annotate hisat2.xml @ 16:21e8ea8e1adb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
author iuc
date Sat, 30 Sep 2017 04:43:26 -0400
parents d5fe9aead222
children 40e1083a4430
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1 <tool id="hisat2" name="HISAT2" version="2.1.0" profile="17.01">
0
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2 <description>A fast and sensitive alignment program</description>
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3 <macros>
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4 <import>hisat2_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="2.1.0">hisat2</requirement>
9
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8 <requirement type="package" version="1.4">samtools</requirement>
0
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9 </requirements>
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10 <stdio>
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11 <regex level="fatal" match="hisat2-align exited with value 1" source="both" />
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12 <regex level="fatal" match="hisat2: not found" source="both" />
0
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13 <exit_code range="1:" />
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14 </stdio>
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15 <version_command>hisat2 --version</version_command>
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16 <command><![CDATA[
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18 ## Prepare HISAT2 index
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20 #if $reference_genome.source == "history":
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21 ln -s '$reference_genome.history_item' genome.fa &&
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22 hisat2-build -p \${GALAXY_SLOTS:-1} genome.fa genome &&
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23 #set index_path = 'genome'
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24 #else:
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25 #set index_path = $reference_genome.index.fields.path
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26 #end if
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29 ## If using known splice sites
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31 #if str($adv.spliced_options.spliced_options_selector) == "advanced" and str($adv.spliced_options.known_splice_gtf) != 'None':
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32 ln -s '${adv.spliced_options.known_splice_gtf}' splice_sites.gtf &&
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33 hisat2_extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&
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34 #end if
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37 ## Link in the input files, so HISAT2 can tell their type
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38
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39 #set compressed="False"
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40 #set reads_are_fastq = True
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41
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42 #if str($library.type) == 'paired':
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43 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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44 #set read1 = "input_f.fastq.gz"
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45 #set compressed = "GZ"
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46 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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47 #set read1 = "input_f.fastq.bz2"
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48 #set compressed = "BZ2"
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49 #else if $library.input_1.is_of_type('fasta'):
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50 #set reads_are_fastq = False
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51 #set read1 = "input_f.fasta"
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52 #else:
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53 #set read1 = "input_f.fastq"
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54 #end if
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55 ln -f -s '${library.input_1}' ${read1} &&
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56
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57 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
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58 #set read2 = "input_r.fastq.gz"
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59 #set compressed = "GZ"
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60 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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61 #set read2 = "input_r.fastq.bz2"
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62 #set compressed = "BZ2"
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63 #else if $library.input_2.is_of_type('fasta'):
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64 #set read2 = "input_r.fasta"
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65 #else:
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66 #set read2 = "input_r.fastq"
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67 #end if
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68 ln -f -s '${library.input_2}' ${read2} &&
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69
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70 #else if str($library.type) == 'paired_collection':
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71 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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72 #set read1 = "input_f.fastq.gz"
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73 #set compressed = "GZ"
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74 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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75 #set read1 = "input_f.fastq.bz2"
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76 #set compressed = "BZ2"
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77 #else if $library.input_1.forward.is_of_type('fasta'):
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78 #set reads_are_fastq = False
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79 #set read1 = "input_f.fasta"
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80 #else:
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81 #set read1 = "input_f.fastq"
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82 #end if
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83 ln -s '${library.input_1.forward}' ${read1} &&
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84
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85 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
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86 #set read2 = "input_r.fastq.gz"
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87 #set compressed = "GZ"
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88 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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89 #set read2 = "input_r.fastq.bz2"
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90 #set compressed = "BZ2"
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91 #else if $library.input_1.reverse.is_of_type("fasta"):
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92 #set read2 = "input_r.fasta"
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93 #else:
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94 #set read2 = "input_r.fastq"
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95 #end if
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96 ln -s '${library.input_1.reverse}' ${read2} &&
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97
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98 #else:
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99 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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100 #set read1 = "input_f.fastq.gz"
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101 #set compressed = "GZ"
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102 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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103 #set read1 = "input_f.fastq.bz2"
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104 #set compressed = "BZ2"
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105 #else if $library.input_1.is_of_type('fasta'):
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106 #set reads_are_fastq = False
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107 #set read1 = "input_f.fasta"
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108 #else:
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109 #set read1 = "input_f.fastq"
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110 #end if
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111 ln -f -s '${library.input_1}' ${read1} &&
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112 #end if
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113
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114
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115 ## Run HISAT2
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116
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117 hisat2
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118
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119 ## number threads
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120 -p \${GALAXY_SLOTS:-1}
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121
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122 ## ref genome index path
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123 -x '${index_path}'
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124
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125 ## input reads are fasta?
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126 #if not $reads_are_fastq:
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127 -f
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128 #end if
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129
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130 ## Input reads
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131
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132 #if str( $library.type ) == "single":
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133
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134 -U '${read1}'
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135
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136 #if str($adv.output_options.output_options_selector) == "advanced":
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137 #if str( $adv.output_options.unaligned_file ) == "true":
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138 #if $compressed == "GZ":
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139 --un-gz '$output_unaligned_reads_l'
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140 #else if $compressed == "BZ2":
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141 --un-bz2 '$output_unaligned_reads_l'
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142 #else:
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143 --un '$output_unaligned_reads_l'
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144 #end if
0
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145 #end if
10
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146
15
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147 #if str( $adv.output_options.aligned_file ) == "true":
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148 #if $compressed == "GZ":
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149 --al-gz '$output_aligned_reads_l'
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150 #else if $compressed == "BZ2":
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151 --al-bz2 '$output_aligned_reads_l'
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152 #else:
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153 --al '$output_aligned_reads_l'
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154 #end if
0
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155 #end if
15
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156 #end if
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157
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158 #else:
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159
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160 -1 '${read1}'
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161 -2 '${read2}'
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162
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163 #if str($adv.output_options.output_options_selector) == "advanced":
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164 #if str( $adv.output_options.unaligned_file ) == "true":
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165 #if $compressed == "GZ":
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166 --un-conc-gz '${output_unaligned_reads_l}'
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167 #else if $compressed == "BZ2":
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168 --un-conc-bz2 '${output_unaligned_reads_l}'
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169 #else:
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170 --un-conc '${output_unaligned_reads_l}'
7
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171 #end if
15
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172 #end if
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173
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174 #if str( $adv.output_options.aligned_file ) == "true":
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175 #if $compressed == "GZ":
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176 --al-conc-gz '${output_aligned_reads_l}'
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177 #else if $compressed == "BZ2":
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178 --al-conc-bz2 '${output_aligned_reads_l}'
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179 #else:
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180 --al-conc '${output_aligned_reads_l}'
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181 #end if
0
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182 #end if
15
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183 #end if
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184
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185 #if str($library.paired_options.paired_options_selector) == "advanced":
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186 ${library.paired_options.fr_rf_ff}
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187 ${library.paired_options.no_mixed}
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188 ${library.paired_options.no_discordant}
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189 #end if
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190
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191 #end if
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192
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193
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194 ## Specify strandedness of reads
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195
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196 #if str($library.rna_strandness):
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197 --rna-strandness ${library.rna_strandness}
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198 #end if
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199
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200
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201 ## Input options
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202
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203 #if str($adv.input_options.input_options_selector) == "advanced":
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204 #if int( $adv.input_options.skip ) > 0:
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205 --skip ${adv.input_options.skip}
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206 #end if
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207 #if int( $adv.input_options.qupto ) > 0:
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208 --qupto ${adv.input_options.qupto}
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209 #end if
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210 --trim5 '${adv.input_options.trim5}'
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211 --trim3 '${adv.input_options.trim3}'
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212 ${adv.input_options.qv_encoding}
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213 ${adv.input_options.solexa_quals}
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214 ${adv.input_options.int_quals}
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215 #end if
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216
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217
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218 ## Alignment options
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219
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220 #if str($adv.alignment_options.alignment_options_selector) == "advanced":
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221 --n-ceil ${adv.alignment_options.function_type},${adv.alignment_options.constant_term},${adv.alignment_options.coefficient}
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222 ${adv.alignment_options.ignore_quals}
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223 ${adv.alignment_options.skip_forward}
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224 ${adv.alignment_options.skip_reverse}
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225 #end if
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226
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227
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228 ## Scoring options
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229
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230 #if str($adv.scoring_options.scoring_options_selector) == "advanced":
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231 --mp ${adv.scoring_options.max_mismatch},${adv.scoring_options.min_mismatch}
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232 ${adv.scoring_options.no_softclip}
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233 --np ${adv.scoring_options.ambiguous_penalty}
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234 --rdg ${adv.scoring_options.read_open_penalty},${adv.scoring_options.read_extend_penalty}
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235 --rfg ${adv.scoring_options.ref_open_penalty},${adv.scoring_options.ref_extend_penalty}
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236 --sp ${scoring_options.soft_clip_penalty_max},${adv.scoring_options.soft_clip_penalty_min}
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237 --score-min ${scoring_options.function_type},${adv.scoring_options.constant_term},${adv.scoring_options.coefficient}
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238 #end if
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239
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240
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241 ## Spliced alignment options
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242
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243 #if str($adv.spliced_options.spliced_options_selector) == "advanced":
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244 --pen-cansplice ${adv.spliced_options.canonical_penalty}
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245 --pen-noncansplice ${adv.spliced_options.noncanonical_penalty}
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246 --pen-canintronlen ${adv.spliced_options.function_type},${adv.spliced_options.constant_term},${adv.spliced_options.coefficient}
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247 --pen-noncanintronlen ${adv.spliced_options.nc_function_type},${adv.spliced_options.nc_constant_term},${adv.spliced_options.nc_coefficient}
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248 #if str($adv.spliced_options.known_splice_gtf) != 'None':
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249 --known-splicesite-infile splice_sites.txt
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250 #end if
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251 ${adv.spliced_options.no_spliced_alignment_options.no_spliced_alignment}
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252 #if $adv.spliced_options.no_spliced_alignment_options.no_spliced_alignment == '--no-spliced-alignment'
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253 -I ${adv.spliced_options.no_spliced_alignment_options.minins}
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254 -X ${adv.spliced_options.no_spliced_alignment_options.maxins}
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255 #end if
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256 --min-intronlen ${adv.spliced_options.min_intron}
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257 --max-intronlen ${adv.spliced_options.max_intron}
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258 ${adv.spliced_options.tma}
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259
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260 #if str($adv.spliced_options.notmplen):
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261 ${adv.spliced_options.notmplen}
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262 #end if
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263 #end if
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264
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265
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266 ## Reporting options
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267
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268 #if str($adv.reporting_options.reporting_options_selector) == "advanced":
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269 -k ${adv.reporting_options.max_primary}
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270 --max-seeds ${adv.reporting_options.max_seeds}
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271 $adv.reporting_options.secondary
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272 #end if
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273
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274
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275 ## Other options
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276
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277 #if str( $adv.other_options.other_options_selector ) == "advanced":
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278 ${adv.other_options.non_deterministic}
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279 --seed '${adv.other_options.seed}'
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280 #end if
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281
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282
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283 ## Output Summary
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284
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285 #if str($sum.new_summary) == "true":
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286 --new-summary
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287 #end if
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288
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289 #if str($sum.summary_file) == "true":
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290 --summary-file summary.txt
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291 #end if
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292
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293 ## Convert SAM output to sorted BAM
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294
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295 | samtools sort - -@ \${GALAXY_SLOTS:-1} -l 6 -o '${output_alignments}'
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296
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297 ## Rename any output fastq files
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298
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299 #if $output_unaligned_reads_l and $output_unaligned_reads_r:
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300 #from os.path import splitext
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301 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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302 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
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303 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
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304 #end if
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305 #if $output_aligned_reads_l and $output_aligned_reads_r:
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306 #from os.path import splitext
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307 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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308 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
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309 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
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310 #end if
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311 ]]></command>
15
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312
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313 <!-- Define inputs -->
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314
0
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315 <inputs>
15
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316
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317 <!-- Reference genome -->
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318 <conditional name="reference_genome">
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319 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options">
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320 <option value="indexed" selected="true">Use a built-in genome</option>
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321 <option value="history">Use a genome from history</option>
0
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322 </param>
15
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323 <when value="indexed">
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324 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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325 <options from_data_table="hisat2_indexes">
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326 <filter type="sort_by" column="2" />
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327 <validator type="no_options" message="No genomes are available for the selected input dataset" />
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328 </options>
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329 </param>
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330 </when>
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331 <when value="history">
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332 <param name="history_item" type="data" format="fasta" label="Select the reference genome" />
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333 </when>
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334 </conditional>
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335
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336 <!-- Reads -->
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337 <conditional name="library">
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338 <param name="type" type="select" label="Single-end or paired-end reads?">
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339 <option value="single">Single-end</option>
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340 <option value="paired">Paired-end</option>
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341 <option value="paired_collection">Paired-end Collection</option>
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342 </param>
15
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343
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344 <when value="single">
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345 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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346 <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand information"
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347 help="'F' means a read corresponds to a transcript. 'R' means a read corresponds to the reverse complemented counterpart of a transcript. With this option being used, every read alignment will have an XS attribute tag: '+' means a read belongs to a transcript on '+' strand of genome. '-' means a read belongs to a transcript on '-' strand of genome.">
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348 <option value="">Unstranded</option>
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349 <option value="F">Forward (F)</option>
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350 <option value="R">Reverse (R)</option>
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351 </param>
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352 </when>
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353
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354 <when value="paired">
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355 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
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356 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
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357 <expand macro="paired_end_options" />
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358 </when>
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359
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360 <when value="paired_collection">
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361 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="Paired Collection" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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362 <expand macro="paired_end_options" />
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363 </when>
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364 </conditional>
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365
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366 <!-- Summary Options -->
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367 <section name="sum" title="Summary Options" expanded="False">
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368 <param name="new_summary" argument="--new-summary" type="boolean" checked="False" label="Output alignment summary in a more machine-friendly style." help="Select this option for compatibility with MultiQC" />
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369 <param name="summary_file" argument="--summary-file" type="boolean" checked="False" label="Print alignment summary to a file." help="Output alignment summary to a file in addition to stderr." />
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370 </section>
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371
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372 <!-- Advanced Options -->
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373 <section name="adv" title="Advanced Options" expanded="False">
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374 <conditional name="input_options">
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375 <param name="input_options_selector" type="select" label="Input options">
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376 <option value="defaults">Use default values</option>
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377 <option value="advanced">Specify input options</option>
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378 </param>
15
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379 <when value="defaults" />
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380 <when value="advanced">
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381 <param name="skip" argument="-s" type="integer" min="0" value="0" label="Skip the first N reads or pairs in the input" help="default: 0" />
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382 <param name="qupto" argument="-u" type="integer" min="0" value="0" label="Align the first N reads or read pairs from the input (after the first N reads or pairs have been skipped), then stop" help="default: no limit" />
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383 <param name="trim5" argument="-5" type="integer" min="0" value="0" label="Trim 5' end" help="Trim N bases from 5' (left) end of each read before alignment, default: 0" />
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384 <param name="trim3" argument="-3" type="integer" min="0" value="0" label="Trim 3' end" help="Trim N bases from 3' (right) end of each read before alignment, default: 0"/>
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385 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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386 <option value="--phred33" selected="True">Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines (--phred33)</option>
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387 <option value="--phred64">Input qualities are ASCII chars equal to the Phred quality plus 64. This is also called the "Phred+64" encoding (--phred64)</option>
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388 </param>
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389 <param name="solexa_quals" argument="--solexa-quals" type="boolean" truevalue="--solexa-quals" falsevalue="" checked="False" label="Convert input qualities from Solexa (which can be negative) to Phred (which can't). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3)" help="--solexa-quals; default: False"/>
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390 <param name="int_quals" argument="--int-quals" type="boolean" truevalue="--int-quals" falsevalue="" checked="False" label="Are quality values provided as space separated integers?" help="Quality values are represented in the read input file as space-separated ASCII integers, e.g., 40 40 30 40..., rather than ASCII characters, e.g., II?I.... Integers are treated as being on the Phred quality scale unless --solexa-quals is also specified [default: False]"/>
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391 </when>
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392 </conditional>
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393
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394 <conditional name="alignment_options">
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395 <param name="alignment_options_selector" type="select" label="Alignment options">
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396 <option value="defaults">Use default values</option>
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397 <option value="advanced">Specify alignment options</option>
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398 </param>
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399 <when value="defaults" />
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400 <when value="advanced">
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401 <param name="function_type" argument="--n-ceil" type="select" display="radio" label="Function governing the maximum number of ambiguous characters (usually Ns and/or .s) allowed in a read as a function of read length" help="Reads exceeding this ceiling are filtered out">
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402 <option value="C">Constant [f(x) = B]</option>
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403 <option value="L" selected="true">Linear [f(x) = B + A * x]</option>
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404 <option value="S">Square root [f(x) = B + A * x&#178;]</option>
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405 <option value="G">Natural logarithm [f(x) = B + A * log(x)]</option>
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406 </param>
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407 <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
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408 <param name="coefficient" type="float" value="0.15" label="Coefficient (A)" help="Coefficient for the above function" />
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409 <param argument="--ignore-quals" name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="Ignore quality values" help="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value. I.e. input is treated as though all quality values are high. This is also the default behavior when the input doesn't specify quality values" />
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410 <param argument="--nofw" name="skip_forward" type="boolean" truevalue="--nofw" falsevalue="" label="Skip forward strand of reference" help="If --nofw is specified, HISAT2 will not attempt to align unpaired reads to the forward (Watson) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes HISAT2 to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand" />
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411 <param argument="--norc" name="skip_reverse" type="boolean" truevalue="--norc" falsevalue="" label="Skip reverse strand of reference" help="If --norc is specified, HISAT2 will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --norc causes HISAT2 to explore only those paired-end configurations corresponding to fragments from the forward-complement (Watson) strand" />
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412 </when>
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413 </conditional>
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414
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415 <conditional name="scoring_options">
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416 <param name="scoring_options_selector" type="select" label="Scoring options">
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417 <option value="defaults">Use default values</option>
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418 <option value="advanced">Specify scoring options</option>
0
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419 </param>
15
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420 <when value="defaults" />
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421 <when value="advanced">
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422 <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
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423 <param name="coefficient" type="float" value="-0.2" label="Coefficient (A)" help="Coefficient for the above function" />
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424 <param argument="--mp" name="max_mismatch" type="integer" value="6" min="0" label="Maximum mismatch penalty" help="Sets the maximum mismatch penalty. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an N. If --ignore-quals is specified, the number subtracted quals MX. Otherwise, the number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value" />
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425 <param argument="--mp" name="min_mismatch" type="integer" value="2" min="0" label="Minimum mismatch penalty" help="Sets the minimum mismatch penalty. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an N. If --ignore-quals is specified, the number subtracted quals MX. Otherwise, the number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value" />
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426 <param argument="--sp" name="soft_clip_penalty_max" type="integer" value="2" min="0" label="Maximum soft-clipping penalty" help="Sets the maximum (MX) penalty for soft-clipping per base. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position. The number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value" />
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427 <param argument="--sp" name="soft_clip_penalty_min" type="integer" value="1" min="0" label="Minimum soft-clipping penalty" help="Sets the minimum (MN) penalty for soft-clipping per base. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position. The number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value" />
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428 <param argument="--no-softclip" name="no_softclip" type="boolean" truevalue="" falsevalue="--no-softclip" label="Allow soft-clipping" />
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429 <param argument="--np" name="ambiguous_penalty" type="integer" value="1" min="0" label="Ambiguous read penalty" help="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N" />
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430 <param argument="--rdg" name="read_open_penalty" type="integer" value="5" min="0" label="Read gap open penalty" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
431 <param argument="--rdg" name="read_extend_penalty" type="integer" value="3" min="0" label="Read gap extend penalty" help="A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
432 <param argument="--rfg" name="ref_open_penalty" type="integer" value="5" min="0" label="Reference gap open penalty" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
433 <param argument="--rfg" name="ref_extend_penalty" type="integer" value="3" min="0" label="Reference gap extend penalty" help="A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
434 <param name="function_type" argument="--score-min" type="select" display="radio" label="Function governing the minimum alignment score needed for an alignment to be considered &quot;valid&quot; (i.e. good enough to report)" help="This is a function of read length">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
435 <option value="C">Constant [f(x) = B]</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
436 <option value="L" selected="true">Linear [f(x) = B + A * x]</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
437 <option value="S">Square root [f(x) = B + A * x&#178;]</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
438 <option value="G">Natural logarithm [f(x) = B + A * log(x)]</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
439 </param>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
440 </when>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
441 </conditional>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
442
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
443 <conditional name="spliced_options">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
444 <param name="spliced_options_selector" type="select" label="Spliced alignment options">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
445 <option value="defaults">Use default values</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
446 <option value="advanced">Specify spliced alignment options</option>
0
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parents:
diff changeset
447 </param>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
448 <when value="defaults" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
449 <when value="advanced">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
450 <param name="canonical_penalty" argument="--pen-cansplice" type="integer" value="0" min="0" label="Penalty for canonical splice sites" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
451 <param name="noncanonical_penalty" argument="--pen-noncansplice" type="integer" value="12" min="0" label="Penalty for non-canonical splice sites" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
452 <param name="function_type" argument="--pen-canintronlen" type="select" display="radio" label="Penalty function for long introns with canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
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453 <option value="C">Constant [f(x) = B]</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
454 <option value="L">Linear [f(x) = B + A * x]</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
455 <option value="S">Square root [f(x) = B + A * x&#178;]</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
456 <option value="G" selected="true">Natural logarithm [f(x) = B + A * log(x)]</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
457 </param>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
458 <param name="constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
459 <param name="coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
460 <param name="nc_function_type" argument="--pen-noncanintronlen" type="select" display="radio" label="Penalty function for long introns with non-canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
461 <option value="C">Constant [f(x) = B]</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
462 <option value="L">Linear [f(x) = B + A * x]</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
463 <option value="S">Square root [f(x) = B + A * x&#178;]</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
464 <option value="G" selected="true">Natural logarithm [f(x) = B + A * log(x)]</option>
9
2dbb7f0ea66f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 1baf0d1eb5d9cb012e4ce1385431461f26f7bc05
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parents: 8
diff changeset
465 </param>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
466 <param name="nc_constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
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467 <param name="nc_coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
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468 <param name="min_intron" type="integer" value="20" min="0" label="Minimum intron length" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
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469 <param name="max_intron" type="integer" value="500000" min="0" label="Maximum intron length" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
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470 <conditional name="no_spliced_alignment_options">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
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471 <param name="no_spliced_alignment" argument="--no-spliced-alignment" type="select" label="Disable spliced alignment">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
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472 <option value="--no-spliced-alignment">True</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
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473 <option value="">False</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
474 </param>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
475 <when value="--no-spliced-alignment">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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476 <param name="minins" argument="-I" type="integer" value="0" min="0" label="Minimum fragment length for valid paired-end alignments" help="E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates. The larger the difference between -I and -X, the slower HISAT2 will run. This is because larger differences between -I and -X require that HISAT2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), HISAT2 is very efficient" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
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477 <param name="maxins" argument="-X" type="integer" value="500" min="0" label="Maximum fragment length for valid paired-end alignments" help="E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates. The larger the difference between -I and -X, the slower HISAT2 will run. This is because larger differences between -I and -X require that HISAT2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), HISAT2 is very efficient" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
478 </when>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
479 <when value="" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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480 </conditional>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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481 <param name="known_splice_gtf" type="data" format="gtf" optional="true" label="GTF file with known splice sites" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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482 <param name="tma" type="select" display="radio" label="Transcriptome assembly reporting">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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483 <option value="">Use default reporting.</option>
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484 <option value="--tmo">Report only those alignments within known transcripts.</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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485 <option value="--dta">Report alignments tailored for transcript assemblers including StringTie.</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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486 <option value="--dta-cufflinks">Report alignments tailored specifically for Cufflinks.</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
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487 </param>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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488 <param name="notmplen" argument="--no-templatelen-adjustment" type="boolean" truevalue="--no-templatelen-adjustment" falsevalue="" label="Disable automatic template length adjustment for RNA-seq reads" help="Default: false" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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489 </when>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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490 </conditional>
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parents: 14
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491
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
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492 <conditional name="reporting_options">
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parents: 14
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493 <param name="reporting_options_selector" type="select" label="Reporting options">
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parents: 14
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494 <option value="defaults">Use default values</option>
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parents: 14
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495 <option value="advanced">Specify reporting options</option>
0
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parents:
diff changeset
496 </param>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
497 <when value="defaults" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
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498 <when value="advanced">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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499 <param name="max_primary" argument="-k" type="integer" min="0" optional="true" label="Primary alignments" help="Search for at most K distinct, primary alignments for each read. Primary alignments mean alignments whose alignment score is equal or higher than any other alignments. The search terminates when it can't find more distinct valid alignments, or when it finds K, whichever happens first. The alignment score for a paired-end alignment equals the sum of the alignment scores of the individual mates. Each reported read or pair alignment beyond the first has the SAM 'secondary' bit (which equals 256) set in its FLAGS field. For reads that have more than K distinct, valid alignments, HISAT2 does not guarantee that the K alignments reported are the best possible in terms of alignment score. HISAT2 is not designed with large values for -k in mind, so when aligning reads to long repetitive genomes, a large K can be very, very slow. Default: 5 (HFM) or 10 (HGFM)" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
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500 <param name="max_seeds" argument="--max-seeds" type="integer" min="0" optional="true" label="Maximum number of seeds that will be extended" help="HISAT2, like other aligners, uses seed-and-extend approaches. HISAT2 tries to extend seeds to full-length alignments. HISAT2 extends up to these many seeds and skips the rest of the seeds. Large values for --max-seeds may improve alignment sensitivity, but HISAT2 is not designed with large values for --max-seeds in mind, and when aligning reads to long repetitive genomes, a large --max-seeds can be very, very slow. Default: 5 (HFM) or 10 (HGFM)" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
501 <param name="secondary" argument="--secondary" type="boolean" truevalue="--secondary" falsevalue="" label="Report secondary alignments" />
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iuc
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diff changeset
502 </when>
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diff changeset
503 </conditional>
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iuc
parents: 14
diff changeset
504
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iuc
parents: 14
diff changeset
505 <conditional name="output_options">
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iuc
parents: 14
diff changeset
506 <param name="output_options_selector" type="select" label="Output options">
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iuc
parents: 14
diff changeset
507 <option value="defaults">Use default values</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
508 <option value="advanced">Specify output options</option>
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iuc
parents: 14
diff changeset
509 </param>
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iuc
parents: 14
diff changeset
510 <when value="defaults" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
511 <when value="advanced">
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parents: 14
diff changeset
512 <param name="unaligned_file" argument="--un/--un-conc" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="This triggers --un parameter for single reads and --un-conc for paired reads" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
513 <param name="aligned_file" argument="--al/--al-conc" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="This triggers --al parameter for single reads and --al-conc for paired reads" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
514 </when>
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parents: 14
diff changeset
515 </conditional>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
516
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
517 <conditional name="other_options">
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iuc
parents: 14
diff changeset
518 <param name="other_options_selector" type="select" label="Other options">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
519 <option value="defaults">Use default values</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
520 <option value="advanced">Specify other options</option>
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parents: 14
diff changeset
521 </param>
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iuc
parents: 14
diff changeset
522 <when value="defaults" />
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iuc
parents: 14
diff changeset
523 <when value="advanced">
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iuc
parents: 14
diff changeset
524 <param name="seed" argument="--seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="Default=0" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
525 <param name="non_deterministic" argument="--non-deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="see Help below for explanation of this option; default: False"/>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
526 </when>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
527 </conditional>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
528 </section>
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parents: 14
diff changeset
529
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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diff changeset
530 </inputs>
15
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iuc
parents: 14
diff changeset
531
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iuc
parents: 14
diff changeset
532 <!-- Define outputs -->
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parents: 14
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533
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
534 <outputs>
15
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iuc
parents: 14
diff changeset
535
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parents: 14
diff changeset
536 <!-- BAM -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
537 <data name="output_alignments" format="bam" label="${tool.name} on ${on_string}: aligned reads (BAM) " />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
538
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
539 <!-- Unaligned fastq (L) -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
540 <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (L)">
16
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iuc
parents: 15
diff changeset
541 <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True</filter>
3
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iuc
parents: 2
diff changeset
542 </data>
15
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parents: 14
diff changeset
543
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
544 <!-- Aligned fastq (L) -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
545 <data name="output_aligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (L)">
16
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iuc
parents: 15
diff changeset
546 <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True</filter>
14
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iuc
parents: 13
diff changeset
547 </data>
15
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iuc
parents: 14
diff changeset
548
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
549 <!-- Unaligned fastq (R) -->
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
550 <data name="output_unaligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (R)">
15
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iuc
parents: 14
diff changeset
551 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection') and (adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True) </filter>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
552 </data>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
553
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
554 <!-- Aligned fastq (R) -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
555 <data name="output_aligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (R)">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
556 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection') and (adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True) </filter>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
557 </data>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
558
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
559 <!-- Alignment summary file -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
560 <data name="summary_file" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary" >
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
561 <filter>sum['summary_file'] is True</filter>
7
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iuc
parents: 6
diff changeset
562 </data>
15
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parents: 14
diff changeset
563
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
564 </outputs>
15
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parents: 14
diff changeset
565
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
566 <!-- Define tests -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
567
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
568 <tests>
16
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iuc
parents: 15
diff changeset
569 <!-- Ensure bam output works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
570 <test expect_num_outputs="1" >
15
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iuc
parents: 14
diff changeset
571 <param name="type" value="paired" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
572 <param name="source" value="history" />
14
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iuc
parents: 13
diff changeset
573 <param name="history_item" ftype="fasta" value="phiX.fa" />
15
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iuc
parents: 14
diff changeset
574 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
575 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
14
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iuc
parents: 13
diff changeset
576 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
0
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iuc
parents:
diff changeset
577 </test>
16
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iuc
parents: 15
diff changeset
578 <!-- Ensure built-in reference works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
579 <test expect_num_outputs="1">
15
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iuc
parents: 14
diff changeset
580 <param name="type" value="paired" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
581 <param name="source" value="indexed" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
582 <param name="input_1" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_forward.fastq" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
583 <param name="input_2" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_reverse.fastq" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
584 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
585 </test>
16
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iuc
parents: 15
diff changeset
586 <!-- Ensure trimming works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
587 <test expect_num_outputs="1">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
588 <param name="type" value="paired" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
589 <param name="source" value="history" />
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
590 <param name="history_item" ftype="fasta" value="phiX.fa" />
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
591 <param name="input_options_selector" value="advanced" />
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
592 <param name="trim3" value="15" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
593 <param name="trim5" value="15" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
594 <param name="input_1" ftype="fastqsanger" value="hisat_input_2_forward.fastq" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
595 <param name="input_2" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" />
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
596 <output name="output_alignments" file="hisat_output_2.bam" ftype="bam" lines_diff="2" />
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
597 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
598 <!-- Ensure paired options works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
599 <test expect_num_outputs="1">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
600 <param name="type" value="paired" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
601 <param name="source" value="history" />
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
602 <param name="history_item" ftype="fasta" value="phiX.fa" />
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
603 <param name="input_options_selector" value="advanced" />
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
604 <param name="trim3" value="15" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
605 <param name="trim5" value="15" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
606 <param name="input_1" ftype="fastqsanger" value="hisat_input_2_forward.fastq" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
607 <param name="input_2" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
608 <param name="paired_options_selector" value="advanced" />
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
609 <param name="no_mixed" value="True" />
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
610 <param name="no_discordant" value="True" />
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
611 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" />
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
612 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
613 <!-- Ensure single unaligned output works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
614 <test expect_num_outputs="2">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
615 <param name="type" value="single" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
616 <param name="source" value="history" />
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
617 <param name="history_item" ftype="fasta" value="phiX.fa" />
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
618 <param name="output_options_selector" value="advanced" />
7
5ba8e317529a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents: 6
diff changeset
619 <param name="unaligned_file" value="true" />
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
620 <param name="history_item" ftype="fasta" value="phiX.fa" />
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
621 <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
622 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />
7
5ba8e317529a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents: 6
diff changeset
623 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
624 <!-- Ensure paired unaligned/aligned output works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
625 <test expect_num_outputs="5">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
626 <param name="type" value="paired" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
627 <param name="source" value="history" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
628 <param name="output_options_selector" value="advanced" />
7
5ba8e317529a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents: 6
diff changeset
629 <param name="unaligned_file" value="true" />
5ba8e317529a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents: 6
diff changeset
630 <param name="aligned_file" value="true" />
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
631 <param name="history_item" ftype="fasta" value="phiX.fa" />
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
632 <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
633 <param name="input_2" ftype="fasta" value="test_unaligned_reads.fasta" />
7
5ba8e317529a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents: 6
diff changeset
634 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />
5ba8e317529a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents: 6
diff changeset
635 <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" />
5ba8e317529a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents: 6
diff changeset
636 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
637 <!-- Ensure fastqsanger.gz works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
638 <test expect_num_outputs="1">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
639 <param name="type" value="paired" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
640 <param name="source" value="history" />
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
641 <param name="history_item" ftype="fasta" value="phiX.fa" />
10
da8d655e2154 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents: 9
diff changeset
642 <param name="input_options_selector" value="advanced" />
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
643 <param name="trim3" value="15" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
644 <param name="trim5" value="15" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
645 <param name="input_1" ftype="fastqsanger.gz" value="hisat_input_2_forward.fastq.gz" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
646 <param name="input_2" ftype="fastqsanger.gz" value="hisat_input_2_reverse.fastq.gz" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
647 <param name="paired_options_selector" value="advanced" />
10
da8d655e2154 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents: 9
diff changeset
648 <param name="no_mixed" value="True" />
da8d655e2154 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents: 9
diff changeset
649 <param name="no_discordant" value="True" />
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
650 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" />
10
da8d655e2154 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents: 9
diff changeset
651 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
652 <!-- Ensure fastqsanger.bz2 works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
653 <test expect_num_outputs="1">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
654 <param name="type" value="paired" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
655 <param name="source" value="history" />
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
656 <param name="history_item" ftype="fasta" value="phiX.fa" />
10
da8d655e2154 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents: 9
diff changeset
657 <param name="input_options_selector" value="advanced" />
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
658 <param name="trim3" value="15" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
659 <param name="trim5" value="15" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
660 <param name="input_1" ftype="fastqsanger.bz2" value="hisat_input_2_forward.fastq.bz2" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
661 <param name="input_2" ftype="fastqsanger.bz2" value="hisat_input_2_reverse.fastq.bz2" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
662 <param name="paired_options_selector" value="advanced" />
10
da8d655e2154 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents: 9
diff changeset
663 <param name="no_mixed" value="True" />
da8d655e2154 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents: 9
diff changeset
664 <param name="no_discordant" value="True" />
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
665 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" />
10
da8d655e2154 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents: 9
diff changeset
666 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
667 <!-- Ensure paired strandness works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
668 <test expect_num_outputs="1">
15
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669 <param name="type" value="paired" />
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670 <param name="source" value="history" />
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671 <param name="history_item" ftype="fasta" value="phiX.fa" />
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672 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
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673 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
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674 <param name="rna_strandness" value="FR" />
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675 <output name="output_alignments" file="hisat_output_4.bam" ftype="bam" lines_diff="2" />
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676 </test>
16
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diff changeset
677 <!-- Ensure summary file output works -->
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678 <test expect_num_outputs="2">
15
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679 <param name="type" value="single" />
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680 <param name="source" value="history" />
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681 <param name="history_item" ftype="fasta" value="phiX.fa" />
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682 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
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683 <param name="rna_strandness" value="R" />
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684 <param name="new_summary" value="true" />
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685 <param name="summary_file" value="true" />
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686 <output name="summary_file" file="hisat_output.summary" ftype="txt" />
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687 </test>
0
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688 </tests>
15
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689
14
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690 <help><![CDATA[
0
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diff changeset
691 Introduction
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692 ============
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693
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694 What is HISAT?
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695 --------------
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diff changeset
696
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diff changeset
697 `HISAT <http://ccb.jhu.edu/software/hisat>`__ is a fast and sensitive
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698 spliced alignment program. As part of HISAT, we have developed a new
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diff changeset
699 indexing scheme based on the Burrows-Wheeler transform
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diff changeset
700 (`BWT <http://en.wikipedia.org/wiki/Burrows-Wheeler_transform>`__) and
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diff changeset
701 the `FM index <http://en.wikipedia.org/wiki/FM-index>`__, called
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parents:
diff changeset
702 hierarchical indexing, that employs two types of indexes: (1) one global
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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diff changeset
703 FM index representing the whole genome, and (2) many separate local FM
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
704 indexes for small regions collectively covering the genome. Our
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
705 hierarchical index for the human genome (about 3 billion bp) includes
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
706 ~48,000 local FM indexes, each representing a genomic region of
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
707 ~64,000bp. As the basis for non-gapped alignment, the FM index is
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
708 extremely fast with a low memory footprint, as demonstrated by
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
709 `Bowtie <http://bowtie-bio.sf.net>`__. In addition, HISAT provides
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
710 several alignment strategies specifically designed for mapping different
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
711 types of RNA-seq reads. All these together, HISAT enables extremely fast
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
712 and sensitive alignment of reads, in particular those spanning two exons
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
713 or more. As a result, HISAT is much faster >50 times than
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
714 `TopHat2 <http://ccb.jhu.edu/software/tophat>`__ with better alignment
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
715 quality. Although it uses a large number of indexes, the memory
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parents:
diff changeset
716 requirement of HISAT is still modest, approximately 4.3 GB for human.
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parents:
diff changeset
717 HISAT uses the `Bowtie2 <http://bowtie-bio.sf.net/bowtie2>`__
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
718 implementation to handle most of the operations on the FM index. In
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
719 addition to spliced alignment, HISAT handles reads involving indels and
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
720 supports a paired-end alignment mode. Multiple processors can be used
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
721 simultaneously to achieve greater alignment speed. HISAT outputs
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
722 alignments in `SAM <http://samtools.sourceforge.net/SAM1.pdf>`__ format,
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
723 enabling interoperation with a large number of other tools (e.g.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
724 `SAMtools <http://samtools.sourceforge.net>`__,
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
725 `GATK <http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit>`__)
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
726 that use SAM. HISAT is distributed under the `GPLv3
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
727 license <http://www.gnu.org/licenses/gpl-3.0.html>`__, and it runs on
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
728 the command line under Linux, Mac OS X and Windows.
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parents:
diff changeset
729
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
730 Running HISAT
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iuc
parents:
diff changeset
731 =============
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parents:
diff changeset
732
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iuc
parents:
diff changeset
733 Reporting
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
734 ---------
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
735
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
736 The reporting mode governs how many alignments HISAT looks for, and how
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
737 to report them.
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parents:
diff changeset
738
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
739 In general, when we say that a read has an alignment, we mean that it
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
740 has a `valid
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
741 alignment <#valid-alignments-meet-or-exceed-the-minimum-score-threshold>`__.
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iuc
parents:
diff changeset
742 When we say that a read has multiple alignments, we mean that it has
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
743 multiple alignments that are valid and distinct from one another.
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parents:
diff changeset
744
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parents:
diff changeset
745 Distinct alignments map a read to different places
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iuc
parents:
diff changeset
746 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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parents:
diff changeset
747
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iuc
parents:
diff changeset
748 Two alignments for the same individual read are "distinct" if they map
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
749 the same read to different places. Specifically, we say that two
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
750 alignments are distinct if there are no alignment positions where a
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
751 particular read offset is aligned opposite a particular reference offset
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iuc
parents:
diff changeset
752 in both alignments with the same orientation. E.g. if the first
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
753 alignment is in the forward orientation and aligns the read character at
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iuc
parents:
diff changeset
754 read offset 10 to the reference character at chromosome 3, offset
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
755 3,445,245, and the second alignment is also in the forward orientation
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
756 and also aligns the read character at read offset 10 to the reference
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
757 character at chromosome 3, offset 3,445,245, they are not distinct
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
758 alignments.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
759
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
760 Two alignments for the same pair are distinct if either the mate 1s in
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
761 the two paired-end alignments are distinct or the mate 2s in the two
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
762 alignments are distinct or both.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
763
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
764 Default mode: search for one or more alignments, report each
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
765 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
766
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
767 HISAT searches for up to N distinct, primary alignments for each read,
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
768 where N equals the integer specified with the ``-k`` parameter. Primary
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
769 alignments mean alignments whose alignment score is equal or higher than
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
770 any other alignments. It is possible that multiple distinct alignments
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
771 whave the same score. That is, if ``-k 2`` is specified, HISAT will
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
772 search for at most 2 distinct alignments. The alignment score for a
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
773 paired-end alignment equals the sum of the alignment scores of the
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
774 individual mates. Each reported read or pair alignment beyond the first
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
775 has the SAM 'secondary' bit (which equals 256) set in its FLAGS field.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
776 See the `SAM specification <http://samtools.sourceforge.net/SAM1.pdf>`__
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
777 for details.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
778
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
779 HISAT does not "find" alignments in any specific order, so for reads
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
780 that have more than N distinct, valid alignments, HISAT does not
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
781 gaurantee that the N alignments reported are the best possible in terms
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
782 of alignment score. Still, this mode can be effective and fast in
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
783 situations where the user cares more about whether a read aligns (or
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
784 aligns a certain number of times) than where exactly it originated.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
785
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
786 Alignment summmary
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
787 ------------------
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
788
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
789 When HISAT finishes running, it prints messages summarizing what happened. These messages are printed to the "standard error" ("stderr") filehandle and can be optionally printed to a file. Choose `--new-summary` under **Summary Options** for compatibility with `MultiQC <http://multiqc.info/docs/#hisat2>`_.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
790 For datasets consisting of unpaired reads, the summary might look like this:
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
791
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
792 ::
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
793
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
794 20000 reads; of these:
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
795 20000 (100.00%) were unpaired; of these:
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
796 1247 (6.24%) aligned 0 times
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
797 18739 (93.69%) aligned exactly 1 time
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
798 14 (0.07%) aligned >1 times
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
799 93.77% overall alignment rate
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
800
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
801 For datasets consisting of pairs, the summary might look like this:
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
802
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
803 ::
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
804
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
805 10000 reads; of these:
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
806 10000 (100.00%) were paired; of these:
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
807 650 (6.50%) aligned concordantly 0 times
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
808 8823 (88.23%) aligned concordantly exactly 1 time
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
809 527 (5.27%) aligned concordantly >1 times
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
810 ----
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
811 650 pairs aligned concordantly 0 times; of these:
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
812 34 (5.23%) aligned discordantly 1 time
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
813 ----
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
814 616 pairs aligned 0 times concordantly or discordantly; of these:
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
815 1232 mates make up the pairs; of these:
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
816 660 (53.57%) aligned 0 times
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
817 571 (46.35%) aligned exactly 1 time
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
818 1 (0.08%) aligned >1 times
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
819 96.70% overall alignment rate
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
820
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
821 The indentation indicates how subtotals relate to totals.
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
822
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
823
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
824 .. class:: infomark
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
825
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
826 **HISAT2 options**
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
827
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
828 Galaxy wrapper for HISAT2 implements most, but not all, options available through the command line. Supported options are described below.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
829
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
830 -----
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
831
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
832 **Inputs**
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
833
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
834 HISAT2 accepts files in FASTQ or FASTA format (single-end or paired-end).
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
835
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
836 Note that if your reads are from a stranded library, you need to choose the appropriate setting under **Specify strand information** above. For single-end reads, use F or R. 'F' means a read corresponds to a transcript. 'R' means a read corresponds to the reverse complemented counterpart of a transcript. For paired-end reads, use either FR or RF. With this option being used, every read alignment will have an XS attribute tag: '+' means a read belongs to a transcript on '+' strand of genome. '-' means a read belongs to a transcript on '-' strand of genome. (TopHat has a similar option, --library-type option, where fr-firststrand corresponds to R and RF; fr-secondstrand corresponds to F and FR.)
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
837
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
838 ------
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
839
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
840 **Input options**::
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
841
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
842 -s/--skip <int>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
843 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
844
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845 -u/--qupto <int>
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846 Align the first `<int>` reads or read pairs from the input (after the
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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847 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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diff changeset
848
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diff changeset
849 -5/--trim5 <int>
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diff changeset
850 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
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851
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852 -3/--trim3 <int>
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diff changeset
853 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
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854
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parents: 14
diff changeset
855 --phred33
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
856 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
857 also called the "Phred+33" encoding, which is used by the very latest Illumina
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
858 pipelines.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
859
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diff changeset
860 --phred64
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
861 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
862 also called the "Phred+64" encoding.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
863
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diff changeset
864 --solexa-quals
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parents: 14
diff changeset
865 Convert input qualities from Solexa Phred quality (which can be negative) to
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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866 Phred Phred quality (which can't). This scheme was used in older Illumina GA
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
867 Pipeline versions (prior to 1.3). Default: off.
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diff changeset
868
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diff changeset
869 --int-quals
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870 Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`....
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871 Integers are treated as being on the Phred quality scale unless
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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872 `--solexa-quals` is also specified. Default: off.
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873
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diff changeset
874 ------
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875
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diff changeset
876 **Alignment options**::
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diff changeset
877
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diff changeset
878 --n-ceil <func>
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diff changeset
879 Sets a function governing the maximum number of ambiguous characters (usually
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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880 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
881 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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882 where x is the read length. Reads exceeding this ceiling are filtered out.
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diff changeset
883 Default: `L,0,0.15`.
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diff changeset
884
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diff changeset
885 --ignore-quals
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886 When calculating a mismatch penalty, always consider the quality value at the
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887 mismatched position to be the highest possible, regardless of the actual value.
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888 I.e. input is treated as though all quality values are high. This is also the
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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889 default behavior when the input doesn't specify quality values (e.g. in `-f`,
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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890 `-r`, or `-c` modes).
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891
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diff changeset
892 --nofw/--norc
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893 If `--nofw` is specified, `hisat2` will not attempt to align unpaired reads to
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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894 the forward (Watson) reference strand. If `--norc` is specified, `hisat2` will not attempt to align unpaired reads against the reverse-complement (Crick)
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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895 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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896 fragments; i.e. specifying `--nofw` causes `hisat2` to explore only those
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897 paired-end configurations corresponding to fragments from the reverse-complement
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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898 (Crick) strand. Default: both strands enabled.
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899
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900 -----
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901
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902 **Scoring options**::
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903
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diff changeset
904 --mp MX,MN
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diff changeset
905 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A number less than or equal to `MX` and greater than or equal to `MN` is
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
906 subtracted from the alignment score for each position where a read character
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907 aligns to a reference character, the characters do not match, and neither is an
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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908 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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diff changeset
909 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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diff changeset
910 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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911
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912 --sp MX,MN
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
913 Sets the maximum (`MX`) and minimum (`MN`) penalties for soft-clipping per base, both integers. A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position. The number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` where Q is the Phred quality value. Default: `MX` = 2, `MN` = 1.
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diff changeset
914
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915 --no-softclip
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diff changeset
916 Disallow soft-clipping.
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diff changeset
917
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diff changeset
918 --np <int>
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diff changeset
919 Sets penalty for positions where the read, reference, or both, contain an
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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920 ambiguous character such as `N`. Default: 1.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
921
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diff changeset
922 --rdg <int1>,<int2>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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923 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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924 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
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diff changeset
925
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iuc
parents: 14
diff changeset
926 --rfg <int1>,<int2>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
927 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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diff changeset
928 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
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diff changeset
929 5, 3.
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parents: 14
diff changeset
930
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diff changeset
931 --score-min <func>
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iuc
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diff changeset
932 Sets a function governing the minimum alignment score needed for an alignment to
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933 be considered "valid" (i.e. good enough to report). This is a function of read
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934 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
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935 to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default is `L,0,-0.2`.
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936
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937 -----
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938
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939 **Spliced alignment options**::
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940
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941 --pen-cansplice <int>
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942 Sets the penalty for each pair of canonical splice sites (e.g. GT/AG). Default: 0.
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943
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944 --pen-noncansplice <int>
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945 Sets the penalty for each pair of non-canonical splice sites (e.g. non-GT/AG). Default: 12.
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946
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947 --pen-canintronlen <func>
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948 Sets the penalty for long introns with canonical splice sites so that alignments with shorter introns are preferred to those with longer ones. Default: G,-8,1
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949
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950 --pen-noncanintronlen <func>
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951 Sets the penalty for long introns with noncanonical splice sites so that alignments with shorter introns are preferred to those with longer ones. Default: G,-8,1
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952
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953 --min-intronlen <int>
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954 Sets minimum intron length. Default: 20
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955
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956 --max-intronlen <int>
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957 Sets maximum intron length. Default: 500000
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958
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959 --no-spliced-alignment
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960 Disable spliced alignment.
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961
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962 -I/--minins <int>
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963 The minimum fragment length for valid paired-end alignments.This option is valid only with `--no-spliced-alignment`. E.g. if `-I 60` is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as `-X` is also satisfied). A 19-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-I` constraint is applied with respect to the untrimmed mates.
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964
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965 The larger the difference between `-I` and `-X`, the slower HISAT2 will run. This is because larger differences between `-I` and `-X` require that HISAT2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), HISAT2 is very efficient.
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966
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967 Default: 0 (essentially imposing no minimum)
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968
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969 -X/--maxins <int>
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970 The maximum fragment length for valid paired-end alignments. This option is valid only with `--no-spliced-alignment`. E.g. if `-X 100` is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates.
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971
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972 The larger the difference between `-I` and `-X`, the slower HISAT2 will run. This is because larger differences between `-I` and `-X` require that HISAT2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), HISAT2 is very efficient.
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973
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974 Default: 500.
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975
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976 --known-splicesite-infile <path>
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977 With this mode, you can provide a list of known splice sites, which HISAT2 makes use of to align reads with small anchors. You can create such a list using python hisat2_extract_splice_sites.py genes.gtf > splicesites.txt, where hisat2_extract_splice_sites.py is included in the HISAT2 package, genes.gtf is a gene annotation file, and splicesites.txt is a list of splice sites with which you provide HISAT2 in this mode. Note that it is better to use indexes built using annotated transcripts (such as genome_tran or genome_snp_tran), which works better than using this option. It has no effect to provide splice sites that are already included in the indexes.
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978
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979 --tmo/--transcriptome-mapping-only
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980 Report only those alignments within known transcripts.
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981
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982 --dta/--downstream-transcriptome-assembly
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983 Report alignments tailored for transcript assemblers including StringTie. With this option, HISAT2 requires longer anchor lengths for de novo discovery of splice sites. This leads to fewer alignments with short-anchors, which helps transcript assemblers improve significantly in computation and memory usage.
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984
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985 --dta-cufflinks
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986 Report alignments tailored specifically for Cufflinks. In addition to what HISAT2 does with the above option (--dta), With this option, HISAT2 looks for novel splice sites with three signals (GT/AG, GC/AG, AT/AC), but all user-provided splice sites are used irrespective of their signals. HISAT2 produces an optional field, XS:A:[+-], for every spliced alignment.
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987
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988 --no-templatelen-adjustment
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989 Disables template length adjustment for RNA-seq reads.
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990
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991 -----
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992
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993 **Reporting options**::
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994
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995 -k <int>
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996 It searches for at most `<int>` distinct, primary alignments for each read. Primary alignments mean alignments whose alignment score is equal or higher than any other alignments. The search terminates when it can't find more distinct valid alignments, or when it finds `<int>`, whichever happens first. The alignment score for a paired-end alignment equals the sum of the alignment scores of the individual mates. Each reported read or pair alignment beyond the first has the SAM 'secondary' bit (which equals 256) set in its FLAGS field. For reads that have more than `<int>` distinct, valid alignments, hisat2 does not guarantee that the `<int>` alignments reported are the best possible in terms of alignment score. Default: 5 (HFM) or 10 (HGFM)
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997
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998 Note: HISAT2 is not designed with large values for `-k` in mind, and when aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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999
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1000 -max-seeds
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1001 HISAT2, like other aligners, uses seed-and-extend approaches. HISAT2 tries to extend seeds to full-length alignments. In HISAT2, `--max-seeds` is used to control the maximum number of seeds that will be extended. HISAT2 extends up to these many seeds and skips the rest of the seeds. Large values for `--max-seeds` may improve alignment sensitivity, but HISAT2 is not designed with large values for `--max-seeds` in mind, and when aligning reads to long, repetitive genomes large `--max-seeds` can be very, very slow. The default value is the maximum of 5 and the value that comes with `-k`.
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1002
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1003 --secondary
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1004 Report secondary alignments.
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1005
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1006 -----
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1007
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1008 **Paired-end options**::
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1009
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1010 --fr/--rf/--ff
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1011 The upstream/downstream mate orientations for a valid paired-end alignment
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1012 against the forward reference strand. E.g., if `--fr` is specified and there is
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1013 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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1014 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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1015 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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1016 complement of mate 1 and all other constraints are met, that too is valid.
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1017 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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1018 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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1019 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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1020 for Illumina's Paired-end Sequencing Assay).
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1021
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1022 --no-mixed
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1023 By default, when `hisat2` cannot find a concordant or discordant alignment for
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1024 a pair, it then tries to find alignments for the individual mates. This option
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1025 disables that behavior.
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1026
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1027 --no-discordant
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1028 By default, `hisat2` looks for discordant alignments if it cannot find any
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1029 concordant alignments. A discordant alignment is an alignment where both mates
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1030 align uniquely, but that does not satisfy the paired-end constraints
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1031 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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1032
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1033
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1034 **Output options**::
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1035
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1036 --un/--un-gz/--un-bz2
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1037 Write unpaired reads that fail to align to file at `<path>`. These reads correspond to the SAM records with the FLAGS `0x4` bit set and neither the `0x40` nor `0x80` bits set. If `--un-gz` is specified, output will be gzip compressed. If `--un-bz2` is specified, output will be bzip2 compressed. Reads written in this way will appear exactly as they did in the input file, without any modification (same sequence, same name, same quality string, same quality encoding). Reads will not necessarily appear in the same order as they did in the input.
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1038
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1039 --al/--al-gz/--al-bz2
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1040 Write unpaired reads that align at least once to file at `<path>`. These reads correspond to the SAM records with the FLAGS `0x4`, `0x40`, and `0x80` bits unset. If `--al-gz` is specified, output will be gzip compressed. If `--al-bz2` is specified, output will be bzip2 compressed. Reads written in this way will appear exactly as they did in the input file, without any modification (same sequence, same name, same quality string, same quality encoding). Reads will not necessarily appear in the same order as they did in the input.
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1041
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1042 --un-conc/--un-conc-gz/--un-conc-bz2
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1043 Write paired-end reads that fail to align concordantly to file(s) at `<path>`. These reads correspond to the SAM records with the FLAGS `0x4` bit set and either the `0x40` or `0x80` bit set (depending on whether it's mate #1 or #2). .1 and .2 strings are added to the filename to distinguish which file contains mate #1 and mate #2. If a percent symbol, %, is used in <path>, the percent symbol is replaced with 1 or 2 to make the per-mate filenames. Otherwise, .1 or .2 are added before the final dot in <path> to make the per-mate filenames. Reads written in this way will appear exactly as they did in the input files, without any modification (same sequence, same name, same quality string, same quality encoding). Reads will not necessarily appear in the same order as they did in the inputs.
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1044
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1045 --al-conc/--al-conc-gz/--al-conc-bz2
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1046 Write paired-end reads that align concordantly at least once to file(s) at `<path>`. These reads correspond to the SAM records with the FLAGS `0x4` bit unset and either the `0x40` or `0x80` bit set (depending on whether it's mate #1 or #2). .1 and .2 strings are added to the filename to distinguish which file contains mate #1 and mate #2. If a percent symbol, %, is used in <path>, the percent symbol is replaced with 1 or 2 to make the per-mate filenames. Otherwise, .1 or .2 are added before the final dot in `<path>` to make the per-mate filenames. Reads written in this way will appear exactly as they did in the input files, without any modification (same sequence, same name, same quality string, same quality encoding). Reads will not necessarily appear in the same order as they did in the inputs.
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1047
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1048
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1049 **Other options**::
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1050
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1051 --seed <int>
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1052 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
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1053
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1054 --non-deterministic
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1055 Normally, HISAT2 re-initializes its pseudo-random generator for each read. It seeds the generator with a number derived from (a) the read name, (b) the nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed` option. This means that if two reads are identical (same name, same nucleotides, same qualities) HISAT2 will find and report the same alignment(s) for both, even if there was ambiguity. When `--non-deterministic` is specified, HISAT2 re-initializes its pseudo-random generator for each read using the current time. This means that HISAT2 will not necessarily report the same alignment for two identical reads. This is counter-intuitive for some users, but might be more appropriate in situations where the input consists of many identical reads.
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1056
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1057 ]]></help>
0
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1058 <citations>
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1059 <citation type="doi">10.1038/nmeth.3317</citation>
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1060 </citations>
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1061 </tool>