Mercurial > repos > iuc > rgrnastar

annotate rg_rnaStar.xml @ 6:2055c2667eb3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 427913231c5894bde2b2ed428da2b8aee30bc311
author iuc
date Thu, 01 Mar 2018 11:56:28 -0500
parents 99b17b74a8cd
children a70a7eebb435
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1 <tool id="rna_star" name="RNA STAR" version="2.5.2b-2" profile="17.01">
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2 <description>Gapped-read mapper for RNA-seq data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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8 <stdio>
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9 <regex match="FATAL error" source="both" level="fatal"/>
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10 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
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11 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
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12 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
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13 </stdio>
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14
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15 <!--
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16 important quote (https://groups.google.com/forum/#!topic/rna-star/q4zGzlPgwXY):
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17 Hi Gary,
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19 if you generate the genome with GTF file, and do not specify the value for - -sjdbOverhang, it will be set to the default 100.
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20 If you want to be able to set arbitrary value of - -sjdbOverhang on the fly, you have to generate the genome without annotations (GTF) - then you supply both the - -sjdbOverhang and GTF file at the mapping step.
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22 Cheers
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23 Alex
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24 -->
1
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25 <command><![CDATA[
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26 ## Create temporary index for custom reference
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27 #if str($refGenomeSource.geneSource) == 'history':
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28 mkdir -p tempstargenomedir &&
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29 STAR
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30 --runMode genomeGenerate
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31 --genomeDir 'tempstargenomedir'
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32 --genomeFastaFiles '$refGenomeSource.genomeFastaFiles'
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33 #if $refGenomeSource.sjdbGTFfile:
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34 --sjdbGTFfile '$refGenomeSource.sjdbGTFfile'
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35 --sjdbOverhang '$refGenomeSource.sjdbOverhang'
2
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36 #end if
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37 --runThreadN \${GALAXY_SLOTS:-4}
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38 &&
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39 #end if
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40
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41 STAR
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42 --runThreadN \${GALAXY_SLOTS:-4}
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43 --genomeLoad NoSharedMemory
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44 --genomeDir
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45 #if str($refGenomeSource.geneSource) == 'history':
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46 'tempstargenomedir'
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47 #if $refGenomeSource.sjdbGTFfile:
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48 --sjdbGTFfile '$refGenomeSource.sjdbGTFfile'
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49 --sjdbOverhang '$refGenomeSource.sjdbOverhang'
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50 #end if
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51 #else
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52 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
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53 #end if
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54
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55 --readFilesIn
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56 #if str($singlePaired.sPaired) == "paired_collection"
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57 '$singlePaired.input.forward' '$singlePaired.input.reverse'
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58
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59 #if $singlePaired.input.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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60 @FASTQ_GZ_OPTION@
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61 #end if
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62 #else
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63 '$singlePaired.input1'
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64 #if str($singlePaired.sPaired) == "paired"
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65 '$singlePaired.input2'
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66 #end if
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67
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68 #if $singlePaired.input1.is_of_type("fastq.gz", "fastqsanger.gz"):
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69 @FASTQ_GZ_OPTION@
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70 #end if
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71 #end if
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72
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73 --outSAMtype BAM SortedByCoordinate
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74
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75 ## Handle difference between indices with/without annotations
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76 #if str($refGenomeSource.geneSource) == 'indexed':
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77 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
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78 #if $refGenomeSource.GTFconditional.sjdbGTFfile:
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79 --sjdbOverhang '$refGenomeSource.GTFconditional.sjdbOverhang'
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80 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
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81 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
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82 --sjdbGTFtagExonParentTranscript Parent
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83 #end if
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84 #end if
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85 #end if
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86 #end if
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87
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88 #if $quantMode:
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89 --quantMode GeneCounts
2
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90 #end if
0
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91
3
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92 ## Output parameters
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93 #if str( $output_params.output_select ) == "yes":
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94 --outSAMattributes $output_params.outSAMattributes
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95 --outSAMstrandField $output_params.outSAMstrandField
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96 --outFilterIntronMotifs $output_params.outFilterIntronMotifs
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97 #if str( $output_params.output_params2.output_select2 ) == "yes":
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98 --outSAMunmapped $output_params.output_params2.outSAMunmapped
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99 --outSAMprimaryFlag $output_params.output_params2.outSAMprimaryFlag
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100 --outSAMmapqUnique "$output_params.output_params2.outSAMmapqUnique"
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101 --outFilterType $output_params.output_params2.outFilterType
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102 --outFilterMultimapScoreRange "$output_params.output_params2.outFilterMultimapScoreRange"
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103 --outFilterMultimapNmax "$output_params.output_params2.outFilterMultimapNmax"
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104 --outFilterMismatchNmax "$output_params.output_params2.outFilterMismatchNmax"
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105 --outFilterMismatchNoverLmax "$output_params.output_params2.outFilterMismatchNoverLmax"
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106 --outFilterMismatchNoverReadLmax "$output_params.output_params2.outFilterMismatchNoverReadLmax"
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107 --outFilterScoreMin "$output_params.output_params2.outFilterScoreMin"
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108 --outFilterScoreMinOverLread "$output_params.output_params2.outFilterScoreMinOverLread"
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109 --outFilterMatchNmin "$output_params.output_params2.outFilterMatchNmin"
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110 --outFilterMatchNminOverLread "$output_params.output_params2.outFilterMatchNminOverLread"
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111 #end if
2
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112 #end if
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113
3
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114 ## Other parameters
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115 #if str( $params.settingsType ) == "star_fusion":
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116 ## Preset parameters for STAR-Fusion
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117 --outReadsUnmapped None
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118 --chimSegmentMin 12
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119 --chimJunctionOverhangMin 12
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120 --alignSJDBoverhangMin 10
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121 --alignMatesGapMax 200000
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122 --alignIntronMax 200000
6
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123 --twopassMode Basic
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124 --twopass1readsN -1
3
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125
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126 ## --chimSegmentReadGapMax 3 ## not an option in STAR 2.4.0
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127 ## --alignSJstitchMismatchNmax 5 -1 5 5 ## not an option in STAR 2.4.0
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128
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129 #elif str( $params.settingsType ) == "full":
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130 ## Extended parameter options
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131
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132 ## Seed parameter options
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133 --seedSearchStartLmax "$params.seed.seedSearchStartLmax"
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134 --seedSearchStartLmaxOverLread "$params.seed.seedSearchStartLmaxOverLread"
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135 --seedSearchLmax "$params.seed.seedSearchLmax"
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136 --seedMultimapNmax "$params.seed.seedMultimapNmax"
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137 --seedPerReadNmax "$params.seed.seedPerReadNmax"
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138 --seedPerWindowNmax "$params.seed.seedPerWindowNmax"
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139 --seedNoneLociPerWindow "$params.seed.seedNoneLociPerWindow"
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140
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141 ## Alignment parameter options
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142 --alignIntronMin "$params.align.alignIntronMin"
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143 --alignIntronMax "$params.align.alignIntronMax"
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144 --alignMatesGapMax "$params.align.alignMatesGapMax"
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145 --alignSJoverhangMin "$params.align.alignSJoverhangMin"
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146 --alignSJDBoverhangMin "$params.align.alignSJDBoverhangMin"
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147 --alignSplicedMateMapLmin "$params.align.alignSplicedMateMapLmin"
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148 --alignSplicedMateMapLminOverLmate "$params.align.alignSplicedMateMapLminOverLmate"
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149 --alignWindowsPerReadNmax "$params.align.alignWindowsPerReadNmax"
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150 --alignTranscriptsPerWindowNmax "$params.align.alignTranscriptsPerWindowNmax"
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151 --alignTranscriptsPerReadNmax "$params.align.alignTranscriptsPerReadNmax"
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152 --alignEndsType $params.align.alignEndsType
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153
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154 ## Two pass mode
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155 --twopassMode "$params.twopass.twopassMode"
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156 #if str( $params.twopass.twopassMode ) == "Basic":
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157 --twopass1readsN "$params.twopass.twopass1readsN"
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158 #end if
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159
3
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160 ## Chimeric alignment parameter options
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161 #if str( $params.chim.chim_select ) == "yes":
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162 --chimSegmentMin "$params.chim.chimSegmentMin"
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163 --chimScoreMin "$params.chim.chimScoreMin"
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164 --chimScoreDropMax "$params.chim.chimScoreDropMax"
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165 --chimScoreSeparation "$params.chim.chimScoreSeparation"
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166 --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG"
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167 --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin"
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168 #end if
5
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169
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170 ## Limits
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171 --limitBAMsortRAM "$params.limits.limitBAMsortRAM"
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172 --limitOutSJoneRead "$params.limits.limitOutSJoneRead"
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173 --limitOutSJcollapsed "$params.limits.limitOutSJcollapsed"
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174 --limitSjdbInsertNsj "$params.limits.limitSjdbInsertNsj"
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175
2
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176 #end if
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177
0
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178 ## Convert chimeric reads.
3
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179 #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0 ):
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180 &&
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181 samtools view
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182 -@ \${GALAXY_SLOTS:-4}
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183 -Shb Chimeric.out.sam |
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184
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185 samtools sort
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186 -@ \${GALAXY_SLOTS:-4} - ChimericSorted
0
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187 #end if
1
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188 ]]></command>
0
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189
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190 <inputs>
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191 <!-- FASTQ input(s) and options specifically for paired-end data. -->
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192 <conditional name="singlePaired">
2
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193 <param name="sPaired" type="select" label="Single-end or paired-end reads">
3
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194 <option value="single" selected="true">Single-end</option>
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195 <option value="paired">Paired-end (as individual datasets)</option>
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196 <option value="paired_collection">Paired-end (as collection)</option>
0
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197 </param>
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198 <when value="single">
3
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199 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file"/>
0
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200 </when>
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201 <when value="paired">
3
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202 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/>
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203 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, reverse reads"/>
2
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204 </when>
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205 <when value="paired_collection">
3
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206 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ/FASTA paired reads"/>
0
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207 </when>
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208 </conditional>
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209
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210 <!-- Genome source. -->
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211 <conditional name="refGenomeSource">
3
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212 <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
0
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213 <option value="indexed" selected="True">Use a built-in index</option>
3
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214 <option value="history">Use reference genome from history and create temporary index</option>
0
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215 </param>
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216 <when value="indexed">
3
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217 <conditional name="GTFconditional">
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218 <param name="GTFselect" type="select" label="Reference genome with or without an annotation" help="Must the index have been created WITH a GTF file (if not you can specify one afterward).">
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219 <option value="without-gtf">use genome reference without builtin gene-model</option>
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220 <option value="with-gtf">use genome reference with builtin gene-model</option>
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221 </param>
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222 <when value="with-gtf">
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223 <param name="genomeDir" argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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224 <options from_data_table="rnastar_index2">
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225 <filter type="static_value" column="4" value="1"/>
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226 <filter type="sort_by" column="2" />
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227 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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228 </options>
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229 </param>
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230 </when>
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231 <when value="without-gtf">
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232 <param argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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233 <options from_data_table="rnastar_index2">
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234 <filter type="static_value" column="4" value="0"/>
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235 <filter type="sort_by" column="2" />
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236 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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237 </options>
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238 </param>
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239
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240 <expand macro="@SJDBOPTIONS@" />
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241 </when>
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242 </conditional>
0
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243 </when>
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244 <when value="history">
3
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245 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
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246 <expand macro="@SJDBOPTIONS@" />
0
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247 </when>
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248 </conditional>
3
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249 <param argument="--quantMode" type="boolean" label="Count number of reads per gene" help="column 1: gene ID, column 2: counts for unstranded RNA-seq, column 3: counts for the 1st read strand aligned with RNA , column 4: counts for the 2nd read strand aligned with RNA. This requires either (A) an index that was built with an annotation (GTF or GFF3 file) or (B) having specified an annotation (GTF or GFF3 file above)."/>
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250
2
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251 <!-- Output parameter settings. -->
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252 <conditional name="output_params">
3
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253 <param name="output_select" type="select" label="Would you like to set output parameters (formatting and filtering)?">
2
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254 <option value="no" selected="true">No</option>
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255 <option value="yes">Yes</option>
3
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256 </param>
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257 <when value="yes">
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258 <param argument="--outSAMattributes" type="select" label="Extra SAM attributes to include" help="See &quot;Extra SAM attributes&quot; below">
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259 <option value="Standard" selected="true">Standard</option>
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260 <option value="All">All</option>
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261 <option value="None">None</option>
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262 </param>
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263 <param argument="--outSAMstrandField" type="select" label="Include strand field flag XS" help="For Cufflinks compatibility with unstranded RNA-seq data, this option is required">
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264 <option value="None" selected="true">No</option>
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265 <option value="intronMotif">Yes -- and reads with inconsistent and/or non-canonical introns are filtered out</option>
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266 </param>
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267 <param argument="--outFilterIntronMotifs" type="select" label="Filter alignments containing non-canonical junctions" help="For Cufflinks compatibility, removing alignments with non-canonical junctions is recommended">
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268 <option value="None" selected="true">No</option>
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269 <option value="RemoveNoncanonical">Remove alignments with non-canonical junctions</option>
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270 <option value="RemoveNoncanonicalUnannotated">Remove alignments with unannotated non-canonical junctions</option>
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271 </param>
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272
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273 <!-- Additional output parameter settings. -->
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274 <conditional name="output_params2">
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275 <param name="output_select2" type="select" label="Would you like to set additional output parameters (formatting and filtering)?">
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276 <option value="no" selected="true">No</option>
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277 <option value="yes">Yes</option>
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278 </param>
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279 <when value="yes">
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280 <param argument="--outSAMunmapped" type="boolean" truevalue="Within" falsevalue="None" checked="false" label="Would you like unmapped reads included in the SAM?"/>
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281 <param argument="--outSAMprimaryFlag" type="boolean" truevalue="AllBestScore" falsevalue="OneBestScore" checked="false" label="Would you like all alignments with the best score labeled primary?"/>
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282 <param argument="--outSAMmapqUnique" type="integer" value="255" min="0" max="255" label="MAPQ value for unique mappers"/>
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283 <param argument="--outFilterType" type="boolean" truevalue="BySJout" falsevalue="Normal" checked="false" label="Would you like to keep only reads that contain junctions that passed filtering?"/>
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284 <param argument="--outFilterMultimapScoreRange" type="integer" value="1" min="0" label="Score range below the maximum score for multimapping alignments"/>
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285 <param argument="--outFilterMultimapNmax" type="integer" value="10" min="1" label="Maximum number of alignments to output a read's alignment results, plus 1" help="Reads with at least this number of alignments will have no alignments output"/>
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286 <param argument="--outFilterMismatchNmax" type="integer" value="10" min="0" label="Maximum number of mismatches to output an alignment, plus 1" help="Alignments with at least this number of mismatches will not be output"/>
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287 <param argument="--outFilterMismatchNoverLmax" type="float" value="0.3" min="0" max="1" label="Maximum ratio of mismatches to mapped length" help="Alignments with a mismatch ratio of at least this value will not be output"/>
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288 <param argument="--outFilterMismatchNoverReadLmax" type="float" value="1" min="0" max="1" label="Maximum ratio of mismatches to read length" help="Alignments with a mismatch ratio of at least this value will not be output"/>
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289 <param argument="--outFilterScoreMin" type="integer" value="0" min="0" label="Minimum alignment score" help="Alignments must have scores higher than this value to be output"/>
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290 <param argument="--outFilterScoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output"/>
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291 <param argument="--outFilterMatchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output"/>
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292 <param argument="--outFilterMatchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output"/>
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293 </when>
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294 <when value="no"/>
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295 </conditional>
2
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296 </when>
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297 <when value="no"/>
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298 </conditional>
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299
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300 <!-- Other parameter settings. -->
0
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301 <conditional name="params">
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302 <param name="settingsType" type="select" label="Other parameters (seed, alignment, limits and chimeric alignment)">
3
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303 <option value="default" selected="true">Use Defaults</option>
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304 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
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305 <option value="full">Extended parameter list</option>
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306 </param>
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307 <when value="default"/>
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308 <when value="star_fusion"/><!-- Set STAR-fusion parameters automatically -->
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309
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310 <when value="full">
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311 <section name="seed" title="Seed parameters" expanded="False">
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312 <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/>
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313 <param argument="--seedSearchStartLmaxOverLread" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length"/>
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314 <param argument="--seedSearchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length"/>
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315 <param argument="--seedMultimapNmax" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching"/>
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316 <param argument="--seedPerReadNmax" type="integer" min="1" value="1000" label="Maximum number of seeds per read"/>
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317 <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/>
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318 <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/>
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319 </section>
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320
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321 <section name="align" title="Alignment parameters" expanded="False">
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322 <param argument="--alignIntronMin" name="alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
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323 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
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324 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
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325 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
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326 <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/>
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327 <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>
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328 <param argument="--alignSplicedMateMapLminOverLmate" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length"/>
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329 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
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330 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
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331 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
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332 <param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/>
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333 </section>
5
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334
6
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335 <section name="twopass" title="Two pass mode" expanded="False">
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336 <param argument="--twopassMode" type="boolean" truevalue="Basic" falsevalue="None" checked="false" label="Use two pass mode to better map reads to unknown splice junctions"/>
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337 <param argument="--twopass1readsN" type="integer" min="-1" value="-1" label="Number of reads to map in the first pass (-1: all)"/>
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338 </section>
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339
5
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340 <section name="limits" title="Limits" expanded="False">
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341 <param argument="--limitBAMsortRAM" type="integer" min="0" value="0" label="Maximum available RAM (in bytes) for sorting" help="If 0, this will be set to the genome index size. This is typically only changed in cases where an error is produced." />
6
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342 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
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343 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
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344 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
5
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345 </section>
3
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346
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347 <conditional name="chim">
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348 <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?">
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349 <option value="no" selected="true">No</option>
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350 <option value="yes">Yes</option>
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351 </param>
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352 <when value="yes">
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353 <param argument="--chimSegmentMin" type="integer" min="0" value="0" label="Minimum length of chimeric segment" help="For small numbers this will cause large number of chimeric alignments. A value of 12 is commonly used. Default of 0 means no chimeric output">
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354 <validator type="in_range" min="1" message="To get chimeric reads this value needs to be larger than 0"/>
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355 </param>
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356 <param argument="--chimScoreMin" type="integer" min="0" value="0" label="Minimum total (summed) score of chimeric segments"/>
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357 <param argument="--chimScoreDropMax" type="integer" min="0" value="20" label="Maximum difference of chimeric score from read length"/>
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358 <param argument="--chimScoreSeparation" type="integer" min="0" value="10" label="Minimum difference between the best chimeric score and the next one"/>
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359 <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1" label="Penalty for a non-GT/AG chimeric junction"/>
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360 <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20" label="Minimum overhang for a chimeric junction"/>
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361 </when>
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362 <when value="no"/>
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363 </conditional>
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364 </when>
0
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365 </conditional>
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366 </inputs>
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367
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368 <outputs>
2
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369 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
3
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370 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction">
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371 <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )</filter>
2
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372 <actions>
3
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373 <conditional name="refGenomeSource.geneSource">
2
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374 <when value="indexed">
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375 <action type="metadata" name="dbkey">
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376 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
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377 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
3
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378 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
2
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379 </option>
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380 </action>
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381 </when>
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382 <when value="history">
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383 <action type="metadata" name="dbkey">
3
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384 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
2
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385 </action>
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386 </when>
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387 </conditional>
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388 </actions>
0
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389 </data>
2
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390
3
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391 <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: chimeric.bam" from_work_dir="ChimericSorted.bam">
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392 <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )</filter>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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393 <actions>
3
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394 <conditional name="refGenomeSource.geneSource">
2
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395 <when value="indexed">
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396 <action type="metadata" name="dbkey">
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397 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
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398 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
3
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399 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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400 </option>
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401 </action>
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402 </when>
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403 <when value="history">
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404 <action type="metadata" name="dbkey">
3
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405 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
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406 </action>
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407 </when>
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408 </conditional>
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409 </actions>
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410 </data>
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411
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iuc
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412 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
413 <actions>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
414 <conditional name="refGenomeSource.geneSource">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
415 <when value="indexed">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
416 <action type="metadata" name="dbkey">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
417 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
418 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
419 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
420 </option>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
421 </action>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
422 </when>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
423 <when value="history">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
424 <action type="metadata" name="dbkey">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
425 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
426 </action>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
427 </when>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
428 </conditional>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
429 </actions>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
430 </data>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
431
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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432 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
433 <actions>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
434 <conditional name="refGenomeSource.geneSource">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
435 <when value="indexed">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
436 <action type="metadata" name="dbkey">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
437 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
438 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
439 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
440 </option>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
441 </action>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
442 </when>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
443 <when value="history">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
444 <action type="metadata" name="dbkey">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
445 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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446 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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447 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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448 </conditional>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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449 </actions>
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
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450 </data>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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451
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
452 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
453 <filter>quantMode is True</filter>
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
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454 </data>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
455 </outputs>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
456
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
457 <tests>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
458 <test>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
459 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
460 <param name="geneSource" value="history" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
461 <param name="genomeFastaFiles" value="tophat_test.fa" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
462 <param name="sPaired" value="single" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
463
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
464 <param name="output_select" value="yes" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
465 <param name="outSAMattributes" value="All" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
466 <param name="outSAMstrandField" value="intronMotif" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
467 <param name="settingsType" value="default" />
1
bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
parents: 0
diff changeset
468
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
469 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
470 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
471 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
472 </test>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
473 <test><!-- tests gtf file and GeneCounts mode -->
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
474 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
475 <param name="geneSource" value="history" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
476 <param name="genomeFastaFiles" value="tophat_test.fa" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
477
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
478 <param name="sjdbOverhang" value="75"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
479 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
480 <param name="quantMode" value="True"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
481
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
482 <param name="sPaired" value="single" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
483 <param name="output_select" value="yes" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
484 <param name="outSAMattributes" value="All" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
485 <param name="outSAMstrandField" value="intronMotif" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
486 <param name="settingsType" value="default" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
487
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
488 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
489 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
490 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
491 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt" />
1
bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
parents: 0
diff changeset
492 </test>
bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
parents: 0
diff changeset
493 <test>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
494 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
495 <param name="geneSource" value="history" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
496 <param name="genomeFastaFiles" value="tophat_test.fa" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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497 <param name="sPaired" value="single" />
1
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iuc
parents: 0
diff changeset
498
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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499 <param name="output_select" value="yes" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
500 <param name="outSAMattributes" value="All" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
501 <param name="outSAMstrandField" value="intronMotif" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
502 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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503
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
504 <param name="output_select2" value="yes" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
505 <param name="outFilterScoreMinOverLread" value="0.9" />
1
bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
parents: 0
diff changeset
506 <param name="settingsType" value="full" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
507 <param name="seed_select" value="yes" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
508 <param name="seedSearchStartLmax" value="25" />
1
bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
parents: 0
diff changeset
509
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
510 <output name="output_log" file="rnastar_test2.log" compare="diff" lines_diff="12"/>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
511 <output name="splice_junctions" file="rnastar_test2_splicejunctions.bed"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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512 <output name="mapped_reads" file="rnastar_test2_mapped_reads.bam" compare="sim_size" delta="200" />
0
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iuc
parents:
diff changeset
513 </test>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
514 <test>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
515 <param name="input1" value="test3.fastqsanger" ftype="fastqsanger" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
516 <param name="geneSource" value="history" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
517 <param name="genomeFastaFiles" value="test3.ref.fa" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
518 <param name="sPaired" value="single" />
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
519
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
520 <param name="output_select" value="yes" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
521 <param name="outSAMattributes" value="All" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
522 <param name="outSAMstrandField" value="intronMotif" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
523 <param name="settingsType" value="star_fusion" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
524
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
525 <output name="chimeric_junctions" file="test3.chimjunc.tabular"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
526 </test>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
527 <test><!-- tests fastqsanger.gz -->
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
528 <param name="input1" value="test3.fastqsanger.gz" ftype="fastqsanger.gz" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
529 <param name="geneSource" value="history" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
530 <param name="genomeFastaFiles" value="test3.ref.fa" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
531 <param name="sPaired" value="single" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
532
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
533 <param name="output_select" value="yes" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
534 <param name="outSAMattributes" value="All" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
535 <param name="outSAMstrandField" value="intronMotif" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
536 <param name="settingsType" value="star_fusion" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
537
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
538 <output name="chimeric_junctions" file="test3.chimjunc.tabular"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
539 </test>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
540 <test>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
541 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
542 <param name="geneSource" value="history" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
543 <param name="genomeFastaFiles" value="tophat_test.fa" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
544 <param name="sPaired" value="single" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
545
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
546 <param name="output_select" value="yes" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
547 <param name="outSAMattributes" value="All" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
548 <param name="outSAMstrandField" value="intronMotif" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
549 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
550
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
551 <param name="output_select2" value="yes" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
552 <param name="settingsType" value="full" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
553 <param name="chim_select" value="false" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
554
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
555 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
556 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
557 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
558 </test>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
559 </tests>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
560 <help>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
561 **What it does**
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
562
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
563 STAR is an ultrafast universal RNA-seq aligner.
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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diff changeset
564
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
565 **Extra SAM attributes**
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
566
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
567 The Standard option includes the following four attributes::
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
568
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
569 NH: Number of reported alignments that contain the query in the current record.
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
570 HI: Query hit index, indicating the alignment record is the i-th one stored in SAM
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
571 AS: Local alignment score (paired for paired-end reads)
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
572 nM: Number of mismatches per (paired) alignment
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
573
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
574 The All option includes the Standard attributes, plus the following four::
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
575
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
576 NM: Edit distance to the reference, including ambiguous bases but excluding clipping
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
577 MD: String for mismatching positions
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
578 jM: Intron motifs for all junctions
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
579 jI: Start and end of introns for all junctions
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
580
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
581 **STAR-Fusion**
0
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582
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583 STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running
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584 STAR prior to STAR-Fusion can be pre-selected, with the following exceptions::
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586 --chimSegmentReadGapMax 3 # not an option in STAR 2.4.0
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587 --alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0
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589 **Attributions**
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590
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591 rna_star - see the web site at rna_star_
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593 For details, please see the rna_starMS_
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594 "STAR: ultrafast universal RNA-seq aligner"
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595 A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635
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596
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597 Galaxy_ (that's what you are using right now!) for gluing everything together
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598
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599 Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper
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601 Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies
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602 and odds and ends of other code and documentation comprising this tool was
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603 written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts
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605 .. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml
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606 .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
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607 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
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608 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs
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609 .. _rna_star: https://github.com/alexdobin/STAR
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610 .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full
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611 .. _Galaxy: http://getgalaxy.org
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612 </help>
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613 <expand macro="citations"/>
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614 </tool>