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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit ac79103bf57c195226877a698dc197a965f82aba
author iuc
date Tue, 24 Jul 2018 09:29:27 -0400
parents 0b1c04a90182
children 6daca6da3059
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21:0b1c04a90182 22:a26ed87f444c
1 <tool id="hisat2" name="HISAT2" version="2.1.0+galaxy1" profile="17.01"> 1 <tool id="hisat2" name="HISAT2" version="2.1.0+galaxy2" profile="17.01">
2 <description>A fast and sensitive alignment program</description> 2 <description>A fast and sensitive alignment program</description>
3 <macros> 3 <macros>
4 <import>hisat2_macros.xml</import> 4 <import>hisat2_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="2.1.0">hisat2</requirement> 7 <requirement type="package" version="2.1.0">hisat2</requirement>
8 <requirement type="package" version="1.8">samtools</requirement> 8 <requirement type="package" version="1.9">samtools</requirement>
9 <requirement type="package" version="1.3">seqtk</requirement>
9 </requirements> 10 </requirements>
10 <stdio> 11 <stdio>
11 <regex level="fatal" match="hisat2-align exited with value 1" source="both" /> 12 <regex level="fatal" match="hisat2-align exited with value 1" source="both" />
12 <regex level="fatal" match="hisat2: not found" source="both" /> 13 <regex level="fatal" match="hisat2: not found" source="both" />
13 <exit_code range="1:" /> 14 <exit_code range="1:" />
40 41
41 #if str($library.type) == 'paired': 42 #if str($library.type) == 'paired':
42 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): 43 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
43 #set read1 = "input_f.fastq.gz" 44 #set read1 = "input_f.fastq.gz"
44 #set compressed = "GZ" 45 #set compressed = "GZ"
45 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): 46 #elif $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
46 #set read1 = "input_f.fastq.bz2" 47 #set read1 = "input_f.fastq.bz2"
47 #set compressed = "BZ2" 48 #set compressed = "BZ2"
48 #else if $library.input_1.is_of_type('fasta'): 49 #elif $library.input_1.is_of_type('fasta'):
49 #set reads_are_fastq = False 50 #set reads_are_fastq = False
50 #set read1 = "input_f.fasta" 51 #set read1 = "input_f.fasta"
51 #else: 52 #else:
52 #set read1 = "input_f.fastq" 53 #set read1 = "input_f.fastq"
53 #end if 54 #end if
54 ln -f -s '${library.input_1}' ${read1} && 55 ln -f -s '${library.input_1}' ${read1} &&
55 56
56 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"): 57 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
57 #set read2 = "input_r.fastq.gz" 58 #set read2 = "input_r.fastq.gz"
58 #set compressed = "GZ" 59 #set compressed = "GZ"
59 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"): 60 #elif $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
60 #set read2 = "input_r.fastq.bz2" 61 #set read2 = "input_r.fastq.bz2"
61 #set compressed = "BZ2" 62 #set compressed = "BZ2"
62 #else if $library.input_2.is_of_type('fasta'): 63 #elif $library.input_2.is_of_type('fasta'):
63 #set read2 = "input_r.fasta" 64 #set read2 = "input_r.fasta"
64 #else: 65 #else:
65 #set read2 = "input_r.fastq" 66 #set read2 = "input_r.fastq"
66 #end if 67 #end if
67 ln -f -s '${library.input_2}' ${read2} && 68 ln -f -s '${library.input_2}' ${read2} &&
68 69
69 #else if str($library.type) == 'paired_collection': 70 #elif str($library.type) == 'paired_collection':
70 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"): 71 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
71 #set read1 = "input_f.fastq.gz" 72 #set read1 = "input_f.fastq.gz"
72 #set compressed = "GZ" 73 #set compressed = "GZ"
73 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): 74 #elif $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
74 #set read1 = "input_f.fastq.bz2" 75 #set read1 = "input_f.fastq.bz2"
75 #set compressed = "BZ2" 76 #set compressed = "BZ2"
76 #else if $library.input_1.forward.is_of_type('fasta'): 77 #elif $library.input_1.forward.is_of_type('fasta'):
77 #set reads_are_fastq = False 78 #set reads_are_fastq = False
78 #set read1 = "input_f.fasta" 79 #set read1 = "input_f.fasta"
79 #else: 80 #else:
80 #set read1 = "input_f.fastq" 81 #set read1 = "input_f.fastq"
81 #end if 82 #end if
82 ln -s '${library.input_1.forward}' ${read1} && 83 ln -s '${library.input_1.forward}' ${read1} &&
83 84
84 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): 85 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
85 #set read2 = "input_r.fastq.gz" 86 #set read2 = "input_r.fastq.gz"
86 #set compressed = "GZ" 87 #set compressed = "GZ"
87 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): 88 #elif $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
88 #set read2 = "input_r.fastq.bz2" 89 #set read2 = "input_r.fastq.bz2"
89 #set compressed = "BZ2" 90 #set compressed = "BZ2"
90 #else if $library.input_1.reverse.is_of_type("fasta"): 91 #elif $library.input_1.reverse.is_of_type("fasta"):
91 #set read2 = "input_r.fasta" 92 #set read2 = "input_r.fasta"
92 #else: 93 #else:
93 #set read2 = "input_r.fastq" 94 #set read2 = "input_r.fastq"
94 #end if 95 #end if
95 ln -s '${library.input_1.reverse}' ${read2} && 96 ln -s '${library.input_1.reverse}' ${read2} &&
96 97 #elif str( $library.type ) == "paired_interleaved":
98 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
99 #set interleaved_reads = "input_f.fastq.gz"
100 #set compressed = "GZ"
101 #elif $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
102 #set interleaved_reads = "input_f.fastq.bz2"
103 #set compressed = "BZ2"
104 #elif $library.input_1.is_of_type('fasta'):
105 #set reads_are_fastq = False
106 #set interleaved_reads = "input_f.fasta"
107 #else:
108 #set interleaved_reads = "input_f.fastq"
109 #end if
110 ln -f -s '${library.input_1}' ${interleaved_reads} &&
111 #if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
112 #set read1 = "<(bzcat input_f.fastq.bz2 | seqtk seq -1 /dev/stdin)"
113 #set read2 = "<(bzcat input_f.fastq.bz2 | seqtk seq -2 /dev/stdin)"
114 #else:
115 #set read1 = "<(seqtk seq -1 %s)" % $interleaved_reads
116 #set read2 = "<(seqtk seq -2 %s)" % $interleaved_reads
117 #end if
97 #else: 118 #else:
98 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): 119 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
99 #set read1 = "input_f.fastq.gz" 120 #set read1 = "input_f.fastq.gz"
100 #set compressed = "GZ" 121 #set compressed = "GZ"
101 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): 122 #elif $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
102 #set read1 = "input_f.fastq.bz2" 123 #set read1 = "input_f.fastq.bz2"
103 #set compressed = "BZ2" 124 #set compressed = "BZ2"
104 #else if $library.input_1.is_of_type('fasta'): 125 #elif $library.input_1.is_of_type('fasta'):
105 #set reads_are_fastq = False 126 #set reads_are_fastq = False
106 #set read1 = "input_f.fasta" 127 #set read1 = "input_f.fasta"
107 #else: 128 #else:
108 #set read1 = "input_f.fastq" 129 #set read1 = "input_f.fastq"
109 #end if 130 #end if
134 155
135 #if str($adv.output_options.output_options_selector) == "advanced": 156 #if str($adv.output_options.output_options_selector) == "advanced":
136 #if str( $adv.output_options.unaligned_file ) == "true": 157 #if str( $adv.output_options.unaligned_file ) == "true":
137 #if $compressed == "GZ": 158 #if $compressed == "GZ":
138 --un-gz '$output_unaligned_reads_l' 159 --un-gz '$output_unaligned_reads_l'
139 #else if $compressed == "BZ2": 160 #elif $compressed == "BZ2":
140 --un-bz2 '$output_unaligned_reads_l' 161 --un-bz2 '$output_unaligned_reads_l'
141 #else: 162 #else:
142 --un '$output_unaligned_reads_l' 163 --un '$output_unaligned_reads_l'
143 #end if 164 #end if
144 #end if 165 #end if
145 166
146 #if str( $adv.output_options.aligned_file ) == "true": 167 #if str( $adv.output_options.aligned_file ) == "true":
147 #if $compressed == "GZ": 168 #if $compressed == "GZ":
148 --al-gz '$output_aligned_reads_l' 169 --al-gz '$output_aligned_reads_l'
149 #else if $compressed == "BZ2": 170 #elif $compressed == "BZ2":
150 --al-bz2 '$output_aligned_reads_l' 171 --al-bz2 '$output_aligned_reads_l'
151 #else: 172 #else:
152 --al '$output_aligned_reads_l' 173 --al '$output_aligned_reads_l'
153 #end if 174 #end if
154 #end if 175 #end if
155 #end if 176 #end if
156 177
157 #else: 178 #else:
158 179 ##quotes are embedded in r1 and r2 variables, needed to allow use of <()
159 -1 '${read1}' 180 #if str( $library.type ) == "paired_interleaved":
160 -2 '${read2}' 181 -1 ${read1}
161 182 -2 ${read2}
183 #else:
184 -1 '${read1}'
185 -2 '${read2}'
186 #end if
162 #if str($adv.output_options.output_options_selector) == "advanced": 187 #if str($adv.output_options.output_options_selector) == "advanced":
163 #if str( $adv.output_options.unaligned_file ) == "true": 188 #if str( $adv.output_options.unaligned_file ) == "true":
164 #if $compressed == "GZ": 189 #if $compressed == "GZ":
165 --un-conc-gz '${output_unaligned_reads_l}' 190 --un-conc-gz '${output_unaligned_reads_l}'
166 #else if $compressed == "BZ2": 191 #elif $compressed == "BZ2":
167 --un-conc-bz2 '${output_unaligned_reads_l}' 192 --un-conc-bz2 '${output_unaligned_reads_l}'
168 #else: 193 #else:
169 --un-conc '${output_unaligned_reads_l}' 194 --un-conc '${output_unaligned_reads_l}'
170 #end if 195 #end if
171 #end if 196 #end if
172 197
173 #if str( $adv.output_options.aligned_file ) == "true": 198 #if str( $adv.output_options.aligned_file ) == "true":
174 #if $compressed == "GZ": 199 #if $compressed == "GZ":
175 --al-conc-gz '${output_aligned_reads_l}' 200 --al-conc-gz '${output_aligned_reads_l}'
176 #else if $compressed == "BZ2": 201 #elif $compressed == "BZ2":
177 --al-conc-bz2 '${output_aligned_reads_l}' 202 --al-conc-bz2 '${output_aligned_reads_l}'
178 #else: 203 #else:
179 --al-conc '${output_aligned_reads_l}' 204 --al-conc '${output_aligned_reads_l}'
180 #end if 205 #end if
181 #end if 206 #end if
290 #end if 315 #end if
291 316
292 ## Convert SAM output to sorted BAM 317 ## Convert SAM output to sorted BAM
293 ## using the two pipe stages has the following effect 318 ## using the two pipe stages has the following effect
294 ## - hisat2 and sort run in parallel, during this time sort produces 319 ## - hisat2 and sort run in parallel, during this time sort produces
295 ## presorted temporary files but does not produce output (hence 320 ## presorted temporary files but does not produce output (hence
296 ## view does not run) 321 ## view does not run)
297 ## - once hisat is finished sort will start to merge the temporary 322 ## - once hisat is finished sort will start to merge the temporary
298 ## files (which should be fast also on a single thread) gives the 323 ## files (which should be fast also on a single thread) gives the
299 ## sorted output to view which only compresses the files (now 324 ## sorted output to view which only compresses the files (now
300 ## using full parallelism again) 325 ## using full parallelism again)
301 326
302 | samtools sort -l 0 -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}' 327 | samtools sort -l 0 -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}'
303 328
304 ## Rename any output fastq files 329 ## Rename any output fastq files
340 </when> 365 </when>
341 </conditional> 366 </conditional>
342 367
343 <!-- Reads --> 368 <!-- Reads -->
344 <conditional name="library"> 369 <conditional name="library">
345 <param name="type" type="select" label="Single-end or paired-end reads?"> 370 <param name="type" type="select" label="Is this a single or paired library">
346 <option value="single">Single-end</option> 371 <option value="single">Single-end</option>
347 <option value="paired">Paired-end</option> 372 <option value="paired">Paired-end</option>
348 <option value="paired_collection">Paired-end Collection</option> 373 <option value="paired_collection">Paired-end Dataset Collection</option>
374 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
349 </param> 375 </param>
350 376
351 <when value="single"> 377 <when value="single">
352 <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;" /> 378 <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;" />
353 <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand information" 379 <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand information"
364 <expand macro="paired_end_options" /> 390 <expand macro="paired_end_options" />
365 </when> 391 </when>
366 392
367 <when value="paired_collection"> 393 <when value="paired_collection">
368 <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;" /> 394 <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;" />
395 <expand macro="paired_end_options" />
396 </when>
397 <when value="paired_interleaved">
398 <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"/>
369 <expand macro="paired_end_options" /> 399 <expand macro="paired_end_options" />
370 </when> 400 </when>
371 </conditional> 401 </conditional>
372 402
373 <!-- Summary Options --> 403 <!-- Summary Options -->
707 <param name="rna_strandness" value="R" /> 737 <param name="rna_strandness" value="R" />
708 <param name="new_summary" value="true" /> 738 <param name="new_summary" value="true" />
709 <param name="summary_file" value="true" /> 739 <param name="summary_file" value="true" />
710 <output name="summary_file" file="hisat_output.summary" ftype="txt" /> 740 <output name="summary_file" file="hisat_output.summary" ftype="txt" />
711 </test> 741 </test>
742 <!-- Ensure interleaved input works -->
743 <test expect_num_outputs="1" >
744 <param name="type" value="paired_interleaved" />
745 <param name="source" value="history" />
746 <param name="history_item" ftype="fasta" value="phiX.fa" />
747 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_interleaved.fastq" />
748 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
749 </test>
750 <!-- Ensure interleaved bz input works -->
751 <test expect_num_outputs="1" >
752 <param name="type" value="paired_interleaved" />
753 <param name="source" value="history" />
754 <param name="history_item" ftype="fasta" value="phiX.fa" />
755 <param name="input_1" ftype="fastqsanger.bz2" value="hisat_input_1_interleaved.fastq.bz2" />
756 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
757 </test>
758 <!-- Ensure interleaved gz input works -->
759 <test expect_num_outputs="1" >
760 <param name="type" value="paired_interleaved" />
761 <param name="source" value="history" />
762 <param name="history_item" ftype="fasta" value="phiX.fa" />
763 <param name="input_1" ftype="fastqsanger.gz" value="hisat_input_1_interleaved.fastq.gz" />
764 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
765 </test>
766 <!-- Ensure interleaved fasta input works -->
767 <test expect_num_outputs="1" >
768 <param name="type" value="paired_interleaved" />
769 <param name="source" value="history" />
770 <param name="history_item" ftype="fasta" value="phiX.fa" />
771 <param name="input_1" ftype="fasta" value="hisat_input_1_interleaved.fasta" />
772 <output name="output_alignments" file="hisat_output_1_noqual.bam" ftype="bam" lines_diff="2" />
773 </test>
712 </tests> 774 </tests>
713 775
714 <help><![CDATA[ 776 <help><![CDATA[
715 Introduction 777 Introduction
716 ============ 778 ============
1075 --seed <int> 1137 --seed <int>
1076 Use `<int>` as the seed for pseudo-random number generator. Default: 0. 1138 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
1077 1139
1078 --non-deterministic 1140 --non-deterministic
1079 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. 1141 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.
1080
1081 ]]></help> 1142 ]]></help>
1082 <citations> 1143 <citations>
1083 <citation type="doi">10.1038/nmeth.3317</citation> 1144 <citation type="doi">10.1038/nmeth.3317</citation>
1084 </citations> 1145 </citations>
1085 </tool> 1146 </tool>