Mercurial > repos > iuc > rgrnastar

annotate rg_rnaStar.xml @ 2:ace9f5a2b40f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
author iuc
date Fri, 05 Feb 2016 11:56:20 -0500
parents bc685d13b637
children 318b2a9d54dd
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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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1 <tool id="rna_star" name="RNA STAR" version="2.4.0d-2">
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2 <description>Gapped-read mapper for RNA-seq data</description>
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3 <requirements>
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4 <requirement type="package" version="2.4.0d">rnastar</requirement>
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5 <requirement type="package" version="0.1.19">samtools</requirement>
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6 </requirements>
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7 <stdio>
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8 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
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9 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
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10 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
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11 <regex match=".*" source="both" level="warning" description="Some stderr/stdout text"/>
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12 </stdio>
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13
1
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14 <command><![CDATA[
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15 ## Create temporary index for custom reference
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16 #if str($refGenomeSource.genomeSource) == 'history':
2
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17 mkdir -p tempstargenomedir &&
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18 STAR
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19 --runMode genomeGenerate
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20 --genomeDir "tempstargenomedir"
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21 --genomeFastaFiles "$refGenomeSource.ownFile"
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22 --runThreadN \${GALAXY_SLOTS:-4}
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23
0
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24 #if str($refGenomeSource.geneModel) != 'None':
2
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25 --sjdbOverhang "$refGenomeSource.overhang"
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26 --sjdbGTFfile "$refGenomeSource.geneModel"
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27
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28 #if str($refGenomeSource.geneModel.ext) == 'gff3':
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29 --sjdbGTFtagExonParentTranscript Parent
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30 #end if
0
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31 #end if
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32 ;
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33 #end if
2
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35
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36 ## Actual alignment
0
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37 STAR
2
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38 --runThreadN \${GALAXY_SLOTS:-4}
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39 --genomeLoad NoSharedMemory
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40 #if str($refGenomeSource.genomeSource) == 'history':
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41 --genomeDir "tempstargenomedir"
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42 #else
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43 --genomeDir "$refGenomeSource.index.fields.path"
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44 #end if
2
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45
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46 --readFilesIn
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47 #if str($singlePaired.sPaired) == "paired_collection"
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48 "$singlePaired.input.forward" "$singlePaired.input.reverse"
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49 #else
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50 "$singlePaired.input1"
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51 #if str($singlePaired.sPaired) == "paired"
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52 "$singlePaired.input2"
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53 #end if
0
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54 #end if
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55
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56 ## Output parameters
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57 #if str( $output_params.output_select ) == "yes":
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58 --outSAMattributes $output_params.outSAMattributes
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59 --outSAMstrandField $output_params.outSAMstrandField
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60 --outFilterIntronMotifs $output_params.outFilterIntronMotifs
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61 #if str( $output_params.output_params2.output_select2 ) == "yes":
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62 --outSAMunmapped $output_params.output_params2.unmapped_opt
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63 --outSAMprimaryFlag $output_params.output_params2.primary_opt
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64 --outSAMmapqUnique "$output_params.output_params2.unique"
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65 --outFilterType $output_params.output_params2.sjfilter_opt
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66 --outFilterMultimapScoreRange "$output_params.output_params2.multiScoreRange"
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67 --outFilterMultimapNmax "$output_params.output_params2.multiNmax"
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68 --outFilterMismatchNmax "$output_params.output_params2.mismatchNmax"
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69 --outFilterMismatchNoverLmax "$output_params.output_params2.mismatchNoverLmax"
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70 --outFilterMismatchNoverReadLmax "$output_params.output_params2.mismatchNoverReadLmax"
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71 --outFilterScoreMin "$output_params.output_params2.scoreMin"
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72 --outFilterScoreMinOverLread "$output_params.output_params2.scoreMinOverLread"
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73 --outFilterMatchNmin "$output_params.output_params2.matchNmin"
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74 --outFilterMatchNminOverLread "$output_params.output_params2.matchNminOverLread"
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75 #end if
0
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76 #end if
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77
2
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78 ## Other parameters
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79 #if str( $params.settingsType ) == "star_fusion":
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80 ## Preset parameters for STAR-Fusion
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81 ## --twopass1readsN 100000000
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82 ## --sjdbOverhang 100
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83 --outReadsUnmapped None
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84 --chimSegmentMin 12
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85 --chimJunctionOverhangMin 12
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86 --alignSJDBoverhangMin 10
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87 --alignMatesGapMax 200000
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88 --alignIntronMax 200000
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89 ## --chimSegmentReadGapMax 3 ## not an option in STAR 2.4.0
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90 ## --alignSJstitchMismatchNmax 5 -1 5 5 ## not an option in STAR 2.4.0
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91
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92 #elif str( $params.settingsType ) == "full":
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93 ## Extended parameter options
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94
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95 ## Seed parameter options
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96 #if str( $params.seed.seed_select ) == "yes":
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97 --seedSearchStartLmax "$params.seed.searchStart"
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98 --seedSearchStartLmaxOverLread "$params.seed.searchStartNorm"
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99 --seedSearchLmax "$params.seed.searchLmax"
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100 --seedMultimapNmax "$params.seed.multimap"
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101 --seedPerReadNmax "$params.seed.readMax"
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102 --seedPerWindowNmax "$params.seed.windowMax"
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103 --seedNoneLociPerWindow "$params.seed.oneSeed"
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104 #end if
0
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105
2
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106 ## Alignment parameter options
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107 #if str( $params.align.align_select ) == "yes":
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108 --alignIntronMin "$params.align.intronMin"
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109 --alignIntronMax "$params.align.intronMax"
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110 --alignMatesGapMax "$params.align.gapMax"
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111 --alignSJoverhangMin "$params.align.sjOverhang"
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112 --alignSJDBoverhangMin "$params.align.sjdbOverhang"
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113 --alignSplicedMateMapLmin "$params.align.splicedMate"
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114 --alignSplicedMateMapLminOverLmate "$params.align.splicedMateNorm"
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115 --alignWindowsPerReadNmax "$params.align.windows"
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116 --alignTranscriptsPerWindowNmax "$params.align.transWindow"
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117 --alignTranscriptsPerReadNmax "$params.align.transRead"
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118 --alignEndsType $params.align.endsType_opt
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119 #end if
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120
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121 ## Chimeric alignment parameter options
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122 #if str( $params.chim.chim_select ) == "yes":
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123 --chimSegmentMin "$params.chim.segmentMin"
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124 --chimScoreMin "$params.chim.scoreMin"
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125 --chimScoreDropMax "$params.chim.scoreDrop"
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126 --chimScoreSeparation "$params.chim.scoreSep"
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127 --chimScoreJunctionNonGTAG "$params.chim.scoreJunction"
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128 --chimJunctionOverhangMin "$params.chim.junctionOverhang"
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129 #end if
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130
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131 #end if
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132
0
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133 ## BAM conversion.
2
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134
0
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135 ## Convert aligned reads.
2
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136 && samtools view -@ \${GALAXY_SLOTS:-4} -Shb Aligned.out.sam | samtools sort -@ \${GALAXY_SLOTS:-4} - AlignedSorted 2>/dev/null
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137
0
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138 ## Convert chimeric reads.
2
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139 #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.segmentMin) > 0 ):
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140 && samtools view -@ \${GALAXY_SLOTS:-4} -Shb Chimeric.out.sam | samtools sort -@ \${GALAXY_SLOTS:-4} - ChimericSorted 2>/dev/null
0
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141 #end if
1
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142 ]]></command>
0
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143
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144 <inputs>
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145 <!-- FASTQ input(s) and options specifically for paired-end data. -->
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146 <conditional name="singlePaired">
2
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147 <param name="sPaired" type="select" label="Single-end or paired-end reads">
0
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148 <option value="single" selected="true">Single-end</option>
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149 <option value="paired">Paired-end (as individual datasets)</option>
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150 <option value="paired_collection">Paired-end (as collection)</option>
0
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151 </param>
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152 <when value="single">
2
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153 <param format="fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file"/>
0
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154 </when>
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155 <when value="paired">
2
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156 <param format="fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/>
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157 <param format="fastq,fasta" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, reverse reads"/>
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158 </when>
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159 <when value="paired_collection">
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160 <param format="fastq,fasta" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ/FASTA paired reads"/>
0
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161 </when>
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162 </conditional>
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163
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164 <!-- Genome source. -->
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165 <conditional name="refGenomeSource">
2
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166 <param name="genomeSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
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167 <option value="indexed" selected="True">Use a built-in index</option>
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168 <option value="history">Index and use a genome fasta and GTF file from history</option>
0
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169 </param>
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170 <when value="indexed">
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171 <param name="index" type="select" label="Select a reference genome">
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172 <options from_data_table="rnastar_index">
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173 <filter type="sort_by" column="2"/>
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174 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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175 </options>
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176 </param>
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177 </when>
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178 <when value="history">
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179 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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180 <param name="geneModel" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions. Leave blank for none"
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181 optional="true" help="Optional. If supplied, the index file will retain exon junction information for mapping splices (--sjdbGTFfile)"/>
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182 <param name="overhang" type="integer" min="0" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1 (--sjdbOverhang)"/>
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183 </when>
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184 </conditional>
2
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185
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186 <!-- Output parameter settings. -->
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187 <conditional name="output_params">
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188 <param name="output_select" type="select" label="Would you like to set output parameters (formatting and filtering)?">
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189 <option value="no" selected="true">No</option>
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190 <option value="yes">Yes</option>
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191 </param>
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192 <when value="yes">
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193 <param name="outSAMattributes" type="select" label="Extra SAM attributes to include" help="See &quot;Extra SAM attributes&quot; below (--outSAMattributes)">
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194 <option value="Standard" selected="true">Standard</option>
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195 <option value="All">All</option>
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196 <option value="None">None</option>
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197 </param>
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198 <param name="outSAMstrandField" type="select" label="Include strand field flag XS" help="For Cufflinks compatibility with unstranded RNA-seq data, this option is required (--outSAMstrandField)">
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199 <option value="None" selected="true">No</option>
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200 <option value="intronMotif">Yes -- and reads with inconsistent and/or non-canonical introns are filtered out</option>
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201 </param>
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202 <param name="outFilterIntronMotifs" type="select" label="Filter alignments containing non-canonical junctions" help="For Cufflinks compatibility, removing alignments with non-canonical junctions is recommended (--outFilterIntronMotifs)">
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203 <option value="None" selected="true">No</option>
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204 <option value="RemoveNoncanonical">Remove alignments with non-canonical junctions</option>
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205 <option value="RemoveNoncanonicalUnannotated">Remove alignments with unannotated non-canonical junctions</option>
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206 </param>
2
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207
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208 <!-- Additional output parameter settings. -->
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209 <conditional name="output_params2">
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210 <param name="output_select2" type="select" label="Would you like to set additional output parameters (formatting and filtering)?">
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211 <option value="no" selected="true">No</option>
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212 <option value="yes">Yes</option>
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213 </param>
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214 <when value="yes">
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215 <param name="unmapped_opt" type="boolean" truevalue="Within" falsevalue="None" checked="false" label="Would you like unmapped reads included in the SAM?" help="(--outSAMunmapped)"/>
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216 <param name="primary_opt" type="boolean" truevalue="AllBestScore" falsevalue="OneBestScore" checked="false" label="Would you like all alignments with the best score labeled primary?" help="(--outSAMprimaryFlag)"/>
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217 <param name="unique" type="integer" value="255" min="0" max="255" label="MAPQ value for unique mappers" help="(--outSAMmapqUnique)"/>
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218 <param name="sjfilter_opt" type="boolean" truevalue="BySJout" falsevalue="Normal" checked="false" label="Would you like to keep only reads that contain junctions that passed filtering?" help="(--outFilterType)"/>
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219 <param name="multiScoreRange" type="integer" value="1" min="0" label="Score range below the maximum score for multimapping alignments" help="(--outFilterMultimapScoreRange)"/>
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220 <param name="multiNmax" 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 (--outFilterMultimapNmax)"/>
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221 <param name="mismatchNmax" 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 (--outFilterMismatchNmax)"/>
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222 <param name="mismatchNoverLmax" 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 (--outFilterMismatchNoverLmax)"/>
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223 <param name="mismatchNoverReadLmax" 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 (--outFilterMismatchNoverReadLmax)"/>
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224 <param name="scoreMin" type="integer" value="0" min="0" label="Minimum alignment score" help="Alignments must have scores higher than this value to be output (--outFilterScoreMin)"/>
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225 <param name="scoreMinOverLread" 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 (--outFilterScoreMinOverLread)"/>
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226 <param name="matchNmin" 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 (--outFilterMatchNmin)"/>
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227 <param name="matchNminOverLread" 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 (--outFilterMatchNminOverLread)"/>
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228 </when>
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229 <when value="no"/>
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230 </conditional>
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231
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232 </when>
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233 <when value="no"/>
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234 </conditional>
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235
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236 <!-- Other parameter settings. -->
0
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237 <conditional name="params">
2
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238 <param name="settingsType" type="select" label="Other parameters (seed, alignment, and chimeric alignment)">
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239 <option value="default" selected="true">Use Defaults</option>
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240 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
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241 <option value="full">Extended parameter list</option>
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242 </param>
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243 <when value="default"/>
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244 <when value="star_fusion"/> <!-- Set STAR-fusion parameters automatically -->
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245
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246 <when value="full">
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247
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248 <!-- Seed parameters -->
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249 <conditional name="seed">
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250 <param name="seed_select" type="select" label="Would you like to set seed parameters?">
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251 <option value="no" selected="true">No</option>
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252 <option value="yes">Yes</option>
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253 </param>
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254 <when value="yes">
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255 <param name="searchStart" type="integer" min="1" value="50" label="Search start point through the read" help="(--seedSearchStartLmax)"/>
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256 <param name="searchStartNorm" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length" help="(--seedSearchStartLmaxOverLread)"/>
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257 <param name="searchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length (--seedSearchLmax)"/>
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258 <param name="multimap" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching" help="(--seedMultimapNmax)"/>
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259 <param name="readMax" type="integer" min="1" value="1000" label="Maximum number of seeds per read" help="(--seedPerReadNmax)"/>
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260 <param name="windowMax" type="integer" min="1" value="50" label="Maximum number of seeds per window" help="(--seedPerWindowNmax)"/>
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261 <param name="oneSeed" type="integer" min="1" value="10" label="Maximum number of one seed loci per window" help="(--seedNoneLociPerWindow)"/>
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262 </when>
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263 <when value="no"/>
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264 </conditional>
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265
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266 <!-- Alignment parameters -->
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267 <conditional name="align">
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268 <param name="align_select" type="select" label="Would you like to set alignment parameters?">
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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 name="intronMin" type="integer" min="0" value="21" label="Minimum intron size" help="(--alignIntronMin)"/>
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274 <param name="intronMax" type="integer" min="0" value="0" label="Maximum intron size" help="(--alignIntronMax)"/>
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275 <param name="gapMax" type="integer" min="0" value="0" label="Maximum gap between two mates" help="(--alignMatesGapMax)"/>
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276 <param name="sjOverhang" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments" help="(--alignSJoverhangMin)"/>
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277 <param name="sjdbOverhang" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments" help="(--alignSJDBoverhangMin)"/>
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278 <param name="splicedMate" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced" help="(--alignSplicedMateMapLmin)"/>
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279 <param name="splicedMateNorm" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length" help="(--alignSplicedMateMapLminOverLmate)"/>
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280 <param name="windows" type="integer" min="1" value="10000" label="Maximum number of windows per read" help="(--alignWindowsPerReadNmax)"/>
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281 <param name="transWindow" type="integer" min="1" value="100" label="Maximum number of transcripts per window" help="(--alignTranscriptsPerWindowNmax)"/>
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282 <param name="transRead" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider" help="(--alignTranscriptsPerReadNmax)"/>
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283 <param name="endsType_opt" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?" help="(--alignEndsType)"/>
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284 </when>
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285 <when value="no"/>
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286 </conditional>
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287
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288 <!-- Chimeric alignment parameters -->
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289 <conditional name="chim">
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290 <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?">
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291 <option value="no" selected="true">No</option>
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292 <option value="yes">Yes</option>
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293 </param>
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294 <when value="yes">
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295 <param name="segmentMin" type="integer" min="0" value="0" label="Minimum length of chimeric segment" help="Default of 0 means no chimeric output (--chimSegmentMin)"/>
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296 <param name="scoreMin" type="integer" min="0" value="0" label="Minimum total (summed) score of chimeric segments" help="(--chimScoreMin)"/>
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297 <param name="scoreDrop" type="integer" min="0" value="20" label="Maximum difference of chimeric score from read length" help="(--chimScoreDropMax)"/>
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298 <param name="scoreSep" type="integer" min="0" value="10" label="Minimum difference between the best chimeric score and the next one" help="(--chimScoreSeparation)"/>
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299 <param name="scoreJunction" type="integer" value="-1" label="Penalty for a non-GT/AG chimeric junction" help="(--chimScoreJunctionNonGTAG)"/>
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300 <param name="junctionOverhang" type="integer" min="0" value="20" label="Minimum overhang for a chimeric junction" help="(--chimJunctionOverhangMin)"/>
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301 </when>
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302 <when value="no"/>
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303 </conditional>
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304
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305 </when>
0
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306 </conditional>
2
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307
0
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308 </inputs>
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309
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310 <outputs>
2
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311 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
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312 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: starchimjunc" from_work_dir="Chimeric.out.junction">
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313 <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['segmentMin'] > 0 )</filter>
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314 <actions>
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315 <conditional name="refGenomeSource.genomeSource">
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316 <when value="indexed">
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317 <action type="metadata" name="dbkey">
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318 <option type="from_data_table" name="rnastar_index" column="1" offset="0">
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319 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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320 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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321 </option>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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322 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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323 </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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324 <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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325 <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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326 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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327 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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328 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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329 </conditional>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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330 </actions>
0
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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331 </data>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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332
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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333 <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: starmappedchim.bam" from_work_dir="ChimericSorted.bam">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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334 <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['segmentMin'] > 0 )</filter>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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335 <actions>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
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336 <conditional name="refGenomeSource.genomeSource">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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337 <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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338 <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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339 <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
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340 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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341 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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342 </option>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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343 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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344 </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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345 <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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346 <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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347 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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348 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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349 </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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350 </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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351 </actions>
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
352 </data>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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353
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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354 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: starsplicejunct.bed" from_work_dir="SJ.out.tab">
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 <actions>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
356 <conditional name="refGenomeSource.genomeSource">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
357 <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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358 <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
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359 <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
360 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
361 <filter type="param_value" ref="refGenomeSource.index" column="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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362 </option>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
363 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
364 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
365 <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
366 <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
367 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
368 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
369 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
370 </conditional>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
371 </actions>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
372 </data>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
373
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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diff changeset
374 <data format="bam" name="mapped_reads" label="${tool.name} on ${on_string}: starmapped.bam" from_work_dir="AlignedSorted.bam">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
375 <actions>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
376 <conditional name="refGenomeSource.genomeSource">
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="indexed">
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">
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
379 <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
380 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
381 <filter type="param_value" ref="refGenomeSource.index" column="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
382 </option>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
383 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
384 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
385 <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
386 <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
387 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
388 </action>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
389 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
390 </conditional>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
391 </actions>
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
392 </data>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff changeset
393 </outputs>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
394
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
395 <tests>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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diff changeset
396 <test>
2
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
397 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
398 <param name="genomeSource" value="history" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
399 <param name="ownFile" value="tophat_test.fa" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
400 <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
401
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents: 1
diff changeset
402 <param name="output_select" value="yes" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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403 <param name="outSAMattributes" value="All" />
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404 <param name="outSAMstrandField" value="intronMotif" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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405 <param name="settingsType" value="default" />
1
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406
2
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407 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff = "10"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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408 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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409 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="200" />
1
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410 </test>
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411 <test>
2
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412 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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413 <param name="genomeSource" value="history" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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414 <param name="ownFile" value="tophat_test.fa" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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415 <param name="sPaired" value="single" />
1
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416
2
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417 <param name="output_select" value="yes" />
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418 <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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419 <param name="outSAMstrandField" value="intronMotif" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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420 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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421
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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422 <param name="output_select2" value="yes" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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423 <param name="scoreMinOverLread" value="0.9" />
1
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424 <param name="settingsType" value="full" />
2
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425 <param name="seed_select" value="yes" />
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426 <param name="searchStart" value="25" />
1
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427
2
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428 <output name="output_log" file="rnastar_test2.log" compare="diff" lines_diff="10"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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429 <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
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430 <output name="mapped_reads" file="rnastar_test2_mapped_reads.bam" compare="sim_size" delta="200" />
0
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431 </test>
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432
2
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433 <test>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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434 <param name="input1" value="test3.fastqsanger" ftype="fastqsanger" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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435 <param name="genomeSource" value="history" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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436 <param name="ownFile" value="test3.ref.fa" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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437 <param name="sPaired" value="single" />
0
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438
2
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439 <param name="output_select" value="yes" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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440 <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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441 <param name="outSAMstrandField" value="intronMotif" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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442 <param name="settingsType" value="star_fusion" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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443
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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444 <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
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445 </test>
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446
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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447 <test>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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448 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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449 <param name="genomeSource" value="history" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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450 <param name="ownFile" value="tophat_test.fa" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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451 <param name="sPaired" value="single" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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452
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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453 <param name="output_select" value="yes" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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454 <param name="outSAMattributes" value="All" />
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455 <param name="outSAMstrandField" value="intronMotif" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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456 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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457
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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458 <param name="output_select2" value="yes" />
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459 <param name="settingsType" value="full" />
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460 <param name="seed_select" value="yes" />
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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461 <param name="align_select" value="yes" />
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462 <param name="chim_select" value="yes" />
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463
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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464 <!-- Uses default settings, should be similar to test1, but tests the parameters -->
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465 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="10"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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466 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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467 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /><!-- header is 434 bytes larger -->
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468 </test>
0
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469
2
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470 </tests>
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471 <help>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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472 **What it does**
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473
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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474 This tool runs STAR, an ultrafast universal RNA-seq aligner.
0
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475
2
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476 **Extra SAM attributes**
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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477
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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478 The Standard option includes the following four attributes::
0
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479
2
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480 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
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481 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
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482 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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483 nM: Number of mismatches per (paired) alignment
0
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484
2
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485 The All option includes the Standard attributes, plus the following four::
0
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486
2
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487 NM: Edit distance to the reference, including ambiguous bases but excluding clipping
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488 MD: String for mismatching positions
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489 jM: Intron motifs for all junctions
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490 jI: Start and end of introns for all junctions
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491
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492 **STAR-Fusion**
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493
2
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494 STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running
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495 STAR prior to STAR-Fusion can be pre-selected, with the following exceptions::
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496
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497 --twopassMode Basic # not an option in STAR 2.4.0
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498 --chimSegmentReadGapMax 3 # not an option in STAR 2.4.0
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499 --alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0
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500
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501 **Attributions**
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502
1
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503 Note that each component has its own license:
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504 - RNA STAR: GPLv3
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505 - samtools: MIT/Expat License
0
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506
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507 rna_star - see the web site at rna_star_
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508
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509 For details, please see the rna_starMS_
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510 "STAR: ultrafast universal RNA-seq aligner"
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511 A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635
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512
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513 Galaxy_ (that's what you are using right now!) for gluing everything together
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514
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515 Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper
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516
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517 Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies
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518 and odds and ends of other code and documentation comprising this tool was
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519 written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts
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520
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521 .. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml
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522 .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
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523 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
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524 .. _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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525 .. _rna_star: https://github.com/alexdobin/STAR
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526 .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full
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527 .. _Galaxy: http://getgalaxy.org
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528 </help>
2
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529 <citations>
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530 <citation type="doi">10.1093/bioinformatics/bts635</citation>
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531 </citations>
0
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532 </tool>