annotate hisat2.xml @ 15:d5fe9aead222 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
author iuc
date Tue, 26 Sep 2017 17:01:28 -0400
parents 526b91fbde60
children 21e8ea8e1adb
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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 = $reference_genome.index.fields.path
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26 #end if
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29 ## If using known splice sites
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30
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31 #if str($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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35
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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
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294 ## Convert SAM output to sorted BAM
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295
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296 | samtools sort - -@ \${GALAXY_SLOTS:-1} -l 6 -o '${output_alignments}'
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297
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298
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299 ## Rename any output fastq files
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300
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301 #if $output_unaligned_reads_l and $output_unaligned_reads_r:
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302 #from os.path import splitext
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303 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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304 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
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305 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
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306 #end if
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307 #if $output_aligned_reads_l and $output_aligned_reads_r:
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308 #from os.path import splitext
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309 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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310 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
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311 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
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312 #end if
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313 ]]></command>
15
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314
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315 <!-- Define inputs -->
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316
0
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317 <inputs>
15
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318
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319 <!-- Reference genome -->
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320 <conditional name="reference_genome">
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321 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options">
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322 <option value="indexed" selected="true">Use a built-in genome</option>
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323 <option value="history">Use a genome from history</option>
0
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324 </param>
15
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325 <when value="indexed">
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326 <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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327 <options from_data_table="hisat2_indexes">
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328 <filter type="sort_by" column="2" />
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329 <validator type="no_options" message="No genomes are available for the selected input dataset" />
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330 </options>
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331 </param>
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332 </when>
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333 <when value="history">
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334 <param name="history_item" type="data" format="fasta" label="Select the reference genome" />
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335 </when>
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336 </conditional>
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337
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338 <!-- Reads -->
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339 <conditional name="library">
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340 <param name="type" type="select" label="Single-end or paired-end reads?">
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341 <option value="single">Single-end</option>
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342 <option value="paired">Paired-end</option>
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343 <option value="paired_collection">Paired-end Collection</option>
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344 </param>
15
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345
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346 <when value="single">
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347 <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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348 <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand information"
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349 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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350 <option value="">Unstranded</option>
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351 <option value="F">Forward (F)</option>
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352 <option value="R">Reverse (R)</option>
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353 </param>
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354 </when>
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355
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356 <when value="paired">
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357 <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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358 <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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359 <expand macro="paired_end_options" />
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360 </when>
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361
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362 <when value="paired_collection">
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363 <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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364 <expand macro="paired_end_options" />
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365 </when>
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366 </conditional>
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367
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368 <!-- Summary Options -->
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369 <section name="sum" title="Summary Options" expanded="False">
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370 <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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371 <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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372 </section>
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373
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374 <!-- Advanced Options -->
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375 <section name="adv" title="Advanced Options" expanded="False">
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376 <conditional name="input_options">
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377 <param name="input_options_selector" type="select" label="Input options">
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378 <option value="defaults">Use default values</option>
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379 <option value="advanced">Specify input options</option>
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380 </param>
15
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381 <when value="defaults" />
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382 <when value="advanced">
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383 <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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384 <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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385 <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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386 <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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387 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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388 <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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389 <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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390 </param>
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391 <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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392 <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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393 </when>
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394 </conditional>
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395
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396 <conditional name="alignment_options">
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397 <param name="alignment_options_selector" type="select" label="Alignment options">
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398 <option value="defaults">Use default values</option>
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399 <option value="advanced">Specify alignment options</option>
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400 </param>
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401 <when value="defaults" />
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402 <when value="advanced">
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403 <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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404 <option value="C">Constant [f(x) = B]</option>
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405 <option value="L" selected="true">Linear [f(x) = B + A * x]</option>
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406 <option value="S">Square root [f(x) = B + A * x&#178;]</option>
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407 <option value="G">Natural logarithm [f(x) = B + A * log(x)]</option>
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408 </param>
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409 <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
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410 <param name="coefficient" type="float" value="0.15" label="Coefficient (A)" help="Coefficient for the above function" />
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411 <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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412 <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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413 <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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414 </when>
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415 </conditional>
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416
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417 <conditional name="scoring_options">
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418 <param name="scoring_options_selector" type="select" label="Scoring options">
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419 <option value="defaults">Use default values</option>
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420 <option value="advanced">Specify scoring options</option>
0
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421 </param>
15
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422 <when value="defaults" />
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423 <when value="advanced">
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424 <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
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425 <param name="coefficient" type="float" value="-0.2" label="Coefficient (A)" help="Coefficient for the above function" />
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426 <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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427 <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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428 <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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429 <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" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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430 <param argument="--no-softclip" name="no_softclip" type="boolean" truevalue="" falsevalue="--no-softclip" label="Allow soft-clipping" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
431 <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" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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432 <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
433 <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
434 <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
435 <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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parents: 14
diff changeset
436 <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
437 <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
438 <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
439 <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
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440 <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
441 </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
442 </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
443 </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
444
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 <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
446 <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
447 <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
448 <option value="advanced">Specify spliced alignment options</option>
0
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parents:
diff changeset
449 </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
450 <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
451 <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
452 <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
453 <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
454 <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
diff changeset
455 <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
456 <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
457 <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
458 <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
459 </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
460 <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
461 <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
462 <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
463 <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
464 <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
465 <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
466 <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
467 </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
468 <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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469 <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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470 <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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471 <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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472 <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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473 <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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474 <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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475 <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
476 </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
477 <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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478 <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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479 <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
480 </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
481 <when value="" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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482 </conditional>
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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483 <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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484 <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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485 <option value="">Use default reporting.</option>
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486 <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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487 <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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488 <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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diff changeset
489 </param>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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490 <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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parents: 14
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491 </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
492 </conditional>
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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493
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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494 <conditional name="reporting_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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495 <param name="reporting_options_selector" type="select" label="Reporting 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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496 <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
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497 <option value="advanced">Specify reporting options</option>
0
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
498 </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
499 <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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500 <when value="advanced">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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501 <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
diff changeset
502 <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)" />
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diff changeset
503 <param name="secondary" argument="--secondary" type="boolean" truevalue="--secondary" falsevalue="" label="Report secondary alignments" />
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diff changeset
504 </when>
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diff changeset
505 </conditional>
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parents: 14
diff changeset
506
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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diff changeset
507 <conditional name="output_options">
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diff changeset
508 <param name="output_options_selector" type="select" label="Output options">
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iuc
parents: 14
diff changeset
509 <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
510 <option value="advanced">Specify output options</option>
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511 </param>
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diff changeset
512 <when value="defaults" />
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parents: 14
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513 <when value="advanced">
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514 <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
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diff changeset
515 <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" />
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516 </when>
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517 </conditional>
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parents: 14
diff changeset
518
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parents: 14
diff changeset
519 <conditional name="other_options">
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parents: 14
diff changeset
520 <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
521 <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
522 <option value="advanced">Specify other options</option>
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parents: 14
diff changeset
523 </param>
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diff changeset
524 <when value="defaults" />
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parents: 14
diff changeset
525 <when value="advanced">
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diff changeset
526 <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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527 <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"/>
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528 </when>
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529 </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
530 </section>
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diff changeset
531
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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diff changeset
532 </inputs>
15
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533
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parents: 14
diff changeset
534 <!-- Define outputs -->
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
535
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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diff changeset
536 <outputs>
15
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parents: 14
diff changeset
537
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diff changeset
538 <!-- BAM -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
539 <data name="output_alignments" format="bam" label="${tool.name} on ${on_string}: aligned reads (BAM) " />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
540
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
541 <!-- Unaligned fastq (L) -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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542 <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (L)">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
543 <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True)</filter>
3
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parents: 2
diff changeset
544 </data>
15
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parents: 14
diff changeset
545
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parents: 14
diff changeset
546 <!-- Aligned fastq (L) -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
547 <data name="output_aligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (L)">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
548 <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True)</filter>
14
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parents: 13
diff changeset
549 </data>
15
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iuc
parents: 14
diff changeset
550
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
551 <!-- Unaligned fastq (R) -->
14
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parents: 13
diff changeset
552 <data name="output_unaligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (R)">
15
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parents: 14
diff changeset
553 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection') and (adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True) </filter>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
554 </data>
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parents: 14
diff changeset
555
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
556 <!-- Aligned fastq (R) -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
557 <data name="output_aligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (R)">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
558 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection') and (adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True) </filter>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
559 </data>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
560
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
561 <!-- Alignment summary file -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
562 <data name="summary_file" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary" >
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diff changeset
563 <filter>sum['summary_file'] is True</filter>
7
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parents: 6
diff changeset
564 </data>
15
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diff changeset
565
0
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diff changeset
566 </outputs>
15
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diff changeset
567
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parents: 14
diff changeset
568 <!-- Define tests -->
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diff changeset
569
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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diff changeset
570 <tests>
15
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diff changeset
571 <test><!-- Ensure bam output works -->
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parents: 14
diff changeset
572 <param name="type" value="paired" />
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diff changeset
573 <param name="source" value="history" />
14
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parents: 13
diff changeset
574 <param name="history_item" ftype="fasta" value="phiX.fa" />
15
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diff changeset
575 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
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diff changeset
576 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
14
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diff changeset
577 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
0
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diff changeset
578 </test>
15
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parents: 14
diff changeset
579 <test><!-- Ensure built-in reference works -->
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parents: 14
diff changeset
580 <param name="type" value="paired" />
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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" />
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diff changeset
585 </test>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
586 <test><!-- Ensure trimming works -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
587 <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
588 <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
589 <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
590 <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
591 <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
592 <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
593 <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
594 <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
595 <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
596 </test>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
597 <test><!-- Ensure paired options works -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
598 <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
599 <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
600 <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
601 <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
602 <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
603 <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
604 <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
605 <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
606 <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
607 <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
608 <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
609 <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
610 </test>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
611 <test><!-- Ensure unaligned output works -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
612 <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
613 <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
614 <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
615 <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
616 <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
617 <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
618 <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
619 <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
620 <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
621 </test>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
622 <test><!-- Ensure paired unaligned output works -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
623 <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
624 <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
625 <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
626 <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
627 <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
628 <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
629 <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
630 <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
631 <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
632 <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
633 </test>
10
da8d655e2154 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents: 9
diff changeset
634 <test><!-- Ensure fastqsanger.gz works -->
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
635 <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
636 <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
637 <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
638 <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
639 <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
640 <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
641 <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
642 <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
643 <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
644 <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
645 <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
646 <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
647 </test>
da8d655e2154 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents: 9
diff changeset
648 <test><!-- Ensure fastqsanger.bz2 works -->
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
649 <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
650 <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
651 <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
652 <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
653 <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
654 <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
655 <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
656 <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
657 <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
658 <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
659 <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
660 <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
661 </test>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
662 <test><!-- Ensure paired strandness works -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
663 <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
664 <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
665 <param name="history_item" ftype="fasta" value="phiX.fa" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
666 <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
iuc
parents: 14
diff changeset
667 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
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668 <param name="rna_strandness" value="FR" />
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669 <output name="output_alignments" file="hisat_output_4.bam" ftype="bam" lines_diff="2" />
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670 </test>
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iuc
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671 <test><!-- Ensure summary file output works -->
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diff changeset
672 <param name="type" value="single" />
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673 <param name="source" value="history" />
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parents: 14
diff changeset
674 <param name="history_item" ftype="fasta" value="phiX.fa" />
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parents: 14
diff changeset
675 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
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676 <param name="rna_strandness" value="R" />
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677 <param name="new_summary" value="true" />
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678 <param name="summary_file" value="true" />
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679 <output name="summary_file" file="hisat_output.summary" ftype="txt" />
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parents: 14
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680 </test>
0
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diff changeset
681 </tests>
15
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diff changeset
682
14
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683 <help><![CDATA[
0
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parents:
diff changeset
684 Introduction
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
685 ============
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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diff changeset
686
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
687 What is HISAT?
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diff changeset
688 --------------
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diff changeset
689
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
690 `HISAT <http://ccb.jhu.edu/software/hisat>`__ is a fast and sensitive
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
691 spliced alignment program. As part of HISAT, we have developed a new
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
692 indexing scheme based on the Burrows-Wheeler transform
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parents:
diff changeset
693 (`BWT <http://en.wikipedia.org/wiki/Burrows-Wheeler_transform>`__) 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
694 the `FM index <http://en.wikipedia.org/wiki/FM-index>`__, called
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
695 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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parents:
diff changeset
696 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
iuc
parents:
diff changeset
697 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
iuc
parents:
diff changeset
698 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
iuc
parents:
diff changeset
699 ~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
700 ~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
701 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
iuc
parents:
diff changeset
702 `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
iuc
parents:
diff changeset
703 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
iuc
parents:
diff changeset
704 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
705 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
706 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
iuc
parents:
diff changeset
707 `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
iuc
parents:
diff changeset
708 quality. Although it uses a large number of indexes, the memory
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
709 requirement of HISAT is still modest, approximately 4.3 GB for human.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
710 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
711 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
712 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
713 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
714 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
715 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
716 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
717 `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
718 `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
719 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
iuc
parents:
diff changeset
720 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
721 the command line under Linux, Mac OS X and Windows.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
722
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
723 Running HISAT
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
724 =============
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
725
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
726 Reporting
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
727 ---------
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
728
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
729 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
730 to report them.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
731
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
732 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
733 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
734 alignment <#valid-alignments-meet-or-exceed-the-minimum-score-threshold>`__.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
735 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
736 multiple alignments that are valid and distinct from one another.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
737
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
738 Distinct alignments map a read to different places
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
739 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
740
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
741 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
742 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
743 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
744 particular read offset is aligned opposite a particular reference offset
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
745 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
746 alignment is in the forward orientation and aligns the read character at
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
747 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
748 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
749 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
750 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
751 alignments.
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iuc
parents:
diff changeset
752
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iuc
parents:
diff changeset
753 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
754 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
755 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
756
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
757 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
758 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 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
761 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
762 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
763 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
764 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
765 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
766 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
767 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
768 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
769 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
770 for details.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
771
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
772 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
773 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
774 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
775 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
776 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
777 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
778
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
779 Alignment summmary
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
780 ------------------
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
781
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
782 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
783 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
784
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
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
787 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
788 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
789 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
790 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
791 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
792 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
793
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
794 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
795
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
796 ::
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
797
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
798 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
799 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
800 650 (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
801 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
802 527 (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
803 ----
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
804 650 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
805 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
806 ----
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
807 616 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
808 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
809 660 (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
810 571 (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
811 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
812 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
813
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
814 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
815
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
816
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
817 .. class:: infomark
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
818
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
819 **HISAT2 options**
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
820
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
821 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
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
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
825 **Inputs**
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
826
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
827 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
828
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
829 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
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
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
833 **Input options**::
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
834
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
835 -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
836 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
837
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
838 -u/--qupto <int>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
839 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
iuc
parents: 14
diff changeset
840 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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 -5/--trim5 <int>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
843 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
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diff changeset
844
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diff changeset
845 -3/--trim3 <int>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
846 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
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847
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diff changeset
848 --phred33
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diff changeset
849 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
850 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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diff changeset
851 pipelines.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
852
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parents: 14
diff changeset
853 --phred64
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diff changeset
854 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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parents: 14
diff changeset
855 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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parents: 14
diff changeset
856
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diff changeset
857 --solexa-quals
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
858 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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parents: 14
diff changeset
859 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
860 Pipeline versions (prior to 1.3). Default: off.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
861
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diff changeset
862 --int-quals
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diff changeset
863 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`....
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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864 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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diff changeset
865 `--solexa-quals` is also specified. Default: off.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
866
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parents: 14
diff changeset
867 ------
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
868
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
869 **Alignment options**::
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
870
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diff changeset
871 --n-ceil <func>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
872 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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873 `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
874 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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diff changeset
875 where x is the read length. Reads exceeding this ceiling are filtered out.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
876 Default: `L,0,0.15`.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
877
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iuc
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diff changeset
878 --ignore-quals
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879 When calculating a mismatch penalty, always consider the quality value at the
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
880 mismatched position to be the highest possible, regardless of the actual value.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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881 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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diff changeset
882 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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parents: 14
diff changeset
883 `-r`, or `-c` modes).
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
884
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
885 --nofw/--norc
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
886 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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diff changeset
887 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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888 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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diff changeset
889 fragments; i.e. specifying `--nofw` causes `hisat2` to explore only those
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
890 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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diff changeset
891 (Crick) strand. Default: both strands enabled.
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diff changeset
892
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diff changeset
893 -----
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diff changeset
894
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diff changeset
895 **Scoring options**::
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
896
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diff changeset
897 --mp MX,MN
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diff changeset
898 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
899 subtracted from the alignment score for each position where a read character
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
900 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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diff changeset
901 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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diff changeset
902 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
903 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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diff changeset
904
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
905 --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
906 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
907
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
908 --no-softclip
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diff changeset
909 Disallow soft-clipping.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
910
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diff changeset
911 --np <int>
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diff changeset
912 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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diff changeset
913 ambiguous character such as `N`. Default: 1.
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diff changeset
914
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diff changeset
915 --rdg <int1>,<int2>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
916 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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diff changeset
917 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
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
918
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
919 --rfg <int1>,<int2>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
920 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
921 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
922 5, 3.
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diff changeset
923
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diff changeset
924 --score-min <func>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
925 Sets a function governing the minimum alignment score needed for an alignment to
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
926 be considered "valid" (i.e. good enough to report). This is a function of read
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
927 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
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 to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default is `L,0,-0.2`.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
929
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
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diff changeset
930 -----
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931
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932 **Spliced alignment options**::
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933
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934 --pen-cansplice <int>
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935 Sets the penalty for each pair of canonical splice sites (e.g. GT/AG). Default: 0.
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936
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937 --pen-noncansplice <int>
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938 Sets the penalty for each pair of non-canonical splice sites (e.g. non-GT/AG). Default: 12.
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939
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940 --pen-canintronlen <func>
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941 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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942
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943 --pen-noncanintronlen <func>
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944 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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945
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946 --min-intronlen <int>
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947 Sets minimum intron length. Default: 20
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948
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949 --max-intronlen <int>
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950 Sets maximum intron length. Default: 500000
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951
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952 --no-spliced-alignment
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953 Disable spliced alignment.
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954
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955 -I/--minins <int>
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956 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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957
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958 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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959
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960 Default: 0 (essentially imposing no minimum)
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961
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962 -X/--maxins <int>
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963 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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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: 500.
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968
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969 --known-splicesite-infile <path>
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970 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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971
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972 --tmo/--transcriptome-mapping-only
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973 Report only those alignments within known transcripts.
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974
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975 --dta/--downstream-transcriptome-assembly
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976 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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977
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978 --dta-cufflinks
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979 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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980
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981 --no-templatelen-adjustment
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982 Disables template length adjustment for RNA-seq reads.
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983
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984 -----
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985
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986 **Reporting options**::
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987
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988 -k <int>
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989 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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990
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991 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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992
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993 -max-seeds
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994 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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995
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996 --secondary
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997 Report secondary alignments.
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998
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999 -----
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1000
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1001 **Paired-end options**::
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1002
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1003 --fr/--rf/--ff
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1004 The upstream/downstream mate orientations for a valid paired-end alignment
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1005 against the forward reference strand. E.g., if `--fr` is specified and there is
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1006 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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1007 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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1008 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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1009 complement of mate 1 and all other constraints are met, that too is valid.
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1010 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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1011 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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1012 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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1013 for Illumina's Paired-end Sequencing Assay).
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1014
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1015 --no-mixed
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1016 By default, when `hisat2` cannot find a concordant or discordant alignment for
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1017 a pair, it then tries to find alignments for the individual mates. This option
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1018 disables that behavior.
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1019
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1020 --no-discordant
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1021 By default, `hisat2` looks for discordant alignments if it cannot find any
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1022 concordant alignments. A discordant alignment is an alignment where both mates
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1023 align uniquely, but that does not satisfy the paired-end constraints
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1024 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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1025
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1026
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1027 **Output options**::
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1028
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1029 --un/--un-gz/--un-bz2
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1030 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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1031
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1032 --al/--al-gz/--al-bz2
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1033 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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1034
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1035 --un-conc/--un-conc-gz/--un-conc-bz2
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1036 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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1037
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1038 --al-conc/--al-conc-gz/--al-conc-bz2
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1039 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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1040
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1041
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1042 **Other options**::
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1043
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1044 --seed <int>
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1045 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
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1046
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1047 --non-deterministic
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1048 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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1049
14
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1050 ]]></help>
0
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1051 <citations>
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1052 <citation type="doi">10.1038/nmeth.3317</citation>
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1053 </citations>
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1054 </tool>