Mercurial > repos > iuc > rgrnastar

annotate rg_rnaStar.xml @ 5:99b17b74a8cd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf
author iuc
date Thu, 12 Oct 2017 04:59:08 -0400
parents 318b2a9d54dd
children 2055c2667eb3
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1 <tool id="rna_star" name="RNA STAR" version="2.5.2b-1" profile="17.01">
0
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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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0
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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 '$refGenomeSource.sjdbOverhang'
2
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36 #end if
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37 --runThreadN \${GALAXY_SLOTS:-4}
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38 &&
0
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39 #end if
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40
3
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41 STAR
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42 --runThreadN \${GALAXY_SLOTS:-4}
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43 --genomeLoad NoSharedMemory
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44 --genomeDir
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45 #if str($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
3
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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 $singlePaired.input1.is_of_type("fastq.gz", "fastqsanger.gz"):
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69 @FASTQ_GZ_OPTION@
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70 #end if
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71 #end if
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72
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73 --outSAMtype BAM SortedByCoordinate
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74
3
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75 ## Handle difference between indices with/without annotations
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76 #if str($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
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123
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124 ## --twopass1readsN 100000000
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125 ## --chimSegmentReadGapMax 3 ## not an option in STAR 2.4.0
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126 ## --alignSJstitchMismatchNmax 5 -1 5 5 ## not an option in STAR 2.4.0
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127
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128 #elif str( $params.settingsType ) == "full":
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129 ## Extended parameter options
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130
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131 ## Seed parameter options
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132 --seedSearchStartLmax "$params.seed.seedSearchStartLmax"
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133 --seedSearchStartLmaxOverLread "$params.seed.seedSearchStartLmaxOverLread"
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134 --seedSearchLmax "$params.seed.seedSearchLmax"
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135 --seedMultimapNmax "$params.seed.seedMultimapNmax"
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136 --seedPerReadNmax "$params.seed.seedPerReadNmax"
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137 --seedPerWindowNmax "$params.seed.seedPerWindowNmax"
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138 --seedNoneLociPerWindow "$params.seed.seedNoneLociPerWindow"
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139
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140 ## Alignment parameter options
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141 --alignIntronMin "$params.align.alignIntronMin"
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142 --alignIntronMax "$params.align.alignIntronMax"
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143 --alignMatesGapMax "$params.align.alignMatesGapMax"
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144 --alignSJoverhangMin "$params.align.alignSJoverhangMin"
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145 --alignSJDBoverhangMin "$params.align.alignSJDBoverhangMin"
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146 --alignSplicedMateMapLmin "$params.align.alignSplicedMateMapLmin"
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147 --alignSplicedMateMapLminOverLmate "$params.align.alignSplicedMateMapLminOverLmate"
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148 --alignWindowsPerReadNmax "$params.align.alignWindowsPerReadNmax"
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149 --alignTranscriptsPerWindowNmax "$params.align.alignTranscriptsPerWindowNmax"
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150 --alignTranscriptsPerReadNmax "$params.align.alignTranscriptsPerReadNmax"
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151 --alignEndsType $params.align.alignEndsType
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152
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153 ## Chimeric alignment parameter options
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154 #if str( $params.chim.chim_select ) == "yes":
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155 --chimSegmentMin "$params.chim.chimSegmentMin"
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156 --chimScoreMin "$params.chim.chimScoreMin"
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157 --chimScoreDropMax "$params.chim.chimScoreDropMax"
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158 --chimScoreSeparation "$params.chim.chimScoreSeparation"
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159 --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG"
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160 --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin"
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161 #end if
5
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162
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163 ## Limits
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164 --limitBAMsortRAM "$params.limits.limitBAMsortRAM"
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165 --limitOutSJoneRead "$params.limits.limitOutSJoneRead"
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166 --limitOutSJcollapsed "$params.limits.limitOutSJcollapsed"
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167 --limitSjdbInsertNsj "$params.limits.limitSjdbInsertNsj"
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168
2
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169 #end if
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170
0
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171 ## Convert chimeric reads.
3
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172 #if str($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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173 &&
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174 samtools view
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175 -@ \${GALAXY_SLOTS:-4}
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176 -Shb Chimeric.out.sam |
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177
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178 samtools sort
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179 -@ \${GALAXY_SLOTS:-4} - ChimericSorted
0
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180 #end if
1
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181 ]]></command>
0
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182
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183 <inputs>
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184 <!-- FASTQ input(s) and options specifically for paired-end data. -->
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185 <conditional name="singlePaired">
2
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186 <param name="sPaired" type="select" label="Single-end or paired-end reads">
3
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187 <option value="single" selected="true">Single-end</option>
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188 <option value="paired">Paired-end (as individual datasets)</option>
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189 <option value="paired_collection">Paired-end (as collection)</option>
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190 </param>
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191 <when value="single">
3
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192 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file"/>
0
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193 </when>
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194 <when value="paired">
3
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195 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/>
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196 <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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197 </when>
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198 <when value="paired_collection">
3
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199 <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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200 </when>
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201 </conditional>
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202
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203 <!-- Genome source. -->
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204 <conditional name="refGenomeSource">
3
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205 <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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206 <option value="indexed" selected="True">Use a built-in index</option>
3
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207 <option value="history">Use reference genome from history and create temporary index</option>
0
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208 </param>
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209 <when value="indexed">
3
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210 <conditional name="GTFconditional">
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211 <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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212 <option value="without-gtf">use genome reference without builtin gene-model</option>
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213 <option value="with-gtf">use genome reference with builtin gene-model</option>
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214 </param>
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215 <when value="with-gtf">
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216 <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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217 <options from_data_table="rnastar_index2">
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218 <filter type="static_value" column="4" value="1"/>
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219 <filter type="sort_by" column="2" />
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220 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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221 </options>
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222 </param>
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223 </when>
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224 <when value="without-gtf">
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225 <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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226 <options from_data_table="rnastar_index2">
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227 <filter type="static_value" column="4" value="0"/>
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228 <filter type="sort_by" column="2" />
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229 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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230 </options>
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231 </param>
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232
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233 <expand macro="@SJDBOPTIONS@" />
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234 </when>
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235 </conditional>
0
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236 </when>
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237 <when value="history">
3
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238 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
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239 <expand macro="@SJDBOPTIONS@" />
0
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240 </when>
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241 </conditional>
3
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242 <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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243
2
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244 <!-- Output parameter settings. -->
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245 <conditional name="output_params">
3
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246 <param name="output_select" type="select" label="Would you like to set output parameters (formatting and filtering)?">
2
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247 <option value="no" selected="true">No</option>
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248 <option value="yes">Yes</option>
3
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249 </param>
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250 <when value="yes">
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251 <param argument="--outSAMattributes" type="select" label="Extra SAM attributes to include" help="See &quot;Extra SAM attributes&quot; below">
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252 <option value="Standard" selected="true">Standard</option>
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253 <option value="All">All</option>
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254 <option value="None">None</option>
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255 </param>
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256 <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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257 <option value="None" selected="true">No</option>
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258 <option value="intronMotif">Yes -- and reads with inconsistent and/or non-canonical introns are filtered out</option>
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259 </param>
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260 <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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261 <option value="None" selected="true">No</option>
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262 <option value="RemoveNoncanonical">Remove alignments with non-canonical junctions</option>
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263 <option value="RemoveNoncanonicalUnannotated">Remove alignments with unannotated non-canonical junctions</option>
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264 </param>
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265
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266 <!-- Additional output parameter settings. -->
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267 <conditional name="output_params2">
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268 <param name="output_select2" type="select" label="Would you like to set additional output parameters (formatting and filtering)?">
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269 <option value="no" selected="true">No</option>
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270 <option value="yes">Yes</option>
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271 </param>
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272 <when value="yes">
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273 <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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274 <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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275 <param argument="--outSAMmapqUnique" type="integer" value="255" min="0" max="255" label="MAPQ value for unique mappers"/>
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276 <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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277 <param argument="--outFilterMultimapScoreRange" type="integer" value="1" min="0" label="Score range below the maximum score for multimapping alignments"/>
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278 <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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279 <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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280 <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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281 <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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282 <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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283 <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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284 <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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285 <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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286 </when>
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287 <when value="no"/>
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288 </conditional>
2
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289 </when>
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290 <when value="no"/>
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291 </conditional>
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292
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293 <!-- Other parameter settings. -->
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294 <conditional name="params">
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295 <param name="settingsType" type="select" label="Other parameters (seed, alignment, limits and chimeric alignment)">
3
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296 <option value="default" selected="true">Use Defaults</option>
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297 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
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298 <option value="full">Extended parameter list</option>
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299 </param>
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300 <when value="default"/>
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301 <when value="star_fusion"/><!-- Set STAR-fusion parameters automatically -->
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302
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303 <when value="full">
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304 <section name="seed" title="Seed parameters" expanded="False">
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305 <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/>
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306 <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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307 <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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308 <param argument="--seedMultimapNmax" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching"/>
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309 <param argument="--seedPerReadNmax" type="integer" min="1" value="1000" label="Maximum number of seeds per read"/>
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310 <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/>
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311 <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/>
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312 </section>
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313
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314 <section name="align" title="Alignment parameters" expanded="False">
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315 <param argument="--alignIntronMin" name="alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
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316 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
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317 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
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318 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
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319 <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/>
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320 <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>
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321 <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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322 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
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323 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
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324 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
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325 <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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326 </section>
5
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327
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328 <section name="limits" title="Limits" expanded="False">
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329 <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." />
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330 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
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331 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
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332 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
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333 </section>
3
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334
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335 <conditional name="chim">
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336 <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?">
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337 <option value="no" selected="true">No</option>
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338 <option value="yes">Yes</option>
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339 </param>
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340 <when value="yes">
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341 <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">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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342 <validator type="in_range" min="1" message="To get chimeric reads this value needs to be larger than 0"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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343 </param>
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344 <param argument="--chimScoreMin" type="integer" min="0" value="0" label="Minimum total (summed) score of chimeric segments"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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345 <param argument="--chimScoreDropMax" type="integer" min="0" value="20" label="Maximum difference of chimeric score from read length"/>
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346 <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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347 <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1" label="Penalty for a non-GT/AG chimeric junction"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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348 <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20" label="Minimum overhang for a chimeric junction"/>
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349 </when>
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350 <when value="no"/>
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351 </conditional>
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352 </when>
0
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353 </conditional>
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354 </inputs>
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355
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356 <outputs>
2
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357 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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358 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction">
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359 <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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360 <actions>
3
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361 <conditional name="refGenomeSource.geneSource">
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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362 <when value="indexed">
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363 <action type="metadata" name="dbkey">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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364 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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365 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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366 <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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367 </option>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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368 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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369 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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370 <when value="history">
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371 <action type="metadata" name="dbkey">
3
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372 <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
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373 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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374 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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375 </conditional>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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376 </actions>
0
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377 </data>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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378
3
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379 <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: chimeric.bam" from_work_dir="ChimericSorted.bam">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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380 <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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381 <actions>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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382 <conditional name="refGenomeSource.geneSource">
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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383 <when value="indexed">
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384 <action type="metadata" name="dbkey">
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385 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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386 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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387 <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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388 </option>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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389 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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390 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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391 <when value="history">
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392 <action type="metadata" name="dbkey">
3
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393 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
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394 </action>
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395 </when>
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396 </conditional>
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397 </actions>
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398 </data>
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399
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400 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab">
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diff changeset
401 <actions>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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402 <conditional name="refGenomeSource.geneSource">
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403 <when value="indexed">
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404 <action type="metadata" name="dbkey">
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405 <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
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406 <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
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407 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
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408 </option>
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409 </action>
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410 </when>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
411 <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
412 <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
413 <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
414 </action>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
415 </when>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
416 </conditional>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
417 </actions>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
418 </data>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
419
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
420 <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
421 <actions>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
422 <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
423 <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
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_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
426 <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
427 <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
428 </option>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
429 </action>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
430 </when>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
431 <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
432 <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
433 <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
diff changeset
434 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
435 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
436 </conditional>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
437 </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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438 </data>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
439
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
440 <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
441 <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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442 </data>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
443 </outputs>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
444
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
445 <tests>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
446 <test>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
447 <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
448 <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
449 <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
450 <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
451
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
452 <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
453 <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
454 <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
455 <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
456
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
457 <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
458 <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
459 <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
460 </test>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
461 <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
462 <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
463 <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
464 <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
465
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
466 <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
467 <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
468 <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
469
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
470 <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
471 <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
472 <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
473 <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
474 <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
475
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
476 <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
477 <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
478 <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
479 <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
480 </test>
bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
parents: 0
diff changeset
481 <test>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
482 <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
483 <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
484 <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
485 <param name="sPaired" value="single" />
1
bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
parents: 0
diff changeset
486
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
487 <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
488 <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
489 <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
490 <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
diff changeset
491
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
492 <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
493 <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
494 <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
495 <param name="seed_select" value="yes" />
3
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iuc
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496 <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
497
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
498 <output name="output_log" file="rnastar_test2.log" compare="diff" lines_diff="12"/>
2
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iuc
parents: 1
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499 <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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500 <output name="mapped_reads" file="rnastar_test2_mapped_reads.bam" compare="sim_size" delta="200" />
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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501 </test>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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502 <test>
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 <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
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504 <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
505 <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
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506 <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
507
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
508 <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
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509 <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
510 <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
511 <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
512
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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diff changeset
513 <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
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514 </test>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
515 <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
516 <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
517 <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
518 <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
519 <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
520
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
521 <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
522 <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
523 <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
524 <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
525
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
526 <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
527 </test>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
528 <test>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
529 <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
530 <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
531 <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
532 <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
533
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
534 <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
535 <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
536 <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
537 <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
538
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
539 <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
540 <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
541 <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
542
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
543 <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
544 <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
545 <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
546 </test>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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diff changeset
547 </tests>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
548 <help>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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diff changeset
549 **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
550
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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diff changeset
551 STAR is an ultrafast universal RNA-seq aligner.
0
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iuc
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diff changeset
552
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
553 **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
554
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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diff changeset
555 The Standard option includes the following four attributes::
0
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iuc
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diff changeset
556
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
557 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
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diff changeset
558 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
559 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
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parents: 1
diff changeset
560 nM: Number of mismatches per (paired) alignment
0
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iuc
parents:
diff changeset
561
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
562 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
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diff changeset
563
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
564 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
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diff changeset
565 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
566 jM: Intron motifs for all junctions
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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diff changeset
567 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:
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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 **STAR-Fusion**
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
570
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
571 STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
572 STAR prior to STAR-Fusion can be pre-selected, with the following exceptions::
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
573
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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diff changeset
574 --twopassMode Basic # not an option in STAR 2.4.0
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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diff changeset
575 --chimSegmentReadGapMax 3 # not an option in STAR 2.4.0
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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diff changeset
576 --alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0
0
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iuc
parents:
diff changeset
577
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
578 **Attributions**
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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579
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580 rna_star - see the web site at rna_star_
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581
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582 For details, please see the rna_starMS_
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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583 "STAR: ultrafast universal RNA-seq aligner"
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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584 A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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585
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586 Galaxy_ (that's what you are using right now!) for gluing everything together
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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587
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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588 Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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589
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590 Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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591 and odds and ends of other code and documentation comprising this tool was
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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592 written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts
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593
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594 .. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml
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595 .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
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596 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
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597 .. _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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598 .. _rna_star: https://github.com/alexdobin/STAR
0
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599 .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full
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600 .. _Galaxy: http://getgalaxy.org
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601 </help>
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602 <expand macro="citations"/>
0
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603 </tool>