Mercurial > repos > iuc > hisat2
comparison hisat2.xml @ 30:6c19daec423d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 591f9e8e46a9429bf28b64bae6f27f744bf08b3c"
author | iuc |
---|---|
date | Sun, 18 Jul 2021 17:50:55 +0000 |
parents | 26371a1df031 |
children | f4af63aaf57a |
comparison
equal
deleted
inserted
replaced
29:26371a1df031 | 30:6c19daec423d |
---|---|
1 <tool id="hisat2" name="HISAT2" version="2.1.0+galaxy7" profile="17.01"> | 1 <tool id="hisat2" name="HISAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> |
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="@TOOL_VERSION@">hisat2</requirement> |
8 <requirement type="package" version="1.11">samtools</requirement> | 8 <requirement type="package" version="1.12">samtools</requirement> |
9 <requirement type="package" version="1.3">seqtk</requirement> | 9 <requirement type="package" version="1.3">seqtk</requirement> |
10 </requirements> | 10 </requirements> |
11 <stdio> | 11 <stdio> |
12 <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" /> |
13 <regex level="fatal" match="hisat2: not found" source="both" /> | 13 <regex level="fatal" match="hisat2: not found" source="both" /> |
14 <exit_code range="1:" /> | 14 <exit_code range="1:" /> |
15 </stdio> | 15 </stdio> |
16 <version_command>hisat2 --version</version_command> | 16 <version_command>hisat2 --version</version_command> |
17 <command><![CDATA[ | 17 <command><![CDATA[ |
18 set -o pipefail; | |
18 ## Prepare HISAT2 index | 19 ## Prepare HISAT2 index |
19 | 20 |
20 #if $reference_genome.source == "history": | 21 #if $reference_genome.source == "history": |
21 ln -s '$reference_genome.history_item' genome.fa && | 22 ln -s '$reference_genome.history_item' genome.fa && |
22 hisat2-build -p \${GALAXY_SLOTS:-1} genome.fa genome && | 23 hisat2-build -p \${GALAXY_SLOTS:-1} genome.fa genome && |
94 #set read2 = "input_r.fastq" | 95 #set read2 = "input_r.fastq" |
95 #end if | 96 #end if |
96 ln -s '${library.input_1.reverse}' ${read2} && | 97 ln -s '${library.input_1.reverse}' ${read2} && |
97 #elif str( $library.type ) == "paired_interleaved": | 98 #elif str( $library.type ) == "paired_interleaved": |
98 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): | 99 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): |
99 #set interleaved_reads = "input_f.fastq.gz" | |
100 #set compressed = "GZ" | 100 #set compressed = "GZ" |
101 #elif $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): | 101 #elif $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
102 #set interleaved_reads = "input_f.fastq.bz2" | |
103 #set compressed = "BZ2" | 102 #set compressed = "BZ2" |
104 #elif $library.input_1.is_of_type('fasta'): | 103 #elif $library.input_1.is_of_type('fasta'): |
105 #set reads_are_fastq = False | 104 #set reads_are_fastq = False |
106 #set interleaved_reads = "input_f.fasta" | 105 #end if |
107 #else: | 106 #set read1 = "input_f.fastq" if reads_are_fastq else "input_f.fasta" |
108 #set interleaved_reads = "input_f.fastq" | 107 #set read2 = "input_r.fastq" if reads_are_fastq else "input_r.fasta" |
109 #end if | |
110 ln -f -s '${library.input_1}' ${interleaved_reads} && | |
111 #if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): | 108 #if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
112 #set read1 = "<(bzcat input_f.fastq.bz2 | seqtk seq -1 /dev/stdin)" | 109 bzcat '${library.input_1}' | seqtk seq -1 /dev/stdin > $read1 && |
113 #set read2 = "<(bzcat input_f.fastq.bz2 | seqtk seq -2 /dev/stdin)" | 110 bzcat '${library.input_1}' | seqtk seq -2 /dev/stdin > $read2 && |
114 #else: | 111 #else |
115 #set read1 = "<(seqtk seq -1 %s)" % $interleaved_reads | 112 seqtk seq -1 '${library.input_1}' > $read1 && |
116 #set read2 = "<(seqtk seq -2 %s)" % $interleaved_reads | 113 seqtk seq -2 '${library.input_1}' > $read2 && |
117 #end if | 114 #end if |
118 #else: | 115 #else: |
119 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): | 116 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): |
120 #set read1 = "input_f.fastq.gz" | 117 #set read1 = "input_f.fastq.gz" |
121 #set compressed = "GZ" | 118 #set compressed = "GZ" |
346 ## - once hisat is finished sort will start to merge the temporary | 343 ## - once hisat is finished sort will start to merge the temporary |
347 ## files (which should be fast also on a single thread) gives the | 344 ## files (which should be fast also on a single thread) gives the |
348 ## sorted output to view which only compresses the files (now | 345 ## sorted output to view which only compresses the files (now |
349 ## using full parallelism again) | 346 ## using full parallelism again) |
350 | 347 |
351 | samtools sort -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}' | 348 | samtools sort --no-PG -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ \${GALAXY_SLOTS:-1} -o '${output_alignments}' |
352 | 349 |
353 ## Rename any output fastq files | 350 ## Rename any output fastq files |
354 | 351 |
355 #if $output_unaligned_reads_l and $output_unaligned_reads_r: | 352 #if $output_unaligned_reads_l and $output_unaligned_reads_r: |
356 #from os.path import splitext | 353 #from os.path import splitext |