annotate hisat2.xml @ 29:26371a1df031 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
author iuc
date Mon, 25 Jan 2021 17:29:15 +0000
parents d4b55e2beb12
children 6c19daec423d
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1 <tool id="hisat2" name="HISAT2" version="2.1.0+galaxy7" 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="1.11">samtools</requirement>
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9 <requirement type="package" version="1.3">seqtk</requirement>
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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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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 '$novel_splicesite_output'
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286 #end if
28
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287
15
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288 #if str($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 ${adv.reporting_options.max_primary}
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299 #end if
15
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300 #end if
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301
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302
29
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303 ## SAM options
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304
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305 #if str($adv.sam_options.sam_options_selector) == "advanced":
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306 #if $adv.sam_options.no_unal:
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307 --no-unal
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308 #end if
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309 #if str($adv.sam_options.read_groups.rg_labels) == "Yes":
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310 --rg-id '$adv.sam_options.read_groups.rg_id'
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311 #if len('$adv.sam_options.read_groups.read_groups'):
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312 #for $i, $id in enumerate($adv.sam_options.read_groups.read_groups):
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313 --rg '$id.rg'
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314 #end for
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315 #end if
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316 #end if
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317 $adv.sam_options.chr_text
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318 #if $adv.sam_options.omit_sec_seq:
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319 --omit-sec-seq
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320 #end if
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321 #end if
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322
15
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323 ## Other options
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324
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325 #if str( $adv.other_options.other_options_selector ) == "advanced":
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326 ${adv.other_options.non_deterministic}
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327 --seed '${adv.other_options.seed}'
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328 #end if
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329
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330
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331 ## Output Summary
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332
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333 #if str($sum.new_summary) == "true":
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334 --new-summary
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335 #end if
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336
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337 #if str($sum.summary_file) == "true":
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338 --summary-file summary.txt
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339 #end if
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340
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341 ## Convert SAM output to sorted BAM
21
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342 ## using the two pipe stages has the following effect
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343 ## - hisat2 and sort run in parallel, during this time sort produces
22
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344 ## presorted temporary files but does not produce output (hence
21
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345 ## view does not run)
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346 ## - once hisat is finished sort will start to merge the temporary
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347 ## files (which should be fast also on a single thread) gives the
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348 ## sorted output to view which only compresses the files (now
21
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349 ## using full parallelism again)
15
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350
27
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351 | samtools sort -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}'
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352
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353 ## Rename any output fastq files
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354
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355 #if $output_unaligned_reads_l and $output_unaligned_reads_r:
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356 #from os.path import splitext
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357 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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358 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
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359 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
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360 #end if
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361 #if $output_aligned_reads_l and $output_aligned_reads_r:
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362 #from os.path import splitext
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363 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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364 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
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365 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
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366 #end if
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367 ]]></command>
15
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368
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369 <!-- Define inputs -->
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370
0
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371 <inputs>
15
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372
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373 <!-- Reference genome -->
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374 <conditional name="reference_genome">
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375 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options">
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376 <option value="indexed" selected="true">Use a built-in genome</option>
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377 <option value="history">Use a genome from history</option>
0
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378 </param>
15
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379 <when value="indexed">
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380 <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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381 <options from_data_table="hisat2_indexes">
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382 <filter type="sort_by" column="2" />
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383 <validator type="no_options" message="No genomes are available for the selected input dataset" />
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384 </options>
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385 </param>
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386 </when>
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387 <when value="history">
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388 <param name="history_item" type="data" format="fasta" label="Select the reference genome" />
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389 </when>
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390 </conditional>
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391
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392 <!-- Reads -->
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393 <conditional name="library">
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394 <param name="type" type="select" label="Is this a single or paired library">
15
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395 <option value="single">Single-end</option>
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396 <option value="paired">Paired-end</option>
22
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397 <option value="paired_collection">Paired-end Dataset Collection</option>
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398 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
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399 </param>
15
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400
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401 <when value="single">
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402 <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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403 <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand information"
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404 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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405 <option value="">Unstranded</option>
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406 <option value="F">Forward (F)</option>
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407 <option value="R">Reverse (R)</option>
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408 </param>
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409 </when>
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410
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411 <when value="paired">
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412 <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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413 <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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414 <expand macro="paired_end_options" />
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415 </when>
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416
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417 <when value="paired_collection">
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418 <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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419 <expand macro="paired_end_options" />
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420 </when>
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421 <when value="paired_interleaved">
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422 <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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423 <expand macro="paired_end_options" />
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424 </when>
15
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425 </conditional>
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426
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427 <!-- Summary Options -->
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428 <section name="sum" title="Summary Options" expanded="False">
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429 <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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430 <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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431 </section>
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432
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433 <!-- Advanced Options -->
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434 <section name="adv" title="Advanced Options" expanded="False">
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435 <conditional name="input_options">
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436 <param name="input_options_selector" type="select" label="Input options">
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437 <option value="defaults">Use default values</option>
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438 <option value="advanced">Specify input options</option>
0
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439 </param>
15
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440 <when value="defaults" />
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441 <when value="advanced">
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442 <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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443 <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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444 <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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445 <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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446 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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447 <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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448 <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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449 </param>
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450 <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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451 <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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452 </when>
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453 </conditional>
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454
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455 <conditional name="alignment_options">
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456 <param name="alignment_options_selector" type="select" label="Alignment options">
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457 <option value="defaults">Use default values</option>
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458 <option value="advanced">Specify alignment options</option>
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459 </param>
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460 <when value="defaults" />
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461 <when value="advanced">
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462 <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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463 <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
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464 <param name="coefficient" type="float" value="0.15" label="Coefficient (A)" help="Coefficient for the above function" />
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465 <param argument="--ignore-quals" name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="Ignore quality values" help="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value. I.e. input is treated as though all quality values are high. This is also the default behavior when the input doesn't specify quality values" />
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466 <param argument="--nofw" name="skip_forward" type="boolean" truevalue="--nofw" falsevalue="" label="Skip forward strand of reference" help="If --nofw is specified, HISAT2 will not attempt to align unpaired reads to the forward (Watson) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes HISAT2 to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand" />
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467 <param argument="--norc" name="skip_reverse" type="boolean" truevalue="--norc" falsevalue="" label="Skip reverse strand of reference" help="If --norc is specified, HISAT2 will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --norc causes HISAT2 to explore only those paired-end configurations corresponding to fragments from the forward-complement (Watson) strand" />
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468 </when>
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469 </conditional>
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470
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471 <conditional name="scoring_options">
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472 <param name="scoring_options_selector" type="select" label="Scoring options">
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473 <option value="defaults">Use default values</option>
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474 <option value="advanced">Specify scoring options</option>
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475 </param>
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476 <when value="defaults" />
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477 <when value="advanced">
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478 <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
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479 <param name="coefficient" type="float" value="-0.2" label="Coefficient (A)" help="Coefficient for the above function" />
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480 <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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481 <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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482 <param argument="--sp" name="soft_clip_penalty_max" type="integer" value="2" min="0" label="Maximum soft-clipping penalty" help="Sets the maximum (MX) penalty for soft-clipping per base. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position. The number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value" />
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483 <param argument="--sp" name="soft_clip_penalty_min" type="integer" value="1" min="0" label="Minimum soft-clipping penalty" help="Sets the minimum (MN) penalty for soft-clipping per base. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position. The number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value" />
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484 <param argument="--no-softclip" name="no_softclip" type="boolean" truevalue="" falsevalue="--no-softclip" label="Allow soft-clipping" />
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485 <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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486 <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]" />
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487 <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]" />
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488 <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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489 <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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490 <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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491 </when>
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492 </conditional>
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493
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494 <conditional name="spliced_options">
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495 <param name="spliced_options_selector" type="select" label="Spliced alignment options">
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496 <option value="defaults">Use default values</option>
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497 <option value="advanced">Specify spliced alignment options</option>
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498 </param>
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499 <when value="defaults" />
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500 <when value="advanced">
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501 <param name="canonical_penalty" argument="--pen-cansplice" type="integer" value="0" min="0" label="Penalty for canonical splice sites" />
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502 <param name="noncanonical_penalty" argument="--pen-noncansplice" type="integer" value="12" min="0" label="Penalty for non-canonical splice sites" />
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503 <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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504 <param name="constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" />
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505 <param name="coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
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506 <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"/>
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507 <param name="nc_constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" />
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508 <param name="nc_coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
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509 <param name="min_intron" type="integer" value="20" min="0" label="Minimum intron length" />
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510 <param name="max_intron" type="integer" value="500000" min="0" label="Maximum intron length" />
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511 <conditional name="no_spliced_alignment_options">
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512 <param name="no_spliced_alignment" argument="--no-spliced-alignment" type="select" label="Disable spliced alignment">
17
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513 <option value="">False</option>
15
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514 <option value="--no-spliced-alignment">True</option>
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515 </param>
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516 <when value="--no-spliced-alignment">
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517 <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" />
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518 <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" />
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519 </when>
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520 <when value="" />
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521 </conditional>
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522 <param name="known_splice_gtf" type="data" format="gtf" optional="true" label="GTF file with known splice sites" />
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523 <param name="tma" type="select" display="radio" label="Transcriptome assembly reporting">
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524 <option value="">Use default reporting</option>
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525 <option value="--tmo">Report only those alignments within known transcripts</option>
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526 <option value="--dta">Report alignments tailored for transcript assemblers including StringTie</option>
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527 <option value="--dta-cufflinks">Report alignments tailored specifically for Cufflinks</option>
15
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528 </param>
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529 <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" />
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530 <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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531 </when>
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532 </conditional>
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533
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534 <conditional name="reporting_options">
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535 <param name="reporting_options_selector" type="select" label="Reporting options">
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536 <option value="defaults">Use default values</option>
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537 <option value="advanced">Specify reporting options</option>
0
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538 </param>
15
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539 <when value="defaults" />
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540 <when value="advanced">
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541 <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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542 </when>
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543 </conditional>
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544
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545 <conditional name="output_options">
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546 <param name="output_options_selector" type="select" label="Output options">
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547 <option value="defaults">Use default values</option>
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548 <option value="advanced">Specify output options</option>
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549 </param>
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550 <when value="defaults" />
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551 <when value="advanced">
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552 <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" />
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553 <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" />
15
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554 </when>
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555 </conditional>
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556
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557 <conditional name="sam_options">
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558 <param name="sam_options_selector" type="select" label="SAM options">
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559 <option value="defaults">Use default values</option>
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560 <option value="advanced">Specify output options</option>
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561 </param>
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562 <when value="defaults" />
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563 <when value="advanced">
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564 <param name="no_unal" argument="--no-unal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress SAM records for reads that failed to align." help="Default: false"/>
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565 <conditional name="read_groups">
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566 <param name="rg_labels" type="select" label="Edit Read Group IDs">
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567 <option value="No" />
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568 <option value="Yes" />
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569 </param>
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570 <when value="No"/>
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571 <when value="Yes">
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572 <param name="rg_id" argument="--rg-id" type="text" value="read_group" label="Read Group ID" help="Set the read group ID to the value set here. This causes the SAM @RG header line to be printed, with this input value as the value associated with the ID: tag. It also causes the RG:Z: extra field to be attached to each SAM output record, with value set to the value set here." />
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573 <repeat name="read_groups" title="Read Groups text">
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574 <param name="rg" argument="--rg" type="text" optional="true" label="Read Group text" help="Add specified text (usually of the form TAG:VAL, e.g. SM:Pool1) as a field on the @RG header line. Note: in order for the @RG line to appear, Read Group ID must also be specified. This is because the ID tag is required by the SAM Spec. Specify --rg multiple times to set multiple fields. See the SAM Spec for details about what fields are legal." />
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575 </repeat>
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576 </when>
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577 </conditional>
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578 <param name="chr_text" type="select" label="Add/remove 'chr' from reference names in alignment files">
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579 <option value="" selected="true">Use default values</option>
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580 <option value="--remove-chrname">Remove ‘chr’ from reference names in alignment (e.g., chr18 to 18)</option>
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581 <option value="--add-chrname">Add ‘chr’ to reference names in alignment (e.g., 18 to chr18)</option>
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582 </param>
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583 <param name="omit_sec_seq" argument="--omit-sec-seq" type="boolean" truevalue="true" falsevalue="false" checked="false" label="When printing secondary alignments, HISAT2 by default will write out the SEQ and QUAL strings. Specifying this option causes HISAT2 to print an asterisk in those fields instead." help="Default: false"/>
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diff changeset
584 </when>
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
585 </conditional>
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
586
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
587 <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
588 <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
589 <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
590 <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
591 </param>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
592 <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
593 <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
594 <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
595 <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
596 </when>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
597 </conditional>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
598 </section>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
599
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
600 </inputs>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
601
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
602 <!-- Define outputs -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
603
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
604 <outputs>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
605
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
606 <!-- BAM -->
20
6ab42baa56e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d9ebd463afa1a41799aa53e9a68d0ea51093007e
iuc
parents: 19
diff changeset
607 <data name="output_alignments" format="bam" label="${tool.name} on ${on_string}: aligned reads (BAM)">
26
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
608 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
609 <expand macro="dbKeyActions" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
610 </actions>
20
6ab42baa56e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d9ebd463afa1a41799aa53e9a68d0ea51093007e
iuc
parents: 19
diff changeset
611 </data>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
612
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
613 <!-- Unaligned fastq (L) -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
614 <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned 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
615 <filter>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
616 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
617 <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
618 <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
619 <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
620 <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
621 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
622 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
623 <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
624 <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
625 <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
626 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
627 </when>
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="paired_collection">
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="forward.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_interleaved">
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="forward.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 </conditional>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
639 <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
640 </actions>
3
b1e25f9b5eab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 9a9d44116b21d9a155b5cc274475e78c14915059
iuc
parents: 2
diff changeset
641 </data>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
642
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
643 <!-- 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
644 <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
645 <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
646 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
647 <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
648 <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
649 <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
650 <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
651 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
652 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
653 <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
654 <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
655 <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
656 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
657 </when>
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="paired_collection">
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="forward.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_interleaved">
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="forward.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 </conditional>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
669 <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
670 </actions>
14
526b91fbde60 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents: 13
diff changeset
671 </data>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
672
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
673 <!-- 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
674 <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
675 <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
676 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
677 <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
678 <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
679 <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
680 <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
681 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
682 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
683 <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
684 <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
685 <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
686 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
687 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
688 <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
689 <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
690 <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
691 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
692 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
693 <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
694 <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
695 <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
696 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
697 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
698 </conditional>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
699 <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
700 </actions>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
701 </data>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
702
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
703 <!-- 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
704 <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
705 <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
706 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
707 <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
708 <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
709 <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
710 <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
711 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
712 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
713 <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
714 <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
715 <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
716 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
717 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
718 <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
719 <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
720 <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
721 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
722 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
723 <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
724 <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
725 <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
726 </action>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
727 </when>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
728 </conditional>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
729 <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
730 </actions>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
731 </data>
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
732
26
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
733 <!-- 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
734 <data name="summary_file" format="txt" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: Mapping summary">
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
735 <filter>sum['summary_file'] is True</filter>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
736 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
737 <expand macro="dbKeyActions" />
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
738 </actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
739 </data>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
740
26
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
741 <!-- Novel Splice file -->
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
742 <data name="novel_splicesite_output" format="tabular" label="${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
743 <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
744 <actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
745 <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
746 </actions>
0c16cad5e03b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 84b71df5668dfd13bdf46e6e6f3d8a6f316ccea6
iuc
parents: 25
diff changeset
747 </data>
25
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
748
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
749
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
750 </outputs>
15
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
751
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
752 <!-- Define tests -->
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
753
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
754 <tests>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
755 <!-- 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
756 <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
757 <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
758 <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
759 <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
760 <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
761 <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
762 <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
763 <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
764 <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
765 </test>
18
764756ab0eb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 4b78174c0753e9f916bf6625490c0ce605979940
iuc
parents: 17
diff changeset
766 <!-- 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
767 <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
768 <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
769 <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
770 <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
771 <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
772 <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
773 <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
774 <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
775 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
776 <!-- 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
777 <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
778 <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
779 <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
780 <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
781 <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
782 <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
783 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
784 <!-- 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
785 <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
786 <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
787 <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
788 <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
789 <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
790 <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
791 <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
792 <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
793 <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
794 <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
795 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
796 <!-- 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
797 <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
798 <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
799 <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
800 <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
801 <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
802 <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
803 <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
804 <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
805 <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
806 <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
807 <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
808 <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
809 <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
810 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
811 <!-- 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
812 <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
813 <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
814 <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
815 <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
816 <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
817 <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
818 <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
819 <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
820 <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
821 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
822 <!-- 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
823 <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
824 <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
825 <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
826 <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
827 <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
828 <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
829 <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
830 <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
831 <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
832 <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
833 <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
834 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
835 <!-- 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
836 <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
837 <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
838 <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
839 <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
840 <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
841 <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
842 <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
843 <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
844 <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
845 <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
846 <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
847 <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
848 <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
849 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
850 <!-- 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
851 <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
852 <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
853 <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
854 <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
855 <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
856 <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
857 <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
858 <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
859 <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
860 <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
861 <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
862 <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
863 <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
864 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
865 <!-- 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
866 <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
867 <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
868 <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
869 <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
870 <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
871 <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
872 <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
873 <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
874 </test>
16
21e8ea8e1adb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632
iuc
parents: 15
diff changeset
875 <!-- 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
876 <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
877 <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
878 <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
879 <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
880 <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
881 <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
882 <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
883 <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
884 <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
885 </test>
22
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
886 <!-- 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
887 <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
888 <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
889 <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
890 <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
891 <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
892 <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
893 </test>
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
894 <!-- 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
895 <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
896 <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
897 <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
898 <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
899 <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
900 <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
901 </test>
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
902 <!-- 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
903 <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
904 <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
905 <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
906 <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
907 <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
908 <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
909 </test>
a26ed87f444c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
iuc
parents: 21
diff changeset
910 <!-- 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
911 <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
912 <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
913 <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
914 <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
915 <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
916 <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
917 </test>
25
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
918 <!-- 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
919 <test>
3fb01a8c902d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652
iuc
parents: 24
diff changeset
920 <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
921 <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
922 <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
923 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_split_forward.fastq" />
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iuc
parents: 24
diff changeset
924 <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
925 <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
926 <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
927 <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
928 <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
iuc
parents: 24
diff changeset
929 </test>
29
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iuc
parents: 28
diff changeset
930 <!-- Ensure SAM output settings work -->
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
931 <test expect_num_outputs="1" >
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
932 <param name="type" value="paired_interleaved" />
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
933 <param name="source" value="history" />
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
934 <param name="history_item" ftype="fasta" value="phiX.fa" />
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
935 <param name="input_1" ftype="fastqsanger.bz2" value="hisat_input_1_interleaved.fastq.bz2" />
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
936 <param name="adv|sam_options|sam_options_selector" value="advanced"/>
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
937 <param name="adv|sam_options|no_unal" value="true"/>
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
938 <param name="adv|sam_options|read_groups|rg_labels" value="Yes"/>
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
939 <repeat name="adv|sam_options|read_groups|read_groups">
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
940 <param name="rg" value="BC:test1"/>
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
941 </repeat>
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
942 <repeat name="adv|sam_options|read_groups|read_groups">
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
943 <param name="rg" value="CN:test2"/>
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
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parents: 28
diff changeset
944 </repeat>
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
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parents: 28
diff changeset
945 <param name="adv|sam_options|chr_text" value="--add-chrname"/>
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
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parents: 28
diff changeset
946 <param name="adv|sam_options|omit_sec_seq" value="True"/>
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
947 <output name="output_alignments" file="hisat_output_5.bam" ftype="bam" lines_diff="2" />
26371a1df031 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit f18e8826ecb395a40fc321b5f3b66ab6d7f51625"
iuc
parents: 28
diff changeset
948 </test>
0
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
949 </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
950
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
951 <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
952 Introduction
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
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parents:
diff changeset
954
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
955 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
956 --------------
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
957
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
958 `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
959 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
960 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
iuc
parents:
diff changeset
961 (`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
962 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
iuc
parents:
diff changeset
963 hierarchical indexing, that employs two types of indexes: (1) one global
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
964 FM index representing the whole genome, and (2) many separate local FM
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
965 indexes for small regions collectively covering the genome. Our
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
966 hierarchical index for the human genome (about 3 billion bp) includes
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
967 ~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
968 ~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
969 extremely fast with a low memory footprint, as demonstrated by
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
970 `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
971 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
972 types of RNA-seq reads. All these together, HISAT enables extremely fast
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
973 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
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parents:
diff changeset
974 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
975 `TopHat2 <http://ccb.jhu.edu/software/tophat>`__ with better alignment
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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parents:
diff changeset
976 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
977 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
978 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
979 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
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parents:
diff changeset
980 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
981 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
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parents:
diff changeset
982 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
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parents:
diff changeset
983 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
984 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"
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parents: 26
diff changeset
985 HISAT is distributed under the `GPLv3
0
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parents:
diff changeset
986 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
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parents:
diff changeset
987 the command line under Linux, Mac OS X and Windows.
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parents:
diff changeset
988
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
989 Running 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
990 =============
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parents:
diff changeset
991
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
992 Reporting
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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diff changeset
993 ---------
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parents:
diff changeset
994
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
995 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
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parents:
diff changeset
996 to report them.
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parents:
diff changeset
997
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
998 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
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parents:
diff changeset
999 has a `valid
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
1000 alignment <#valid-alignments-meet-or-exceed-the-minimum-score-threshold>`__.
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parents:
diff changeset
1001 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
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parents:
diff changeset
1002 multiple alignments that are valid and distinct from one another.
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parents:
diff changeset
1003
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parents:
diff changeset
1004 Distinct alignments map a read to different places
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diff changeset
1005 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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diff changeset
1006
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parents:
diff changeset
1007 Two alignments for the same individual read are "distinct" if they map
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parents:
diff changeset
1008 the same read to different places. Specifically, we say that two
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iuc
parents:
diff changeset
1009 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
1010 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
1011 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
1012 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
1013 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
1014 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
1015 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
1016 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
1017 alignments.
5bafe7d7a55e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff changeset
1018
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iuc
parents:
diff changeset
1019 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
1020 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
1021 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
1022
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iuc
parents:
diff changeset
1023 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
1024 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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iuc
parents:
diff changeset
1025
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iuc
parents:
diff changeset
1026 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
1027 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
1028 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
1029 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
1030 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
1031 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
1032 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
1033 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
1034 has the SAM 'secondary' bit (which equals 256) set in its FLAGS field.
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iuc
parents:
diff changeset
1035 See the `SAM specification <http://samtools.sourceforge.net/SAM1.pdf>`__
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iuc
parents:
diff changeset
1036 for details.
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iuc
parents:
diff changeset
1037
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iuc
parents:
diff changeset
1038 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
1039 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
1040 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
1041 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
1042 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
1043 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
1044
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iuc
parents:
diff changeset
1045 Alignment summmary
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iuc
parents:
diff changeset
1046 ------------------
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iuc
parents:
diff changeset
1047
15
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parents: 14
diff changeset
1048 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>`_.
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iuc
parents: 14
diff changeset
1049 For datasets consisting of unpaired reads, the summary might look like this:
0
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iuc
parents:
diff changeset
1050
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iuc
parents:
diff changeset
1051 ::
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iuc
parents:
diff changeset
1052
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iuc
parents:
diff changeset
1053 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
1054 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
1055 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
1056 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
1057 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
1058 93.77% overall alignment rate
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iuc
parents:
diff changeset
1059
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iuc
parents:
diff changeset
1060 For datasets consisting of pairs, the summary might look like this:
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iuc
parents:
diff changeset
1061
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iuc
parents:
diff changeset
1062 ::
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iuc
parents:
diff changeset
1063
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iuc
parents:
diff changeset
1064 10000 reads; of these:
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iuc
parents:
diff changeset
1065 10000 (100.00%) were paired; of these:
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iuc
parents:
diff changeset
1066 650 (6.50%) aligned concordantly 0 times
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iuc
parents:
diff changeset
1067 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
1068 527 (5.27%) aligned concordantly >1 times
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iuc
parents:
diff changeset
1069 ----
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iuc
parents:
diff changeset
1070 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
1071 34 (5.23%) aligned discordantly 1 time
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iuc
parents:
diff changeset
1072 ----
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iuc
parents:
diff changeset
1073 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
1074 1232 mates make up the pairs; of these:
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iuc
parents:
diff changeset
1075 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
1076 571 (46.35%) aligned exactly 1 time
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iuc
parents:
diff changeset
1077 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
1078 96.70% overall alignment rate
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iuc
parents:
diff changeset
1079
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iuc
parents:
diff changeset
1080 The indentation indicates how subtotals relate to totals.
15
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iuc
parents: 14
diff changeset
1081
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iuc
parents: 14
diff changeset
1082
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iuc
parents: 14
diff changeset
1083 .. class:: infomark
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iuc
parents: 14
diff changeset
1084
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iuc
parents: 14
diff changeset
1085 **HISAT2 options**
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iuc
parents: 14
diff changeset
1086
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
1087 Galaxy wrapper for HISAT2 implements most, but not all, options available through the command line. Supported options are described below.
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iuc
parents: 14
diff changeset
1088
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iuc
parents: 14
diff changeset
1089 -----
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iuc
parents: 14
diff changeset
1090
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iuc
parents: 14
diff changeset
1091 **Inputs**
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iuc
parents: 14
diff changeset
1092
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iuc
parents: 14
diff changeset
1093 HISAT2 accepts files in FASTQ or FASTA format (single-end or paired-end).
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
1094
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iuc
parents: 14
diff changeset
1095 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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iuc
parents: 14
diff changeset
1096
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1097 ------
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1098
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1099 **Input options**::
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1100
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1101 -s/--skip <int>
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1102 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
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1103
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1104 -u/--qupto <int>
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1105 Align the first `<int>` reads or read pairs from the input (after the
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1106 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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1107
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1108 -5/--trim5 <int>
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1109 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
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1110
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1111 -3/--trim3 <int>
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1112 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
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1113
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1114 --phred33
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1115 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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1116 also called the "Phred+33" encoding, which is used by the very latest Illumina
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1117 pipelines.
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1118
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1119 --phred64
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1120 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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1121 also called the "Phred+64" encoding.
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1122
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1123 --solexa-quals
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1124 Convert input qualities from Solexa Phred quality (which can be negative) to
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1125 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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1126 Pipeline versions (prior to 1.3). Default: off.
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1127
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1128 --int-quals
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1129 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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1130 Integers are treated as being on the Phred quality scale unless
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1131 `--solexa-quals` is also specified. Default: off.
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1132
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1133 ------
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1134
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1135 **Alignment options**::
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1136
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1137 --n-ceil <func>
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1138 Sets a function governing the maximum number of ambiguous characters (usually
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1139 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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1140 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
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1141 where x is the read length. Reads exceeding this ceiling are filtered out.
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1142 Default: `L,0,0.15`.
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1143
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1144 --ignore-quals
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1145 When calculating a mismatch penalty, always consider the quality value at the
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1146 mismatched position to be the highest possible, regardless of the actual value.
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1147 I.e. input is treated as though all quality values are high. This is also the
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1148 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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1149 `-r`, or `-c` modes).
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1150
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1151 --nofw/--norc
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1152 If `--nofw` is specified, `hisat2` will not attempt to align unpaired reads to
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1153 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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1154 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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1155 fragments; i.e. specifying `--nofw` causes `hisat2` to explore only those
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1156 paired-end configurations corresponding to fragments from the reverse-complement
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1157 (Crick) strand. Default: both strands enabled.
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1158
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1159 -----
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1160
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diff changeset
1161 **Scoring options**::
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1162
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1163 --mp MX,MN
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1164 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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1165 subtracted from the alignment score for each position where a read character
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1166 aligns to a reference character, the characters do not match, and neither is an
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1167 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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1168 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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1169 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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diff changeset
1170
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1171 --sp MX,MN
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1172 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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1173
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1174 --no-softclip
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1175 Disallow soft-clipping.
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1176
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1177 --np <int>
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1178 Sets penalty for positions where the read, reference, or both, contain an
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1179 ambiguous character such as `N`. Default: 1.
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diff changeset
1180
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1181 --rdg <int1>,<int2>
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1182 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
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1183 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
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diff changeset
1184
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1185 --rfg <int1>,<int2>
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1186 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
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1187 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
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1188 5, 3.
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1189
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1190 --score-min <func>
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1191 Sets a function governing the minimum alignment score needed for an alignment to
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1192 be considered "valid" (i.e. good enough to report). This is a function of read
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1193 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
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diff changeset
1194 to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default is `L,0,-0.2`.
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1195
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1196 -----
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1197
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1198 **Spliced alignment options**::
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1199
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1200 --pen-cansplice <int>
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1201 Sets the penalty for each pair of canonical splice sites (e.g. GT/AG). Default: 0.
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1202
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1203 --pen-noncansplice <int>
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1204 Sets the penalty for each pair of non-canonical splice sites (e.g. non-GT/AG). Default: 12.
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1205
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1206 --pen-canintronlen <func>
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1207 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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1208
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1209 --pen-noncanintronlen <func>
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1210 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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1211
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1212 --min-intronlen <int>
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1213 Sets minimum intron length. Default: 20
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1214
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1215 --max-intronlen <int>
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1216 Sets maximum intron length. Default: 500000
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1217
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1218 --no-spliced-alignment
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1219 Disable spliced alignment.
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1220
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1221 -I/--minins <int>
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1222 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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1223
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1224 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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1225
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1226 Default: 0 (essentially imposing no minimum)
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1227
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1228 -X/--maxins <int>
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1229 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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1230
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1231 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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1232
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1233 Default: 500.
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1234
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1235 --known-splicesite-infile <path>
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1236 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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1237
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1238 --tmo/--transcriptome-mapping-only
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1239 Report only those alignments within known transcripts.
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1240
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1241 --dta/--downstream-transcriptome-assembly
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1242 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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1243
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1244 --dta-cufflinks
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1245 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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1246
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1247 --no-templatelen-adjustment
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1248 Disables template length adjustment for RNA-seq reads.
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1249
25
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1250 --novel-splicesite-outfile
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1251 In this mode, HISAT2 reports a list of splice sites in the file :
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1252 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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1253
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1254 -----
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diff changeset
1255
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1256 **Reporting options**::
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1257
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1258 -k <int>
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1259 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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1260
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1261 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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1262
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1263 -----
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diff changeset
1264
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1265 **Paired-end options**::
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diff changeset
1266
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
1267 --fr/--rf/--ff
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
1268 The upstream/downstream mate orientations for a valid paired-end alignment
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
1269 against the forward reference strand. E.g., if `--fr` is specified and there is
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
1270 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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
1271 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
1272 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
1273 complement of mate 1 and all other constraints are met, that too is valid.
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
1274 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
iuc
parents: 14
diff changeset
1275 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
1276 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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
1277 for Illumina's Paired-end Sequencing Assay).
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
1278
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parents: 14
diff changeset
1279 --no-mixed
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
1280 By default, when `hisat2` cannot find a concordant or discordant alignment for
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
1281 a pair, it then tries to find alignments for the individual mates. This option
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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parents: 14
diff changeset
1282 disables that behavior.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
1283
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
1284 --no-discordant
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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diff changeset
1285 By default, `hisat2` looks for discordant alignments if it cannot find any
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
1286 concordant alignments. A discordant alignment is an alignment where both mates
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
1287 align uniquely, but that does not satisfy the paired-end constraints
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diff changeset
1288 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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1289
29
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diff changeset
1290 -----
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1291
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diff changeset
1292 ** SAM options
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diff changeset
1293
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diff changeset
1294 --no-unal
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1295 Suppress SAM records for reads that failed to align.
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diff changeset
1296 --rg-id <text>
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diff changeset
1297
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diff changeset
1298 Set the read group ID to <text>. This causes the SAM @RG header line to be printed, with <text> as the value associated with the ID: tag. It also causes the RG:Z: extra field to be attached to each SAM output record, with value set to <text>.
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diff changeset
1299 --rg <text>
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diff changeset
1300 Add <text> (usually of the form TAG:VAL, e.g. SM:Pool1) as a field on the @RG header line. Note: in order for the @RG line to appear, --rg-id must also be specified. This is because the ID tag is required by the SAM Spec. Specify --rg multiple times to set multiple fields. See the SAM Spec for details about what fields are legal.
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diff changeset
1301
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diff changeset
1302 --remove-chrname
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diff changeset
1303 Remove ‘chr’ from reference names in alignment (e.g., chr18 to 18)
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diff changeset
1304
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diff changeset
1305 --add-chrname
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1306 Add ‘chr’ to reference names in alignment (e.g., 18 to chr18)
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1307
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diff changeset
1308 --omit-sec-seq
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1309 When printing secondary alignments, HISAT2 by default will write out the SEQ and QUAL strings. Specifying this option causes HISAT2 to print an asterisk in those fields instead.
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diff changeset
1310
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1311 -----
15
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1312
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diff changeset
1313 **Output options**::
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1314
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1315 --un/--un-gz/--un-bz2
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1316 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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1317
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1318 --al/--al-gz/--al-bz2
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1319 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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1320
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1321 --un-conc/--un-conc-gz/--un-conc-bz2
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1322 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.
d5fe9aead222 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 48012d1879395ecf1b4e6cd962f325c372164a33
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1323
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1324 --al-conc/--al-conc-gz/--al-conc-bz2
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1325 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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1326
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1327
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1328 **Other options**::
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1329
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1330 --seed <int>
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1331 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
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1332
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1333 --non-deterministic
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1334 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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1335 ]]></help>
0
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1336 <citations>
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1337 <citation type="doi">10.1038/nmeth.3317</citation>
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1338 </citations>
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1339 </tool>