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1 <macros>
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2 <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
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3 whenever you make changes to the following two version tokens!
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4 The data manager uses a symlink to this macro file to keep the STAR and
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5 the index versions in sync, but you should manually adjust the +galaxy
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6 version number. -->
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7 <!-- STAR version to be used -->
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8 <token name="@VERSION@">2.7.8a</token>
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9 <!-- STAR index version compatible with this version of STAR
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10 This is the STAR version that introduced the index structure expected
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11 by the current version.
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12 It can be found for any specific version of STAR with:
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13 STAR -h | grep versionGenome
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14 or by looking for the versionGenome parameter in source/parametersDefault
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15 of STAR's source code -->
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2
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16 <token name="@IDX_VERSION@">2.7.4b</token>
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0
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17 <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
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18
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19 <xml name="requirements">
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20 <requirements>
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21 <requirement type="package" version="@VERSION@">star</requirement>
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22 <requirement type="package" version="1.9">samtools</requirement>
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23 <yield />
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24 </requirements>
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25 </xml>
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26
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27 <xml name="edam">
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28 <edam_topics>
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29 <edam_topic>topic_3170</edam_topic>
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30 <edam_topic>topic_3308</edam_topic>
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31 </edam_topics>
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32 <edam_operations>
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33 <edam_operation>operation_0292</edam_operation>
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34 </edam_operations>
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35 </xml>
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36
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37 <xml name="index_selection" token_with_gene_model="0">
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38 <param argument="--genomeDir" name="genomeDir" type="select"
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39 label="Select reference genome"
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40 help="If your genome of interest is not listed, contact the Galaxy team">
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41 <options from_data_table="@IDX_DATA_TABLE@">
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42 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
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43 <filter type="static_value" column="5" value="@IDX_VERSION@" />
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44 <filter type="sort_by" column="2" />
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45 <validator type="no_options" message="No indexes are available for the selected input dataset" />
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46 </options>
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47 </param>
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48 </xml>
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49
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50 <token name="@FASTQ_GZ_OPTION@">
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51 --readFilesCommand zcat
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52 </token>
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53 <xml name="citations">
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54 <citations>
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55 <citation type="doi">10.1093/bioinformatics/bts635</citation>
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56 </citations>
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57 </xml>
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58 <xml name="@SJDBOPTIONS@" token_optional="true">
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59 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/>
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60 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
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61 </xml>
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62 <xml name="dbKeyActions">
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63 <actions>
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64 <conditional name="refGenomeSource.geneSource">
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65 <when value="indexed">
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66 <action type="metadata" name="dbkey">
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67 <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
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68 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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69 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
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70 </option>
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71 </action>
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72 </when>
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73 <when value="history">
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74 <action type="metadata" name="dbkey">
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75 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
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76 </action>
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77 </when>
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78 </conditional>
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79 </actions>
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80 </xml>
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81 <token name="@TEMPINDEX@"><![CDATA[
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82 ## Create temporary index for custom reference
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83 #if str($refGenomeSource.geneSource) == 'history':
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84 mkdir -p tempstargenomedir &&
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85 STAR
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86 --runMode genomeGenerate
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87 --genomeDir 'tempstargenomedir'
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88 --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}'
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89 ## Handle difference between indices with/without annotations
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90 #if 'GTFconditional' in $refGenomeSource:
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91 ## GTFconditional exists only in STAR, but not STARsolo
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92 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
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93 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
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94 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
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95 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
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96 --sjdbGTFtagExonParentTranscript Parent
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97 #end if
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98 #end if
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99 #else:
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100 ## ref genome selection is less complex for STARsolo cause
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101 ## with-gtf is mandatory there
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102 --sjdbOverhang '${refGenomeSource.sjdbOverhang}'
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103 --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}'
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104 #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3':
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105 --sjdbGTFtagExonParentTranscript Parent
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106 #end if
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107 #end if
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108 #if str($refGenomeSource.genomeSAindexNbases):
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109 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
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110 #end if
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111 --runThreadN \${GALAXY_SLOTS:-4}
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112 &&
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113 #end if
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114 ]]></token>
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115 <token name="@REFGENOMEHANDLING@" ><![CDATA[
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116 --runThreadN \${GALAXY_SLOTS:-4}
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117 --genomeLoad NoSharedMemory
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118 --genomeDir
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119 #if str($refGenomeSource.geneSource) == 'history':
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120 tempstargenomedir
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121 #else:
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122 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
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123 ## Handle difference between indices with/without annotations
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124 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
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125 #if $refGenomeSource.GTFconditional.sjdbGTFfile:
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126 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
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127 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
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128 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
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129 --sjdbGTFtagExonParentTranscript Parent
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130 #end if
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131 #end if
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132 #end if
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133 #end if
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134 ]]></token>
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135 <token name="@READSHANDLING@" ><![CDATA[
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136 ## Check that the input pairs are of the same type
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137 ## otherwise STARsolo will run for a long time and then error out.
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138 ## We consume either repeats of two inputs R1 + R2
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139 ## or a collection of paired reads.
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140 #if str($sc.input_types.use) == "repeat":
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141 #set $reads1 = []
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142 #set $reads2 = []
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143 #for $r1, $r2 in zip($sc.input_types.input1, $sc.input_types.input2):
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144 #assert $r1.datatype == $r2.datatype
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145 #silent $reads1.append(str($r1))
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146 #silent $reads2.append(str($r2))
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147 #end for
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148 #set $reads1 = ','.join($reads1)
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149 #set $reads2 = ','.join($reads2)
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150 #elif str($sc.input_types.use) == "list_paired":
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151 #set $r1 = $sc.input_types.input_collection.forward
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152 #set $r2 = $sc.input_types.input_collection.reverse
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153 #set $reads1 = $r1
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154 #set $reads2 = $r2
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155 #end if
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156 ## cDNA sequence(s) [R2] always go first, then barcode(s) [R1]
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157 ## see: Section 3.2 of STAR manual for multiple inputs, and Section 13 for STARsolo inputs
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158 --readFilesIn $reads2 $reads1
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159 --soloCBmatchWLtype $sc.soloCBmatchWLtype
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160 #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'):
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161 @FASTQ_GZ_OPTION@
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162 #end if
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163 ]]></token>
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164 <xml name="ref_selection">
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165 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
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166 <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/>
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167 </xml>
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168 <xml name="stdio" >
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169 <stdio>
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170 <regex match="FATAL error" source="both" level="fatal"/>
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171 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
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172 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
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173 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
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174 <yield />
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175 </stdio>
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176 </xml>
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177 <xml name="input_selection">
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178 <conditional name="input_types" >
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179 <param name="use" type="select" label="Input Type" >
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180 <option value="repeat" >Separate barcode and cDNA reads</option>
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181 <option value="list_paired" >Paired collection of barcode and cDNA reads</option>
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182 </param>
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183 <when value="repeat">
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184 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" multiple="true"
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185 label="RNA-Seq FASTQ/FASTA file, Barcode reads" />
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186 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" multiple="true"
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187 label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>
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188 </when>
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189 <when value="list_paired">
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190 <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs" />
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191 </when>
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192 </conditional>
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193 </xml>
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194 <xml name="input_selection_smart_seq">
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195 <conditional name="input_types_smart_seq" >
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196 <param name="use" type="select" label="Input Type" >
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197 <option value="list_single_end" >Single-end FASTQ collection</option>
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198 <option value="list_paired_end" >Paired FASTQ collection</option>
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199 </param>
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200 <when value="list_single_end">
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201 <param name="single_end_collection" collection_type="list" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of single-end FASTQ files" />
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202 </when>
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203 <when value="list_paired_end">
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204 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" />
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205 </when>
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206 </conditional>
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207 </xml>
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208 <xml name="umidedup_options">
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209 <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other</option>
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210 <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option>
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211 <option value="1MM_Directional" >Directional with stringent UMI deduplication</option>
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212 </xml>
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213 <xml name="anchor_types">
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214 <option value="0">Read start</option>
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215 <option value="1">Read end</option>
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216 <option value="2">Adapter start</option>
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217 <option value="3">Adapter end</option>
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218 </xml>
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219 <xml name="cb_match_wl_common">
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220 <option value="Exact" >Exact</option>
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221 <option value="1MM" >Single match</option>
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222 </xml>
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223 <xml name="cb_match_wl_cellranger">
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224 <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2)</option>
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225 <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option>
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226 <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3)</option>
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227 </xml>
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228 <xml name="solo_adapter_params">
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229 <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." >
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230 <sanitizer>
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231 <valid initial="string.digits">
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232 <add value="-"/>
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233 <add value="A"/>
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234 <add value="T"/>
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235 <add value="C"/>
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236 <add value="G"/>
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237 <add value="N"/>
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238 </valid>
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239 </sanitizer>
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240 </param>
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241 <param argument="--soloAdapterMismatchesNmax" type="integer" min="1" value="1" label="Maximum number of mismatches allowed in adapter sequence" />
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242 <param argument="--clipAdapterType" type="select" >
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243 <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option>
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244 <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option>
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245 <option value="None" >No adapter clipping</option>
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246 </param>
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247 </xml>
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248 </macros>
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