parameters">
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151 <conditional name="advanced_parameters">
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152 <param name="advanced_parameters_enabled" type="boolean" label="Configure Advanced Parameters" />
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153 <when value="true">
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154 <yield />
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155 </when>
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156 <when value="false" />
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157 </conditional>
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158 </xml>
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159
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160 <xml name="macro_tests">
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161 <tests>
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162
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163 </tests>
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164 </xml>
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165
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166 </macros>