annotate hisat2.xml @ 28:d4b55e2beb12 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 0c0447365a23d4382b04745f22290608b47e5ff5"
author iuc
date Thu, 26 Nov 2020 10:10:04 +0000
parents a86e80d3c09c
children 26371a1df031
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d4b55e2beb12 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 0c0447365a23d4382b04745f22290608b47e5ff5"
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1 <tool id="hisat2" name="HISAT2" version="2.1.0+galaxy6" 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>
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8 <requirement type="package" version="1.9">samtools</requirement>
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9 <requirement type="package" version="1.3">seqtk</requirement>
0
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10 </requirements>
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11 <stdio>
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12 <regex level="fatal" match="hisat2-align exited with value 1" source="both" />
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13 <regex level="fatal" match="hisat2: not found" source="both" />
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14 <exit_code range="1:" />
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15 </stdio>
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16 <version_command>hisat2 --version</version_command>
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17 <command><![CDATA[
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18 ## Prepare HISAT2 index
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20 #if $reference_genome.source == "history":
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21 ln -s '$reference_genome.history_item' genome.fa &&
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22 hisat2-build -p \${GALAXY_SLOTS:-1} genome.fa genome &&
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23 #set index_path = 'genome'
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24 #else:
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25 #set index_path = $reference_genome.index.fields.path
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26 #end if
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29 ## If using known splice sites
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31 #if str($adv.spliced_options.spliced_options_selector) == "advanced" and str($adv.spliced_options.known_splice_gtf) != 'None':
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32 ln -s '${adv.spliced_options.known_splice_gtf}' splice_sites.gtf &&
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33 hisat2_extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&
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34 #end if
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37 ## Link in the input files, so HISAT2 can tell their type
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38
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39 #set compressed="False"
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40 #set reads_are_fastq = True
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41
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42 #if str($library.type) == 'paired':
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43 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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44 #set read1 = "input_f.fastq.gz"
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45 #set compressed = "GZ"
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46 #elif $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 #elif $library.input_1.is_of_type('fasta'):
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50 #set reads_are_fastq = False
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51 #set read1 = "input_f.fasta"
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52 #else:
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53 #set read1 = "input_f.fastq"
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54 #end if
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55 ln -f -s '${library.input_1}' ${read1} &&
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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 #elif $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 #elif $library.input_2.is_of_type('fasta'):
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64 #set read2 = "input_r.fasta"
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65 #else:
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66 #set read2 = "input_r.fastq"
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67 #end if
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68 ln -f -s '${library.input_2}' ${read2} &&
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69
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70 #elif str($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 #elif $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 #elif $library.input_1.forward.is_of_type('fasta'):
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78 #set reads_are_fastq = False
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79 #set read1 = "input_f.fasta"
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80 #else:
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81 #set read1 = "input_f.fastq"
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82 #end if
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83 ln -s '${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 #elif $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 #elif $library.input_1.reverse.is_of_type("fasta"):
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92 #set read2 = "input_r.fasta"
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93 #else:
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94 #set read2 = "input_r.fastq"
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95 #end if
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96 ln -s '${library.input_1.reverse}' ${read2} &&
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97 #elif str( $library.type ) == "paired_interleaved":
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98 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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99 #set interleaved_reads = "input_f.fastq.gz"
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100 #set compressed = "GZ"
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101 #elif $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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102 #set interleaved_reads = "input_f.fastq.bz2"
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103 #set compressed = "BZ2"
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104 #elif $library.input_1.is_of_type('fasta'):
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105 #set reads_are_fastq = False
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106 #set interleaved_reads = "input_f.fasta"
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107 #else:
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108 #set interleaved_reads = "input_f.fastq"
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109 #end if
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110 ln -f -s '${library.input_1}' ${interleaved_reads} &&
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111 #if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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112 #set read1 = "<(bzcat input_f.fastq.bz2 | seqtk seq -1 /dev/stdin)"
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113 #set read2 = "<(bzcat input_f.fastq.bz2 | seqtk seq -2 /dev/stdin)"
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114 #else:
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115 #set read1 = "<(seqtk seq -1 %s)" % $interleaved_reads
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116 #set read2 = "<(seqtk seq -2 %s)" % $interleaved_reads
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117 #end if
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118 #else:
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119 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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120 #set read1 = "input_f.fastq.gz"
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121 #set compressed = "GZ"
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122 #elif $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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123 #set read1 = "input_f.fastq.bz2"
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124 #set compressed = "BZ2"
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125 #elif $library.input_1.is_of_type('fasta'):
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126 #set reads_are_fastq = False
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127 #set read1 = "input_f.fasta"
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128 #else:
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129 #set read1 = "input_f.fastq"
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130 #end if
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131 ln -f -s '${library.input_1}' ${read1} &&
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132 #end if
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133
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134
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135 ## Run HISAT2
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136
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137 hisat2
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138
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139 ## number threads
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140 -p \${GALAXY_SLOTS:-1}
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141
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142 ## ref genome index path
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143 -x '${index_path}'
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144
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145 ## input reads are fasta?
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146 #if not $reads_are_fastq:
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147 -f
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148 #end if
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149
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150 ## Input reads
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151
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152 #if str( $library.type ) == "single":
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153
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154 -U '${read1}'
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155
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156 #if str($adv.output_options.output_options_selector) == "advanced":
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157 #if str( $adv.output_options.unaligned_file ) == "true":
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158 #if $compressed == "GZ":
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159 --un-gz '$output_unaligned_reads_l'
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160 #elif $compressed == "BZ2":
15
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161 --un-bz2 '$output_unaligned_reads_l'
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162 #else:
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163 --un '$output_unaligned_reads_l'
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164 #end if
0
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165 #end if
10
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166
15
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167 #if str( $adv.output_options.aligned_file ) == "true":
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168 #if $compressed == "GZ":
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169 --al-gz '$output_aligned_reads_l'
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170 #elif $compressed == "BZ2":
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171 --al-bz2 '$output_aligned_reads_l'
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172 #else:
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173 --al '$output_aligned_reads_l'
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174 #end if
0
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175 #end if
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176 #end if
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177
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178 #else:
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179 ##quotes are embedded in r1 and r2 variables, needed to allow use of <()
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180 #if str( $library.type ) == "paired_interleaved":
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181 -1 ${read1}
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182 -2 ${read2}
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183 #else:
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184 -1 '${read1}'
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185 -2 '${read2}'
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186 #end if
15
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187 #if str($adv.output_options.output_options_selector) == "advanced":
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188 #if str( $adv.output_options.unaligned_file ) == "true":
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189 #if $compressed == "GZ":
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190 --un-conc-gz '${output_unaligned_reads_l}'
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191 #elif $compressed == "BZ2":
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192 --un-conc-bz2 '${output_unaligned_reads_l}'
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193 #else:
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194 --un-conc '${output_unaligned_reads_l}'
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195 #end if
15
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196 #end if
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197
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198 #if str( $adv.output_options.aligned_file ) == "true":
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199 #if $compressed == "GZ":
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200 --al-conc-gz '${output_aligned_reads_l}'
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201 #elif $compressed == "BZ2":
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202 --al-conc-bz2 '${output_aligned_reads_l}'
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203 #else:
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204 --al-conc '${output_aligned_reads_l}'
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205 #end if
0
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206 #end if
15
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207 #end if
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208
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209 #if str($library.paired_options.paired_options_selector) == "advanced":
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210 ${library.paired_options.fr_rf_ff}
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211 ${library.paired_options.no_mixed}
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212 ${library.paired_options.no_discordant}
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213 #end if
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214
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215 #end if
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216
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217
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218 ## Specify strandedness of reads
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219
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220 #if str($library.rna_strandness):
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221 --rna-strandness ${library.rna_strandness}
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222 #end if
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223
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224
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225 ## Input options
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226
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227 #if str($adv.input_options.input_options_selector) == "advanced":
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228 #if int( $adv.input_options.skip ) > 0:
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229 --skip ${adv.input_options.skip}
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230 #end if
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231 #if int( $adv.input_options.qupto ) > 0:
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232 --qupto ${adv.input_options.qupto}
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233 #end if
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234 --trim5 '${adv.input_options.trim5}'
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235 --trim3 '${adv.input_options.trim3}'
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236 ${adv.input_options.qv_encoding}
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237 ${adv.input_options.solexa_quals}
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238 ${adv.input_options.int_quals}
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239 #end if
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240
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241
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242 ## Alignment options
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243
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244 #if str($adv.alignment_options.alignment_options_selector) == "advanced":
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245 --n-ceil ${adv.alignment_options.function_type},${adv.alignment_options.constant_term},${adv.alignment_options.coefficient}
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246 ${adv.alignment_options.ignore_quals}
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247 ${adv.alignment_options.skip_forward}
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248 ${adv.alignment_options.skip_reverse}
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249 #end if
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250
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251
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252 ## Scoring options
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253
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254 #if str($adv.scoring_options.scoring_options_selector) == "advanced":
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255 --mp ${adv.scoring_options.max_mismatch},${adv.scoring_options.min_mismatch}
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256 ${adv.scoring_options.no_softclip}
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257 --np ${adv.scoring_options.ambiguous_penalty}
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258 --rdg ${adv.scoring_options.read_open_penalty},${adv.scoring_options.read_extend_penalty}
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259 --rfg ${adv.scoring_options.ref_open_penalty},${adv.scoring_options.ref_extend_penalty}
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260 --sp ${adv.scoring_options.soft_clip_penalty_max},${adv.scoring_options.soft_clip_penalty_min}
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261 --score-min ${adv.scoring_options.function_type},${adv.scoring_options.constant_term},${adv.scoring_options.coefficient}
15
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262 #end if
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263
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264
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265 ## Spliced alignment options
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266
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267 #if str($adv.spliced_options.spliced_options_selector) == "advanced":
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268 --pen-cansplice ${adv.spliced_options.canonical_penalty}
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269 --pen-noncansplice ${adv.spliced_options.noncanonical_penalty}
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270 --pen-canintronlen ${adv.spliced_options.function_type},${adv.spliced_options.constant_term},${adv.spliced_options.coefficient}
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271 --pen-noncanintronlen ${adv.spliced_options.nc_function_type},${adv.spliced_options.nc_constant_term},${adv.spliced_options.nc_coefficient}
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272 #if str($adv.spliced_options.known_splice_gtf) != 'None':
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273 --known-splicesite-infile splice_sites.txt
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274 #end if
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275 ${adv.spliced_options.no_spliced_alignment_options.no_spliced_alignment}
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276 #if $adv.spliced_options.no_spliced_alignment_options.no_spliced_alignment == '--no-spliced-alignment'
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277 -I ${adv.spliced_options.no_spliced_alignment_options.minins}
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278 -X ${adv.spliced_options.no_spliced_alignment_options.maxins}
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279 #end if
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280 --min-intronlen ${adv.spliced_options.min_intron}
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281 --max-intronlen ${adv.spliced_options.max_intron}
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282 ${adv.spliced_options.tma}
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283
25
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284 #if str($adv.spliced_options.novel_splicesite_outfile) == "true":
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285 --novel-splicesite-outfile '$novel_splicesite_output'
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286 #end if
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287
15
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288 #if str($adv.spliced_options.notmplen):
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289 ${adv.spliced_options.notmplen}
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290 #end if
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291 #end if
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292
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293
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294 ## Reporting options
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295
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296 #if str($adv.reporting_options.reporting_options_selector) == "advanced":
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297 #if str($adv.reporting_options.max_primary) != '':
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298 -k ${adv.reporting_options.max_primary}
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299 #end if
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300 #end if
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301
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302
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303 ## Other options
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304
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305 #if str( $adv.other_options.other_options_selector ) == "advanced":
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306 ${adv.other_options.non_deterministic}
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307 --seed '${adv.other_options.seed}'
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308 #end if
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309
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310
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311 ## Output Summary
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312
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313 #if str($sum.new_summary) == "true":
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314 --new-summary
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315 #end if
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316
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317 #if str($sum.summary_file) == "true":
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318 --summary-file summary.txt
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319 #end if
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320
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321 ## Convert SAM output to sorted BAM
21
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322 ## using the two pipe stages has the following effect
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323 ## - hisat2 and sort run in parallel, during this time sort produces
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324 ## presorted temporary files but does not produce output (hence
21
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325 ## view does not run)
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326 ## - once hisat is finished sort will start to merge the temporary
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327 ## files (which should be fast also on a single thread) gives the
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328 ## sorted output to view which only compresses the files (now
21
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329 ## using full parallelism again)
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330
27
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331 | samtools sort -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}'
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332
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333 ## Rename any output fastq files
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334
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335 #if $output_unaligned_reads_l and $output_unaligned_reads_r:
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336 #from os.path import splitext
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337 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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338 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
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339 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
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340 #end if
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341 #if $output_aligned_reads_l and $output_aligned_reads_r:
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342 #from os.path import splitext
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343 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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344 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
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345 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
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346 #end if
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347 ]]></command>
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348
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349 <!-- Define inputs -->
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350
0
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351 <inputs>
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352
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353 <!-- Reference genome -->
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354 <conditional name="reference_genome">
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355 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options">
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356 <option value="indexed" selected="true">Use a built-in genome</option>
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357 <option value="history">Use a genome from history</option>
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358 </param>
15
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359 <when value="indexed">
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360 <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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361 <options from_data_table="hisat2_indexes">
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362 <filter type="sort_by" column="2" />
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363 <validator type="no_options" message="No genomes are available for the selected input dataset" />
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364 </options>
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365 </param>
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366 </when>
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367 <when value="history">
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368 <param name="history_item" type="data" format="fasta" label="Select the reference genome" />
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369 </when>
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370 </conditional>
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371
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372 <!-- Reads -->
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373 <conditional name="library">
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374 <param name="type" type="select" label="Is this a single or paired library">
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375 <option value="single">Single-end</option>
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376 <option value="paired">Paired-end</option>
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377 <option value="paired_collection">Paired-end Dataset Collection</option>
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378 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
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379 </param>
15
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380
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381 <when value="single">
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382 <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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383 <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand information"
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384 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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385 <option value="">Unstranded</option>
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386 <option value="F">Forward (F)</option>
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387 <option value="R">Reverse (R)</option>
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388 </param>
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389 </when>
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390
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391 <when value="paired">
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392 <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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393 <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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394 <expand macro="paired_end_options" />
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395 </when>
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396
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397 <when value="paired_collection">
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398 <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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399 <expand macro="paired_end_options" />
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400 </when>
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401 <when value="paired_interleaved">
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402 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
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403 <expand macro="paired_end_options" />
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404 </when>
15
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405 </conditional>
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406
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407 <!-- Summary Options -->
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408 <section name="sum" title="Summary Options" expanded="False">
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409 <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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410 <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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411 </section>
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412
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413 <!-- Advanced Options -->
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414 <section name="adv" title="Advanced Options" expanded="False">
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415 <conditional name="input_options">
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416 <param name="input_options_selector" type="select" label="Input options">
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417 <option value="defaults">Use default values</option>
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418 <option value="advanced">Specify input options</option>
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419 </param>
15
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420 <when value="defaults" />
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421 <when value="advanced">
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422 <param name="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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423 <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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424 <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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425 <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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426 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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427 <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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428 <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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429 </param>
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430 <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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431 <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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432 </when>
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433 </conditional>
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434
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435 <conditional name="alignment_options">
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436 <param name="alignment_options_selector" type="select" label="Alignment options">
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437 <option value="defaults">Use default values</option>
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438 <option value="advanced">Specify alignment options</option>
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439 </param>
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440 <when value="defaults" />
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441 <when value="advanced">
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442 <expand macro="nc_function" name="function_type" argument="--n-ceil" 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" lselected="true"/>
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443 <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
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444 <param name="coefficient" type="float" value="0.15" label="Coefficient (A)" help="Coefficient for the above function" />
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445 <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" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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446 <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" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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447 <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" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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448 </when>
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449 </conditional>
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450
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451 <conditional name="scoring_options">
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452 <param name="scoring_options_selector" type="select" label="Scoring options">
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453 <option value="defaults">Use default values</option>
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454 <option value="advanced">Specify scoring options</option>
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455 </param>
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456 <when value="defaults" />
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457 <when value="advanced">
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458 <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
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459 <param name="coefficient" type="float" value="-0.2" label="Coefficient (A)" help="Coefficient for the above function" />
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460 <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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461 <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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462 <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" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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463 <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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464 <param argument="--no-softclip" name="no_softclip" type="boolean" truevalue="" falsevalue="--no-softclip" label="Allow soft-clipping" />
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465 <param argument="--np" name="ambiguous_penalty" type="integer" value="1" min="0" label="Ambiguous read penalty" help="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N" />
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466 <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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467 <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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468 <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]" />
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469 <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]" />
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470 <expand macro="nc_function" name="function_type" argument="--score-min" 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" lselected="true"/>
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471 </when>
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472 </conditional>
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473
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474 <conditional name="spliced_options">
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475 <param name="spliced_options_selector" type="select" label="Spliced alignment options">
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476 <option value="defaults">Use default values</option>
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477 <option value="advanced">Specify spliced alignment options</option>
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478 </param>
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479 <when value="defaults" />
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480 <when value="advanced">
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481 <param name="canonical_penalty" argument="--pen-cansplice" type="integer" value="0" min="0" label="Penalty for canonical splice sites" />
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482 <param name="noncanonical_penalty" argument="--pen-noncansplice" type="integer" value="12" min="0" label="Penalty for non-canonical splice sites" />
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483 <expand macro="nc_function" name="function_type" argument="--pen-canintronlen" label="Penalty function for long introns with canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones" gselected="true"/>
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484 <param name="constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" />
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485 <param name="coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
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486 <expand macro="nc_function" name="nc_function_type" argument="--pen-noncanintronlen" label="Penalty function for long introns with non-canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones" gselected="true"/>
15
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487 <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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488 <param name="nc_coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
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489 <param name="min_intron" type="integer" value="20" min="0" label="Minimum intron length" />
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490 <param name="max_intron" type="integer" value="500000" min="0" label="Maximum intron length" />
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491 <conditional name="no_spliced_alignment_options">
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492 <param name="no_spliced_alignment" argument="--no-spliced-alignment" type="select" label="Disable spliced alignment">
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493 <option value="">False</option>
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494 <option value="--no-spliced-alignment">True</option>
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495 </param>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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496 <when value="--no-spliced-alignment">
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497 <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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498 <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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499 </when>
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500 <when value="" />
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501 </conditional>
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502 <param name="known_splice_gtf" type="data" format="gtf" optional="true" label="GTF file with known splice sites" />
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503 <param name="tma" type="select" display="radio" label="Transcriptome assembly reporting">
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504 <option value="">Use default reporting</option>
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iuc
parents: 16
diff changeset
505 <option value="--tmo">Report only those alignments within known transcripts</option>
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iuc
parents: 16
diff changeset
506 <option value="--dta">Report alignments tailored for transcript assemblers including StringTie</option>
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iuc
parents: 16
diff changeset
507 <option value="--dta-cufflinks">Report alignments tailored specifically for Cufflinks</option>
15
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iuc
parents: 14
diff changeset
508 </param>
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parents: 14
diff changeset
509 <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" />
25
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iuc
parents: 24
diff changeset
510 <param name="novel_splicesite_outfile" type="boolean" checked="false" label="reports a list of novel splice sites" help="Default: false" />
15
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iuc
parents: 14
diff changeset
511 </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
512 </conditional>
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iuc
parents: 14
diff changeset
513
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
514 <conditional name="reporting_options">
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iuc
parents: 14
diff changeset
515 <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
iuc
parents: 14
diff changeset
516 <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
517 <option value="advanced">Specify reporting options</option>
0
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iuc
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diff changeset
518 </param>
15
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iuc
parents: 14
diff changeset
519 <when value="defaults" />
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iuc
parents: 14
diff changeset
520 <when value="advanced">
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iuc
parents: 14
diff changeset
521 <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)" />
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iuc
parents: 14
diff changeset
522 </when>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
523 </conditional>
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iuc
parents: 14
diff changeset
524
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
525 <conditional name="output_options">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
526 <param name="output_options_selector" type="select" label="Output options">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
527 <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
528 <option value="advanced">Specify output options</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
529 </param>
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parents: 14
diff changeset
530 <when value="defaults" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
531 <when value="advanced">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
532 <param name="unaligned_file" argument="--un/--un-conc" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="This triggers --un parameter for single reads and --un-conc for paired reads" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
533 <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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iuc
parents: 14
diff changeset
534 </when>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
535 </conditional>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
536
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
537 <conditional name="other_options">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
538 <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
539 <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
540 <option value="advanced">Specify other options</option>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
541 </param>
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iuc
parents: 14
diff changeset
542 <when value="defaults" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
543 <when value="advanced">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
544 <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
iuc
parents: 14
diff changeset
545 <param name="non_deterministic" argument="--non-deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="see Help below for explanation of this option; default: False"/>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
546 </when>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
547 </conditional>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
548 </section>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
549
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
550 </inputs>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
551
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
552 <!-- Define outputs -->
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iuc
parents: 14
diff changeset
553
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
554 <outputs>
15
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iuc
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 <!-- BAM -->
20
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iuc
parents: 19
diff changeset
557 <data name="output_alignments" format="bam" label="${tool.name} on ${on_string}: aligned reads (BAM)">
26
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iuc
parents: 25
diff changeset
558 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
559 <expand macro="dbKeyActions" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
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parents: 25
diff changeset
560 </actions>
20
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iuc
parents: 19
diff changeset
561 </data>
15
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parents: 14
diff changeset
562
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
563 <!-- Unaligned fastq (L) -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
564 <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (L)">
16
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parents: 15
diff changeset
565 <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True</filter>
26
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iuc
parents: 25
diff changeset
566 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
567 <conditional name="library.type">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
568 <when value="single">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
569 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
570 <option type="from_param" name="library.input_1" param_attribute="ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
571 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
572 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
573 <when value="paired">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
574 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
575 <option type="from_param" name="library.input_1" param_attribute="ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
576 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
577 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
578 <when value="paired_collection">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
579 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
580 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
581 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
582 </when>
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iuc
parents: 25
diff changeset
583 <when value="paired_interleaved">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
584 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
585 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
586 </action>
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parents: 25
diff changeset
587 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
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diff changeset
588 </conditional>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
589 <expand macro="dbKeyActions" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
590 </actions>
3
b1e25f9b5eab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059
iuc
parents: 2
diff changeset
591 </data>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
592
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
593 <!-- Aligned fastq (L) -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
594 <data name="output_aligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (L)">
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
595 <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True</filter>
26
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
596 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
597 <conditional name="library.type">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
598 <when value="single">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
599 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
600 <option type="from_param" name="library.input_1" param_attribute="ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
601 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
602 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
603 <when value="paired">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
604 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
605 <option type="from_param" name="library.input_1" param_attribute="ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
606 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
607 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
608 <when value="paired_collection">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
609 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
610 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
611 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
612 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
613 <when value="paired_interleaved">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
614 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
615 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
616 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
617 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
618 </conditional>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
619 <expand macro="dbKeyActions" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
620 </actions>
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
621 </data>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
622
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
623 <!-- Unaligned fastq (R) -->
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
624 <data name="output_unaligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (R)">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
625 <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>
26
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
626 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
627 <conditional name="library.type">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
628 <when value="single">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
629 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
630 <option type="from_param" name="library.input_1" param_attribute="ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
631 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
632 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
633 <when value="paired">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
634 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
635 <option type="from_param" name="library.input_1" param_attribute="ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
636 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
637 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
638 <when value="paired_collection">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
639 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
640 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
641 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
642 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
643 <when value="paired_interleaved">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
644 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
645 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
646 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
647 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
648 </conditional>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
649 <expand macro="dbKeyActions" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
650 </actions>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
651 </data>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
652
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
653 <!-- Aligned fastq (R) -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
654 <data name="output_aligned_reads_r" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (R)">
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
655 <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>
26
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
656 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
657 <conditional name="library.type">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
658 <when value="single">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
659 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
660 <option type="from_param" name="library.input_1" param_attribute="ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
661 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
662 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
663 <when value="paired">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
664 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
665 <option type="from_param" name="library.input_1" param_attribute="ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
666 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
667 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
668 <when value="paired_collection">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
669 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
670 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
671 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
672 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
673 <when value="paired_interleaved">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
674 <action type="format">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
675 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
676 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
677 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
678 </conditional>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
679 <expand macro="dbKeyActions" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
680 </actions>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
681 </data>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
682
26
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
683 <!-- Alignment summary file -->
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
684 <data name="summary_file" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
685 <filter>sum['summary_file'] is True</filter>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
686 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
687 <expand macro="dbKeyActions" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
688 </actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
689 </data>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
690
26
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
691 <!-- Novel Splice file -->
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
692 <data name="novel_splicesite_output" format="tabular" label="${tool.name} on ${on_string}: Novel Splice Sites">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
693 <filter>adv['spliced_options']['spliced_options_selector'] == 'advanced' and adv['spliced_options']['novel_splicesite_outfile'] is True</filter>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
694 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
695 <expand macro="dbKeyActions" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
696 </actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
697 </data>
25
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
698
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
699
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
700 </outputs>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
701
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
702 <!-- Define tests -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
703
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
704 <tests>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
705 <!-- Ensure bam output works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
706 <test expect_num_outputs="1" >
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
707 <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
708 <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
709 <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
710 <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
711 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
24
61ee47027bd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 67cc9b86dcb40c7691cc85b77428117be25d6046
iuc
parents: 23
diff changeset
712 <param name="adv|reporting_options|reporting_options_selector" value="advanced"/>
25
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
713 <param name="novel_splicesite_outfile" value="false" />
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
714 <output name="output_alignments" file="hisat_output_1.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
715 </test>
18
764756ab0eb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 4b78174c0753e9f916bf6625490c0ce605979940
iuc
parents: 17
diff changeset
716 <!-- Ensure advanced scoring options work -->
764756ab0eb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 4b78174c0753e9f916bf6625490c0ce605979940
iuc
parents: 17
diff changeset
717 <test expect_num_outputs="1" >
764756ab0eb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 4b78174c0753e9f916bf6625490c0ce605979940
iuc
parents: 17
diff changeset
718 <param name="type" value="paired" />
764756ab0eb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 4b78174c0753e9f916bf6625490c0ce605979940
iuc
parents: 17
diff changeset
719 <param name="source" value="history" />
764756ab0eb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 4b78174c0753e9f916bf6625490c0ce605979940
iuc
parents: 17
diff changeset
720 <param name="history_item" ftype="fasta" value="phiX.fa" />
764756ab0eb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 4b78174c0753e9f916bf6625490c0ce605979940
iuc
parents: 17
diff changeset
721 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
764756ab0eb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 4b78174c0753e9f916bf6625490c0ce605979940
iuc
parents: 17
diff changeset
722 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
764756ab0eb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 4b78174c0753e9f916bf6625490c0ce605979940
iuc
parents: 17
diff changeset
723 <param name="adv|scoring_options|coefficient" value="-0.3"/>
764756ab0eb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 4b78174c0753e9f916bf6625490c0ce605979940
iuc
parents: 17
diff changeset
724 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
764756ab0eb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 4b78174c0753e9f916bf6625490c0ce605979940
iuc
parents: 17
diff changeset
725 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
726 <!-- Ensure built-in reference works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
727 <test expect_num_outputs="1">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
728 <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
729 <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
730 <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
731 <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
732 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
733 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
734 <!-- Ensure trimming works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
735 <test expect_num_outputs="1">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
736 <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
737 <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
738 <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
739 <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
740 <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
741 <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
742 <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
743 <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
744 <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
745 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
746 <!-- Ensure paired options works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
747 <test expect_num_outputs="1">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
748 <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
749 <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
750 <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
751 <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
752 <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
753 <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
754 <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
755 <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
756 <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
757 <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
758 <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
759 <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
760 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
761 <!-- Ensure single unaligned output works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
762 <test expect_num_outputs="2">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
763 <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
764 <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
765 <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
766 <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
767 <param name="unaligned_file" value="true" />
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
768 <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
769 <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" />
27
a86e80d3c09c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ee1e956ad8c2841d6b4861f6b5415f68d84e6ab7"
iuc
parents: 26
diff changeset
770 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" sort="true"/>
7
5ba8e317529a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents: 6
diff changeset
771 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
772 <!-- Ensure paired unaligned/aligned output works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
773 <test expect_num_outputs="5">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
774 <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
775 <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
776 <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
777 <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
778 <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
779 <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
780 <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
781 <param name="input_2" ftype="fasta" value="test_unaligned_reads.fasta" />
27
a86e80d3c09c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ee1e956ad8c2841d6b4861f6b5415f68d84e6ab7"
iuc
parents: 26
diff changeset
782 <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" sort="true"/>
a86e80d3c09c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ee1e956ad8c2841d6b4861f6b5415f68d84e6ab7"
iuc
parents: 26
diff changeset
783 <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" sort="true"/>
7
5ba8e317529a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents: 6
diff changeset
784 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
785 <!-- Ensure fastqsanger.gz works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
786 <test expect_num_outputs="1">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
787 <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
788 <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
789 <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
790 <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
791 <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
792 <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
793 <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
794 <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
795 <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
796 <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
797 <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
798 <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
799 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
800 <!-- Ensure fastqsanger.bz2 works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
801 <test expect_num_outputs="1">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
802 <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
803 <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
804 <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
805 <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
806 <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
807 <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
808 <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
809 <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
810 <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
811 <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
812 <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
813 <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
814 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
815 <!-- Ensure paired strandness works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
816 <test expect_num_outputs="1">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
817 <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
818 <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
819 <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
820 <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
821 <param name="input_2" ftype="fastqsanger" 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
822 <param name="rna_strandness" value="FR" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
823 <output name="output_alignments" file="hisat_output_4.bam" ftype="bam" lines_diff="2" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
824 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
825 <!-- Ensure summary file output works -->
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
826 <test expect_num_outputs="2">
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
827 <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
828 <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
829 <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
830 <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
831 <param name="rna_strandness" value="R" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
832 <param name="new_summary" value="true" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
833 <param name="summary_file" value="true" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
834 <output name="summary_file" file="hisat_output.summary" ftype="txt" />
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
835 </test>
22
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
836 <!-- Ensure interleaved input works -->
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
837 <test expect_num_outputs="1" >
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
838 <param name="type" value="paired_interleaved" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
839 <param name="source" value="history" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
840 <param name="history_item" ftype="fasta" value="phiX.fa" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
841 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_interleaved.fastq" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
842 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
843 </test>
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
844 <!-- Ensure interleaved bz input works -->
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
845 <test expect_num_outputs="1" >
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
846 <param name="type" value="paired_interleaved" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
847 <param name="source" value="history" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
848 <param name="history_item" ftype="fasta" value="phiX.fa" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
849 <param name="input_1" ftype="fastqsanger.bz2" value="hisat_input_1_interleaved.fastq.bz2" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
850 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
851 </test>
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
852 <!-- Ensure interleaved gz input works -->
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
853 <test expect_num_outputs="1" >
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
854 <param name="type" value="paired_interleaved" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
855 <param name="source" value="history" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
856 <param name="history_item" ftype="fasta" value="phiX.fa" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
857 <param name="input_1" ftype="fastqsanger.gz" value="hisat_input_1_interleaved.fastq.gz" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
858 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
859 </test>
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
860 <!-- Ensure interleaved fasta input works -->
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
861 <test expect_num_outputs="1" >
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
862 <param name="type" value="paired_interleaved" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
863 <param name="source" value="history" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
864 <param name="history_item" ftype="fasta" value="phiX.fa" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
865 <param name="input_1" ftype="fasta" value="hisat_input_1_interleaved.fasta" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
866 <output name="output_alignments" file="hisat_output_1_noqual.bam" ftype="bam" lines_diff="2" />
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
867 </test>
25
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
868 <!-- Ensure novel splicesite file output works -->
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
869 <test>
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iuc
parents: 24
diff changeset
870 <param name="type" value="single" />
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
871 <param name="source" value="history" />
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
872 <param name="history_item" ftype="fasta" value="phiX.fa" />
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
873 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_split_forward.fastq" />
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
874 <param name="rna_strandness" value="R" />
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
875 <param name="adv|spliced_options|spliced_options_selector" value="advanced"/>
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
876 <param name="adv|spliced_options|novel_splicesite_outfile" value="true" />
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
877 <output name="output_alignments" file="hisat_output_spliced_1.bam" ftype="bam" lines_diff="2" />
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
878 <output name="novel_splicesite_output" file="novel_splicesite_out.tab" ftype="tabular" />
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
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parents: 24
diff changeset
879 </test>
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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diff changeset
880 </tests>
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
881
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
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parents: 13
diff changeset
882 <help><![CDATA[
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
883 Introduction
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
884 ============
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
885
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
886 What is HISAT?
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
887 --------------
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
888
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
889 `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
iuc
parents:
diff changeset
890 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
iuc
parents:
diff changeset
891 indexing scheme based on the Burrows-Wheeler transform
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
892 (`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
893 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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diff changeset
894 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
iuc
parents:
diff changeset
895 FM index representing the whole genome, and (2) many separate local FM
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
896 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
897 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
898 ~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
899 ~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
iuc
parents:
diff changeset
900 extremely fast with a low memory footprint, as demonstrated by
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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diff changeset
901 `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
902 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
903 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
iuc
parents:
diff changeset
904 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
905 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
906 `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
907 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
908 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
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parents:
diff changeset
909 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
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parents:
diff changeset
910 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
911 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
912 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
913 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
914 alignments in `SAM <http://samtools.sourceforge.net/SAM1.pdf>`__ format,
27
a86e80d3c09c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ee1e956ad8c2841d6b4861f6b5415f68d84e6ab7"
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parents: 26
diff changeset
915 enabling interoperation with a large number of other tools that use SAM.
a86e80d3c09c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ee1e956ad8c2841d6b4861f6b5415f68d84e6ab7"
iuc
parents: 26
diff changeset
916 HISAT is distributed under the `GPLv3
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
917 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
918 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
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parents:
diff changeset
919
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
920 Running HISAT
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
921 =============
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
922
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
923 Reporting
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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924 ---------
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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diff changeset
925
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
926 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
927 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
928
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
929 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
930 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
931 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
932 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
933 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
934
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
935 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
936 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
937
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
938 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
939 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
940 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
941 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
942 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
943 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
944 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
945 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
946 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
947 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
948 alignments.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
949
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
950 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
951 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
952 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
953
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
954 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
955 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
956
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
957 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
958 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
959 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
960 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
961 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
962 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
963 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
964 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
965 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
966 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
967 for details.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
968
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
969 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
970 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
971 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
972 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
973 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
974 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
975
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
976 Alignment summmary
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
977 ------------------
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
978
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
979 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
980 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
981
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
982 ::
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
983
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
984 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
985 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
986 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
987 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
988 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
989 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
990
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
991 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
992
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
993 ::
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
994
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
995 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
996 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
997 650 (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
998 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
999 527 (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
1000 ----
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
1001 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
1002 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
1003 ----
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
1004 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
1005 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
1006 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
1007 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
1008 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
1009 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
1010
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
1011 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
1012
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
1013
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
1014 .. class:: infomark
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
1015
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
1016 **HISAT2 options**
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1017
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1018 Galaxy wrapper for HISAT2 implements most, but not all, options available through the command line. Supported options are described below.
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1019
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1020 -----
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1021
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1022 **Inputs**
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1023
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1024 HISAT2 accepts files in FASTQ or FASTA format (single-end or paired-end).
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1025
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1026 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.)
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1027
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1028 ------
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1029
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1030 **Input options**::
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1031
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1032 -s/--skip <int>
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1033 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
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1034
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1035 -u/--qupto <int>
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1036 Align the first `<int>` reads or read pairs from the input (after the
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1037 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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1038
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1039 -5/--trim5 <int>
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1040 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
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1041
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1042 -3/--trim3 <int>
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1043 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
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1044
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1045 --phred33
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1046 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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1047 also called the "Phred+33" encoding, which is used by the very latest Illumina
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1048 pipelines.
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1049
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1050 --phred64
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1051 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
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1052 also called the "Phred+64" encoding.
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1053
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1054 --solexa-quals
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1055 Convert input qualities from Solexa Phred quality (which can be negative) to
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1056 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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1057 Pipeline versions (prior to 1.3). Default: off.
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1058
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1059 --int-quals
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1060 Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`....
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1061 Integers are treated as being on the Phred quality scale unless
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1062 `--solexa-quals` is also specified. Default: off.
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1063
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1064 ------
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1065
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1066 **Alignment options**::
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1067
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1068 --n-ceil <func>
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1069 Sets a function governing the maximum number of ambiguous characters (usually
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1070 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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1071 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
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1072 where x is the read length. Reads exceeding this ceiling are filtered out.
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1073 Default: `L,0,0.15`.
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1074
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1075 --ignore-quals
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1076 When calculating a mismatch penalty, always consider the quality value at the
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1077 mismatched position to be the highest possible, regardless of the actual value.
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1078 I.e. input is treated as though all quality values are high. This is also the
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1079 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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1080 `-r`, or `-c` modes).
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1081
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1082 --nofw/--norc
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1083 If `--nofw` is specified, `hisat2` will not attempt to align unpaired reads to
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1084 the forward (Watson) reference strand. If `--norc` is specified, `hisat2` will not attempt to align unpaired reads against the reverse-complement (Crick)
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1085 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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1086 fragments; i.e. specifying `--nofw` causes `hisat2` to explore only those
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1087 paired-end configurations corresponding to fragments from the reverse-complement
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1088 (Crick) strand. Default: both strands enabled.
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1089
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1090 -----
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1091
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1092 **Scoring options**::
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1093
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1094 --mp MX,MN
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1095 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
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1096 subtracted from the alignment score for each position where a read character
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1097 aligns to a reference character, the characters do not match, and neither is an
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1098 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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1099 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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1100 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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1101
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1102 --sp MX,MN
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1103 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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1104
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1105 --no-softclip
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1106 Disallow soft-clipping.
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1107
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1108 --np <int>
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1109 Sets penalty for positions where the read, reference, or both, contain an
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1110 ambiguous character such as `N`. Default: 1.
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1111
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1112 --rdg <int1>,<int2>
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1113 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
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1114 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
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1115
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1116 --rfg <int1>,<int2>
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1117 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
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1118 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
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1119 5, 3.
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1120
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1121 --score-min <func>
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1122 Sets a function governing the minimum alignment score needed for an alignment to
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1123 be considered "valid" (i.e. good enough to report). This is a function of read
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1124 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
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1125 to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default is `L,0,-0.2`.
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1126
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1127 -----
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1128
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1129 **Spliced alignment options**::
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1130
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1131 --pen-cansplice <int>
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1132 Sets the penalty for each pair of canonical splice sites (e.g. GT/AG). Default: 0.
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1133
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1134 --pen-noncansplice <int>
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1135 Sets the penalty for each pair of non-canonical splice sites (e.g. non-GT/AG). Default: 12.
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1136
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1137 --pen-canintronlen <func>
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1138 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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1139
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1140 --pen-noncanintronlen <func>
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1141 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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1142
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1143 --min-intronlen <int>
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1144 Sets minimum intron length. Default: 20
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1145
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1146 --max-intronlen <int>
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1147 Sets maximum intron length. Default: 500000
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1148
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1149 --no-spliced-alignment
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1150 Disable spliced alignment.
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1151
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1152 -I/--minins <int>
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1153 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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1154
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1155 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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1156
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1157 Default: 0 (essentially imposing no minimum)
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1158
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1159 -X/--maxins <int>
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1160 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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1161
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1162 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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1163
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1164 Default: 500.
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1165
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1166 --known-splicesite-infile <path>
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1167 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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1168
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1169 --tmo/--transcriptome-mapping-only
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1170 Report only those alignments within known transcripts.
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1171
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1172 --dta/--downstream-transcriptome-assembly
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1173 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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1174
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1175 --dta-cufflinks
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1176 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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1177
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1178 --no-templatelen-adjustment
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1179 Disables template length adjustment for RNA-seq reads.
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1180
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1181 --novel-splicesite-outfile
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1182 In this mode, HISAT2 reports a list of splice sites in the file :
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1183 chromosome name <tab> genomic position of the flanking base on the left side of an intron <tab> genomic position of the flanking base on the right <tab> strand (+, -, and .) '.' indicates an unknown strand for non-canonical splice sites.
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1184
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1185 -----
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1186
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1187 **Reporting options**::
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1188
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1189 -k <int>
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1190 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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1191
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1192 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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1193
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1194 -----
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1195
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1196 **Paired-end options**::
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1197
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1198 --fr/--rf/--ff
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1199 The upstream/downstream mate orientations for a valid paired-end alignment
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1200 against the forward reference strand. E.g., if `--fr` is specified and there is
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1201 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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1202 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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1203 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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1204 complement of mate 1 and all other constraints are met, that too is valid.
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1205 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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1206 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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1207 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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1208 for Illumina's Paired-end Sequencing Assay).
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1209
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1210 --no-mixed
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1211 By default, when `hisat2` cannot find a concordant or discordant alignment for
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1212 a pair, it then tries to find alignments for the individual mates. This option
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1213 disables that behavior.
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1214
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1215 --no-discordant
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1216 By default, `hisat2` looks for discordant alignments if it cannot find any
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1217 concordant alignments. A discordant alignment is an alignment where both mates
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1218 align uniquely, but that does not satisfy the paired-end constraints
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1219 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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1220
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1221
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1222 **Output options**::
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1223
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1224 --un/--un-gz/--un-bz2
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1225 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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1226
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1227 --al/--al-gz/--al-bz2
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1228 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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1229
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1230 --un-conc/--un-conc-gz/--un-conc-bz2
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1231 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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1232
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1233 --al-conc/--al-conc-gz/--al-conc-bz2
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1234 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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1235
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1236
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1237 **Other options**::
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1238
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1239 --seed <int>
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1240 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
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1241
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1242 --non-deterministic
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1243 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.
14
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1244 ]]></help>
0
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1245 <citations>
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1246 <citation type="doi">10.1038/nmeth.3317</citation>
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1247 </citations>
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1248 </tool>