Mercurial > repos > devteam > hisat

comparison hisat.xml @ 1:8bb3efa0dae8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 8000b1dd0d6b336707cf84867d11f690f6a26f5c
author devteam
date Tue, 21 Jul 2015 15:33:12 -0400
parents e3fe061597ac
children 4d91675e16e8
comparison
equal deleted inserted replaced
0:e3fe061597ac 1:8bb3efa0dae8
1 <tool id="hisat" name="HISAT" version="1.0.1"> 1 <tool id="hisat" name="HISAT" version="1.0.2">
2 <description>spliced aligner</description> 2 <description>spliced aligner</description>
3 <macros> 3 <macros>
4 <import>hisat_macros.xml</import> 4 <import>hisat_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
10 <stdio> 10 <stdio>
11 <exit_code range="1:" /> 11 <exit_code range="1:" />
12 </stdio> 12 </stdio>
13 <version_command>hisat --version</version_command> 13 <version_command>hisat --version</version_command>
14 <command><![CDATA[ 14 <command><![CDATA[
15 #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gff) != 'None': 15 #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != 'None':
16 ln -s "${spliced_options.known_splice_gff}" splice_sites.gff && 16 ln -s "${spliced_options.known_splice_gtf}" splice_sites.gtf &&
17 extract_splice_sites.py splice_sites.gff > splice_sites.txt && 17 extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&
18 #end if 18 #end if
19 #if $reference_genome.reference_genome_source == "history": 19 #if $reference_genome.reference_genome_source == "history":
20 ln -s "$reference_genome.history_item" genome.fa && 20 ln -s "$reference_genome.history_item" genome.fa &&
21 hisat-build genome.fa genome && 21 hisat-build genome.fa genome &&
22 #set index_path = 'genome' 22 #set index_path = 'genome'
56 ${alignment_options.skip_forward} ${alignment_options.skip_reverse} 56 ${alignment_options.skip_forward} ${alignment_options.skip_reverse}
57 #end if 57 #end if
58 #if str($spliced_options.spliced_options_selector) == "advanced": 58 #if str($spliced_options.spliced_options_selector) == "advanced":
59 --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty} 59 --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty}
60 --pen-intronlen ${spliced_options.function_type},${spliced_options.constant_term},${spliced_options.coefficient_term} 60 --pen-intronlen ${spliced_options.function_type},${spliced_options.constant_term},${spliced_options.coefficient_term}
61 #if str($spliced_options.known_splice_gff) != 'None': 61 #if str($spliced_options.known_splice_gtf) != 'None':
62 --known-splicesite-infile splice_sites.txt 62 --known-splicesite-infile splice_sites.txt
63 #end if 63 #end if
64 #end if 64 #end if
65 | samtools view -bS - | samtools sort - -o hsbam > "${output_alignments}" 65 | samtools view -bS - | samtools sort - -o hsbam > "${output_alignments}"
66 ]]></command> 66 ]]></command>
181 <expand macro="function"> 181 <expand macro="function">
182 <label>Sets the penalty for long introns so that alignments with shorter introns are preferred to those with longer ones.</label> 182 <label>Sets the penalty for long introns so that alignments with shorter introns are preferred to those with longer ones.</label>
183 </expand> 183 </expand>
184 <param name="min_intron" label="Minimum intron length" type="integer" value="20" /> 184 <param name="min_intron" label="Minimum intron length" type="integer" value="20" />
185 <param name="max_intron" label="Maximum intron length" type="integer" value="500000" /> 185 <param name="max_intron" label="Maximum intron length" type="integer" value="500000" />
186 <param name="known_splice_gff" label="GTF/GFF file with known splice sites" type="data" format="gff" optional="True" /> 186 <param name="known_splice_gtf" label="GTF file with known splice sites" type="data" format="gtf" optional="True" />
187 </when> 187 </when>
188 </conditional> 188 </conditional>
189 </inputs> 189 </inputs>
190 <tests> 190 <tests>
191 <test> 191 <test>