Mercurial > repos > iuc > rgrnastar

annotate rg_rnaStar.xml @ 4:d681e989ac95 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 4c4199b39a51216c83594762baadcadd81c519b2
author iuc
date Fri, 09 Jun 2017 07:34:30 -0400
parents 318b2a9d54dd
children 99b17b74a8cd
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1 <tool id="rna_star" name="RNA STAR" version="2.5.2b-0" profile="17.01">
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2 <description>Gapped-read mapper for RNA-seq data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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8 <stdio>
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9 <regex match="FATAL error" source="both" level="fatal"/>
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10 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
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11 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
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12 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
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13 </stdio>
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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
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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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 '$refGenomeSource.sjdbOverhang'
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36 #end if
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37 --runThreadN \${GALAXY_SLOTS:-4}
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38 &&
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39 #end if
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40
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41 STAR
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42 --runThreadN \${GALAXY_SLOTS:-4}
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43 --genomeLoad NoSharedMemory
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44 --genomeDir
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45 #if str($refGenomeSource.geneSource) == 'history':
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46 'tempstargenomedir'
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47 #if $refGenomeSource.sjdbGTFfile:
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48 --sjdbGTFfile '$refGenomeSource.sjdbGTFfile'
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49 --sjdbOverhang '$refGenomeSource.sjdbOverhang'
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50 #end if
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51 #else
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52 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
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53 #end if
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54
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55 --readFilesIn
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56 #if str($singlePaired.sPaired) == "paired_collection"
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57 '$singlePaired.input.forward' '$singlePaired.input.reverse'
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58
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59 #if $singlePaired.input.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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60 @FASTQ_GZ_OPTION@
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61 #end if
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62 #else
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63 '$singlePaired.input1'
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64 #if str($singlePaired.sPaired) == "paired"
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65 '$singlePaired.input2'
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66 #end if
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67
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68 #if $singlePaired.input1.is_of_type("fastq.gz", "fastqsanger.gz"):
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69 @FASTQ_GZ_OPTION@
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70 #end if
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71 #end if
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72
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73 --outSAMtype BAM SortedByCoordinate
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74
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75 ## Handle difference between indices with/without annotations
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76 #if str($refGenomeSource.geneSource) == 'indexed':
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77 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
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78 #if $refGenomeSource.GTFconditional.sjdbGTFfile:
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79 --sjdbOverhang '$refGenomeSource.GTFconditional.sjdbOverhang'
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80 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
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81 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
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82 --sjdbGTFtagExonParentTranscript Parent
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83 #end if
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84 #end if
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85 #end if
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86 #end if
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87
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88 #if $quantMode:
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89 --quantMode GeneCounts
2
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90 #end if
0
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91
3
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92 ## Output parameters
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93 #if str( $output_params.output_select ) == "yes":
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94 --outSAMattributes $output_params.outSAMattributes
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95 --outSAMstrandField $output_params.outSAMstrandField
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96 --outFilterIntronMotifs $output_params.outFilterIntronMotifs
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97 #if str( $output_params.output_params2.output_select2 ) == "yes":
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98 --outSAMunmapped $output_params.output_params2.outSAMunmapped
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99 --outSAMprimaryFlag $output_params.output_params2.outSAMprimaryFlag
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100 --outSAMmapqUnique "$output_params.output_params2.outSAMmapqUnique"
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101 --outFilterType $output_params.output_params2.outFilterType
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102 --outFilterMultimapScoreRange "$output_params.output_params2.outFilterMultimapScoreRange"
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103 --outFilterMultimapNmax "$output_params.output_params2.outFilterMultimapNmax"
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104 --outFilterMismatchNmax "$output_params.output_params2.outFilterMismatchNmax"
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105 --outFilterMismatchNoverLmax "$output_params.output_params2.outFilterMismatchNoverLmax"
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106 --outFilterMismatchNoverReadLmax "$output_params.output_params2.outFilterMismatchNoverReadLmax"
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107 --outFilterScoreMin "$output_params.output_params2.outFilterScoreMin"
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108 --outFilterScoreMinOverLread "$output_params.output_params2.outFilterScoreMinOverLread"
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109 --outFilterMatchNmin "$output_params.output_params2.outFilterMatchNmin"
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110 --outFilterMatchNminOverLread "$output_params.output_params2.outFilterMatchNminOverLread"
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111 #end if
2
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112 #end if
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113
3
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114 ## Other parameters
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115 #if str( $params.settingsType ) == "star_fusion":
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116 ## Preset parameters for STAR-Fusion
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117 --outReadsUnmapped None
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118 --chimSegmentMin 12
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119 --chimJunctionOverhangMin 12
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120 --alignSJDBoverhangMin 10
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121 --alignMatesGapMax 200000
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122 --alignIntronMax 200000
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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 "$params.chim.chimJunctionOverhangMin"
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161 #end if
2
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162 #end if
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163
0
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164 ## Convert chimeric reads.
3
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165 #if str($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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166 &&
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167 samtools view
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168 -@ \${GALAXY_SLOTS:-4}
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169 -Shb Chimeric.out.sam |
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170
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171 samtools sort
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172 -@ \${GALAXY_SLOTS:-4} - ChimericSorted
0
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173 #end if
1
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174 ]]></command>
0
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175
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176 <inputs>
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177 <!-- FASTQ input(s) and options specifically for paired-end data. -->
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178 <conditional name="singlePaired">
2
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179 <param name="sPaired" type="select" label="Single-end or paired-end reads">
3
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180 <option value="single" selected="true">Single-end</option>
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181 <option value="paired">Paired-end (as individual datasets)</option>
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182 <option value="paired_collection">Paired-end (as collection)</option>
0
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183 </param>
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184 <when value="single">
3
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185 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file"/>
0
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186 </when>
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187 <when value="paired">
3
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188 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/>
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189 <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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190 </when>
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191 <when value="paired_collection">
3
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192 <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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193 </when>
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194 </conditional>
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195
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196 <!-- Genome source. -->
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197 <conditional name="refGenomeSource">
3
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198 <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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199 <option value="indexed" selected="True">Use a built-in index</option>
3
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200 <option value="history">Use reference genome from history and create temporary index</option>
0
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201 </param>
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202 <when value="indexed">
3
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203 <conditional name="GTFconditional">
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204 <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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205 <option value="without-gtf">use genome reference without builtin gene-model</option>
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206 <option value="with-gtf">use genome reference with builtin gene-model</option>
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207 </param>
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208 <when value="with-gtf">
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209 <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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210 <options from_data_table="rnastar_index2">
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211 <filter type="static_value" column="4" value="1"/>
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212 <filter type="sort_by" column="2" />
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213 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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214 </options>
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215 </param>
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216 </when>
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217 <when value="without-gtf">
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218 <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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219 <options from_data_table="rnastar_index2">
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220 <filter type="static_value" column="4" value="0"/>
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221 <filter type="sort_by" column="2" />
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222 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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223 </options>
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224 </param>
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225
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226 <expand macro="@SJDBOPTIONS@" />
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227 </when>
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228 </conditional>
0
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229 </when>
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230 <when value="history">
3
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231 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
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232 <expand macro="@SJDBOPTIONS@" />
0
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233 </when>
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234 </conditional>
3
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235 <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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236
2
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237 <!-- Output parameter settings. -->
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238 <conditional name="output_params">
3
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239 <param name="output_select" type="select" label="Would you like to set output parameters (formatting and filtering)?">
2
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240 <option value="no" selected="true">No</option>
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241 <option value="yes">Yes</option>
3
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242 </param>
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243 <when value="yes">
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244 <param argument="--outSAMattributes" type="select" label="Extra SAM attributes to include" help="See &quot;Extra SAM attributes&quot; below">
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245 <option value="Standard" selected="true">Standard</option>
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246 <option value="All">All</option>
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247 <option value="None">None</option>
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248 </param>
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249 <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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250 <option value="None" selected="true">No</option>
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251 <option value="intronMotif">Yes -- and reads with inconsistent and/or non-canonical introns are filtered out</option>
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252 </param>
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253 <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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254 <option value="None" selected="true">No</option>
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255 <option value="RemoveNoncanonical">Remove alignments with non-canonical junctions</option>
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256 <option value="RemoveNoncanonicalUnannotated">Remove alignments with unannotated non-canonical junctions</option>
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257 </param>
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258
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259 <!-- Additional output parameter settings. -->
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260 <conditional name="output_params2">
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261 <param name="output_select2" type="select" label="Would you like to set additional output parameters (formatting and filtering)?">
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262 <option value="no" selected="true">No</option>
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263 <option value="yes">Yes</option>
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264 </param>
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265 <when value="yes">
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266 <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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267 <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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268 <param argument="--outSAMmapqUnique" type="integer" value="255" min="0" max="255" label="MAPQ value for unique mappers"/>
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269 <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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270 <param argument="--outFilterMultimapScoreRange" type="integer" value="1" min="0" label="Score range below the maximum score for multimapping alignments"/>
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271 <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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272 <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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273 <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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274 <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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275 <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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276 <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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277 <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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278 <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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279 </when>
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280 <when value="no"/>
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281 </conditional>
2
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282 </when>
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283 <when value="no"/>
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284 </conditional>
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285
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286 <!-- Other parameter settings. -->
0
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287 <conditional name="params">
3
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288 <param name="settingsType" type="select" label="Other parameters (seed, alignment, and chimeric alignment)">
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289 <option value="default" selected="true">Use Defaults</option>
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290 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
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291 <option value="full">Extended parameter list</option>
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292 </param>
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293 <when value="default"/>
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294 <when value="star_fusion"/><!-- Set STAR-fusion parameters automatically -->
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295
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296 <when value="full">
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297 <section name="seed" title="Seed parameters" expanded="False">
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298 <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/>
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299 <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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300 <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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301 <param argument="--seedMultimapNmax" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching"/>
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302 <param argument="--seedPerReadNmax" type="integer" min="1" value="1000" label="Maximum number of seeds per read"/>
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303 <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/>
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304 <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/>
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305 </section>
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306
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307 <section name="align" title="Alignment parameters" expanded="False">
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308 <param argument="--alignIntronMin" name="alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
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309 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
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310 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
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311 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
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312 <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/>
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313 <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>
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314 <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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315 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
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316 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
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317 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
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318 <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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319 </section>
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320
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321 <conditional name="chim">
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322 <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?">
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323 <option value="no" selected="true">No</option>
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324 <option value="yes">Yes</option>
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325 </param>
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326 <when value="yes">
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327 <param argument="--chimSegmentMin" type="integer" min="0" value="0" label="Minimum length of chimeric segment" help="For small numbers this will cause large number of chimeric alignments. A value of 12 is commonly used. Default of 0 means no chimeric output">
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328 <validator type="in_range" min="1" message="To get chimeric reads this value needs to be larger than 0"/>
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329 </param>
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330 <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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331 <param argument="--chimScoreDropMax" type="integer" min="0" value="20" label="Maximum difference of chimeric score from read length"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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332 <param argument="--chimScoreSeparation" type="integer" min="0" value="10" label="Minimum difference between the best chimeric score and the next one"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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333 <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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334 <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20" label="Minimum overhang for a chimeric junction"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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335 </when>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
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336 <when value="no"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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337 </conditional>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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338 </when>
0
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339 </conditional>
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iuc
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340 </inputs>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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341
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iuc
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342 <outputs>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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parents: 1
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343 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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344 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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345 <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
iuc
parents: 1
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346 <actions>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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347 <conditional name="refGenomeSource.geneSource">
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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348 <when value="indexed">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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349 <action type="metadata" name="dbkey">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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350 <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
iuc
parents: 1
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351 <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
iuc
parents: 2
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352 <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
iuc
parents: 1
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353 </option>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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354 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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355 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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356 <when value="history">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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357 <action type="metadata" name="dbkey">
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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358 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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359 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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360 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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361 </conditional>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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362 </actions>
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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363 </data>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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364
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
365 <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
iuc
parents: 2
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366 <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
iuc
parents: 1
diff changeset
367 <actions>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
368 <conditional name="refGenomeSource.geneSource">
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
369 <when value="indexed">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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370 <action type="metadata" name="dbkey">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
371 <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
iuc
parents: 1
diff changeset
372 <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
iuc
parents: 2
diff changeset
373 <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
iuc
parents: 1
diff changeset
374 </option>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
375 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
376 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
377 <when value="history">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
378 <action type="metadata" name="dbkey">
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
379 <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
380 </action>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
381 </when>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
382 </conditional>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
383 </actions>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
384 </data>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
385
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
386 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
387 <actions>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
388 <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
389 <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
390 <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
391 <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
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392 <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
393 <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
394 </option>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
395 </action>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
396 </when>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
397 <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
398 <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
399 <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
400 </action>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
401 </when>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
402 </conditional>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
403 </actions>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
404 </data>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
405
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
406 <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
407 <actions>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
408 <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
409 <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
410 <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
411 <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
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412 <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
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413 <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
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414 </option>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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415 </action>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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416 </when>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
417 <when value="history">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
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418 <action type="metadata" name="dbkey">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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parents: 2
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419 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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420 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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421 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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422 </conditional>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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423 </actions>
0
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424 </data>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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425
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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426 <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
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427 <filter>quantMode is True</filter>
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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428 </data>
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429 </outputs>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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430
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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431 <tests>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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432 <test>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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433 <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
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434 <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
435 <param name="genomeFastaFiles" value="tophat_test.fa" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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436 <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
437
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
438 <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
439 <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
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440 <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
441 <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
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442
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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443 <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
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444 <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
445 <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
446 </test>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
447 <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
448 <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
449 <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
450 <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
451
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
452 <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
453 <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
454 <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
455
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
456 <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
457 <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
458 <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
459 <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
460 <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
461
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
462 <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
463 <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
464 <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
465 <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
466 </test>
bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
parents: 0
diff changeset
467 <test>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
468 <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
469 <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
470 <param name="genomeFastaFiles" value="tophat_test.fa" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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471 <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
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472
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
473 <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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474 <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
475 <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
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476 <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
477
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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478 <param name="output_select2" value="yes" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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479 <param name="outFilterScoreMinOverLread" value="0.9" />
1
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parents: 0
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480 <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
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481 <param name="seed_select" value="yes" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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482 <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
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483
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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484 <output name="output_log" file="rnastar_test2.log" compare="diff" lines_diff="12"/>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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485 <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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486 <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
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487 </test>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
488 <test>
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="input1" value="test3.fastqsanger" ftype="fastqsanger" />
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents: 2
diff changeset
490 <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
491 <param name="genomeFastaFiles" value="test3.ref.fa" />
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
492 <param name="sPaired" value="single" />
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
493
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
494 <param name="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
495 <param name="outSAMattributes" value="All" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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496 <param name="outSAMstrandField" value="intronMotif" />
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497 <param name="settingsType" value="star_fusion" />
3
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498
2
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499 <output name="chimeric_junctions" file="test3.chimjunc.tabular"/>
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500 </test>
3
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501 <test><!-- tests fastqsanger.gz -->
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502 <param name="input1" value="test3.fastqsanger.gz" ftype="fastqsanger.gz" />
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503 <param name="geneSource" value="history" />
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504 <param name="genomeFastaFiles" value="test3.ref.fa" />
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505 <param name="sPaired" value="single" />
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506
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507 <param name="output_select" value="yes" />
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508 <param name="outSAMattributes" value="All" />
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509 <param name="outSAMstrandField" value="intronMotif" />
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510 <param name="settingsType" value="star_fusion" />
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511
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512 <output name="chimeric_junctions" file="test3.chimjunc.tabular"/>
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513 </test>
2
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514 <test>
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515 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
3
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516 <param name="geneSource" value="history" />
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517 <param name="genomeFastaFiles" value="tophat_test.fa" />
2
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518 <param name="sPaired" value="single" />
3
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519
2
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520 <param name="output_select" value="yes" />
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521 <param name="outSAMattributes" value="All" />
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522 <param name="outSAMstrandField" value="intronMotif" />
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523 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
3
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524
2
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525 <param name="output_select2" value="yes" />
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526 <param name="settingsType" value="full" />
3
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527 <param name="chim_select" value="false" />
2
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528
3
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529 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>
2
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530 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
3
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531 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
2
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532 </test>
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533 </tests>
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534 <help>
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535 **What it does**
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536
3
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537 STAR is an ultrafast universal RNA-seq aligner.
0
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538
2
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539 **Extra SAM attributes**
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540
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541 The Standard option includes the following four attributes::
0
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542
2
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543 NH: Number of reported alignments that contain the query in the current record.
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544 HI: Query hit index, indicating the alignment record is the i-th one stored in SAM
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545 AS: Local alignment score (paired for paired-end reads)
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546 nM: Number of mismatches per (paired) alignment
0
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547
2
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548 The All option includes the Standard attributes, plus the following four::
0
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549
2
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550 NM: Edit distance to the reference, including ambiguous bases but excluding clipping
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551 MD: String for mismatching positions
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552 jM: Intron motifs for all junctions
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553 jI: Start and end of introns for all junctions
0
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554
2
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555 **STAR-Fusion**
0
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556
2
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557 STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running
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558 STAR prior to STAR-Fusion can be pre-selected, with the following exceptions::
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559
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560 --twopassMode Basic # not an option in STAR 2.4.0
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561 --chimSegmentReadGapMax 3 # not an option in STAR 2.4.0
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562 --alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0
0
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563
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564 **Attributions**
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565
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566 rna_star - see the web site at rna_star_
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567
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568 For details, please see the rna_starMS_
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569 "STAR: ultrafast universal RNA-seq aligner"
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570 A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635
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571
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572 Galaxy_ (that's what you are using right now!) for gluing everything together
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573
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574 Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper
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575
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576 Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies
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577 and odds and ends of other code and documentation comprising this tool was
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578 written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts
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579
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580 .. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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581 .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
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ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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582 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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583 .. _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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bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
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584 .. _rna_star: https://github.com/alexdobin/STAR
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b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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585 .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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586 .. _Galaxy: http://getgalaxy.org
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318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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587 </help>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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588 <expand macro="citations"/>
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b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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589 </tool>