hisat: hisat.xml annotate

annotate hisat.xml @ 0:faed168e996f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b

author	devteam
date	Mon, 09 Nov 2015 11:39:20 -0500
parents
children

rev	line source
0 faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	1 <tool id="hisat" name="HISAT" version="1.0.3">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	2 <description>spliced aligner</description>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	3 <macros>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	4 <import>hisat_macros.xml</import>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	5 </macros>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	6 <requirements>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	7 <requirement type="package" version="0.1.6">hisat</requirement>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	8 <requirement type="package" version="1.2">samtools</requirement>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	9 </requirements>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	10 <stdio>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	11 <exit_code range="1:" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	12 </stdio>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	13 <version_command>hisat --version</version_command>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	14 <command><![CDATA[
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	15 #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != 'None':
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	16 ln -s "${spliced_options.known_splice_gtf}" splice_sites.gtf &&
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	17 extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	18 #end if
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	19 #if $reference_genome.reference_genome_source == "history":
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	20 ln -s "$reference_genome.history_item" genome.fa &&
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	21 hisat-build genome.fa genome &&
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	22 #set index_path = 'genome'
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	23 #else:
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	24 #set index_path = $reference_genome.index.fields.path
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	25 #end if
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	26 hisat -p \${GALAXY_SLOTS:-1} -x "${index_path}"
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	27 #if str($input_format.paired.paired_selector) == 'paired':
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	28 -1 "${reads_f}" -2 "${reads_r}"
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	29 #else if str($input_format.paired.paired_selector) == 'paired_collection':
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	30 -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}"
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	31 #else:
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	32 -U "${reads}"
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	33 #end if
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	34 #if $input_format.input_format_selector == 'fasta':
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	35 -f
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	36 #end if
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	37 #if str($input_options.input_options_selector) == "advanced":
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	38 -s ${input_options.skip} -u ${input_options.stop_after} -5 ${input_options.trim_five} -3 ${input_options.trim_three}
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	39 #end if
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	40 #if str($scoring_options.scoring_options_selector) == "advanced":
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	41 --ma ${scoring_options.match_bonus} --mp ${scoring_options.max_mismatch},${scoring_options.min_mismatch}
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	42 --np ${scoring_options.ambiguous_penalty} --rdg ${scoring_options.read_open_penalty},${scoring_options.read_extend_penalty}
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	43 --rfg ${scoring_options.ref_open_penalty},${scoring_options.ref_extend_penalty}
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	44 #end if
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	45 #if str($alignment_options.alignment_options_selector) == "advanced":
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	46 --n-ceil ${alignment_options.function_type},${alignment_options.constant_term},${alignment_options.coefficient_term}
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	47 ${alignment_options.skip_forward} ${alignment_options.skip_reverse}
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	48 #end if
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	49 #if str($spliced_options.spliced_options_selector) == "advanced":
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	50 --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty}
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	51 --pen-intronlen ${spliced_options.function_type},${spliced_options.constant_term},${spliced_options.coefficient_term}
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	52 #if str($spliced_options.known_splice_gtf) != 'None':
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	53 --known-splicesite-infile splice_sites.txt
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	54 #end if
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	55 #end if
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	56 \| samtools view -bS - \| samtools sort - -o hsbam > "${output_alignments}"
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	57 ]]></command>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	58 <inputs>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	59 <conditional name="input_format">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	60 <param name="input_format_selector" label="Input data format" type="select">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	61 <option value="fastq" selected="selected">FASTQ</option>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	62 <option value="fasta">FASTA</option>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	63 </param>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	64 <when value="fasta">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	65 <conditional name="paired">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	66 <expand macro="single_paired_selector" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	67 <when value="paired_collection">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	68 <param format="fasta" name="reads" type="data_collection" collection_type="paired" label="Paired reads" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	69 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	70 <when value="paired_list">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	71 <param format="fasta" name="reads" type="data_collection" collection_type="list:paired" label="Paired reads" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	72 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	73 <when value="paired">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	74 <param label="Forward reads" type="data" name="reads_f" multiple="true" format="fasta" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	75 <param label="Reverse reads" type="data" name="reads_r" multiple="true" format="fasta" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	76 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	77 <when value="single">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	78 <param label="Reads" type="data" name="reads" multiple="true" format="fasta" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	79 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	80 </conditional>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	81 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	82 <when value="fastq">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	83 <conditional name="paired">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	84 <expand macro="single_paired_selector" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	85 <when value="paired_collection">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	86 <param format="fastq" name="reads" type="data_collection" collection_type="paired" label="Paired reads" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	87 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	88 <when value="paired">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	89 <param label="Forward reads" type="data" name="reads_f" multiple="true" format="fastq" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	90 <param label="Reverse reads" type="data" name="reads_r" multiple="true" format="fastq" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	91 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	92 <when value="single">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	93 <param label="Reads" type="data" name="reads" multiple="true" format="fastq" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	94 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	95 </conditional>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	96 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	97 </conditional>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	98 <conditional name="reference_genome">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	99 <param name="reference_genome_source" type="select" label="Source for the reference genome to align against" help="Built-in references were created using default options">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	100 <option value="indexed" selected="True">Use a built-in genome</option>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	101 <option value="history">Use a genome from history</option>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	102 </param>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	103 <when value="indexed">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	104 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	105 <options from_data_table="hisat_indexes">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	106 <filter type="sort_by" column="2"/>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	107 <validator type="no_options" message="No genomes are available for the selected input dataset"/>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	108 </options>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	109 </param>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	110 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	111 <when value="history">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	112 <param name="history_item" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	113 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	114 </conditional>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	115 <conditional name="alignment_options">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	116 <param label="Alignment options" name="alignment_options_selector" type="select">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	117 <option value="defaults">Use default values</option>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	118 <option value="advanced">Specify alignment parameters</option>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	119 </param>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	120 <when value="defaults" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	121 <when value="advanced">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	122 <expand macro="function">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	123 <label>Sets a function governing the maximum number of ambiguous characters</label>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	124 </expand>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	125 <param name="ignore_quals" label="Ignore quality values" type="boolean" truevalue="--ignore-quals" falsevalue="" help="(--ignore-quals) 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." />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	126 <param name="skip_forward" label="Skip forward strand of reference" type="boolean" truevalue="--nofw" falsevalue="" help="(--nofw) If --nofw is specified, hisat 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 hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand." />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	127 <param name="skip_reverse" label="Skip reference strand of reference" type="boolean" truevalue="--norc" falsevalue="" help="(--norc) If --norc is specified, hisat 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 --nofw causes hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand." />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	128 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	129 </conditional>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	130 <conditional name="input_options">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	131 <param label="Input options" name="input_options_selector" type="select">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	132 <option value="defaults">Use default values</option>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	133 <option value="advanced">Specify input parameters</option>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	134 </param>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	135 <when value="defaults" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	136 <when value="advanced">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	137 <param name="skip" label="Skip the first N reads or pairs in the input" help="-s" type="integer" value="0" default="0" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	138 <param name="stop_after" label="Stop after aligning N reads" help="(-u) Align the first N reads or read pairs from the input (after the first N reads or pairs have been skipped), then stop." type="integer" value="0" default="0" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	139 <param name="trim_five" label="Trim 5' end" help="(-5) Trim N bases from 5' (left) end of each read before alignment" type="integer" value="0" default="0" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	140 <param name="trim_three" label="Trim 3' end" help="(-3) Trim N bases from 3' (right) end of each read before alignment" type="integer" value="0" default="0" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	141 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	142 </conditional>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	143 <conditional name="scoring_options">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	144 <param label="Scoring options" name="scoring_options_selector" type="select">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	145 <option value="defaults">Use default values</option>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	146 <option value="advanced">Specify scoring parameters</option>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	147 </param>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	148 <when value="defaults" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	149 <when value="advanced">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	150 <param name="match_bonus" label="Set match bonus" help="(--ma) In local mode N is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in end-to-end mode" type="integer" value="2" default="2" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	151 <param name="max_mismatch" label="Maximum mismatch penalty" help="(--mp) 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." type="integer" value="6" default="6" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	152 <param name="min_mismatch" label="Minimum mismatch penalty" help="(--mp) 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." type="integer" value="2" default="2" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	153 <param name="ambiguous_penalty" label="Ambiguous read penalty" help="(--np) Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N" type="integer" value="1" default="1" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	154 <param name="read_open_penalty" label="Read gap open penalty." type="integer" help="(--rdg) A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" value="5" default="5" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	155 <param name="read_extend_penalty" label="Read gap extend penalty." type="integer" help="(--rdg) A read gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" value="3" default="3" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	156 <param name="ref_open_penalty" label="Reference gap open penalty." help="(--rfg) A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" type="integer" value="5" default="5" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	157 <param name="ref_extend_penalty" label="Reference gap extend penalty." help="(--rfg) A reference gap of length N gets a penalty of [open_penalty] + N * [extend_penalty]" type="integer" value="3" default="3" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	158 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	159 </conditional>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	160 <conditional name="spliced_options">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	161 <param label="Spliced alignment parameters" name="spliced_options_selector" type="select">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	162 <option value="defaults">Use default values</option>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	163 <option value="advanced">Specify spliced alignment parameters</option>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	164 </param>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	165 <when value="defaults" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	166 <when value="advanced">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	167 <param name="canonical_penalty" label="Penalty for canonical splice sites" type="integer" value="0" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	168 <param name="noncanonical_penalty" label="Penalty for non-canonical splice sites" type="integer" value="3" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	169 <expand macro="function">
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	170 <label>Sets the penalty for long introns so that alignments with shorter introns are preferred to those with longer ones.</label>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	171 </expand>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	172 <param name="min_intron" label="Minimum intron length" type="integer" value="20" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	173 <param name="max_intron" label="Maximum intron length" type="integer" value="500000" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	174 <param name="known_splice_gtf" label="GTF file with known splice sites" type="data" format="gtf" optional="True" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	175 </when>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	176 </conditional>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	177 </inputs>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	178 <tests>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	179 <test>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	180 <param name="input_format_selector" value="fastq" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	181 <param name="paired_selector" value="paired" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	182 <param name="reference_genome_source" value="history" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	183 <param name="history_item" value="phiX.fa" ftype="fasta" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	184 <param name="reads_f" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	185 <param name="reads_r" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	186 <output name="output_alignments" ftype="bam" file="hisat_output_1.bam" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	187 </test>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	188 <test>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	189 <param name="input_format_selector" value="fastq" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	190 <param name="paired_selector" value="paired" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	191 <param name="reference_genome_source" value="history" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	192 <param name="history_item" value="phiX.fa" ftype="fasta" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	193 <param name="input_options_selector" value="advanced" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	194 <param name="trim_three" value="15" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	195 <param name="trim_five" value="15" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	196 <param name="reads_f" ftype="fastqsanger" value="hisat_input_2_forward.fastq" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	197 <param name="reads_r" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	198 <output name="output_alignments" ftype="bam" file="hisat_output_2.bam" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	199 </test>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	200 </tests>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	201 <outputs>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	202 <data name="output_alignments" format="bam" />
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	203 </outputs>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	204 <help><![CDATA[
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	205 Introduction
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	206 ============
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	207
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	208 What is HISAT?
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	209 --------------
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	210
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	211 `HISAT <http://ccb.jhu.edu/software/hisat>`__ is a fast and sensitive
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	212 spliced alignment program. As part of HISAT, we have developed a new
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	213 indexing scheme based on the Burrows-Wheeler transform
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	214 (`BWT <http://en.wikipedia.org/wiki/Burrows-Wheeler_transform>`__) and
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	215 the `FM index <http://en.wikipedia.org/wiki/FM-index>`__, called
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	216 hierarchical indexing, that employs two types of indexes: (1) one global
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	217 FM index representing the whole genome, and (2) many separate local FM
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	218 indexes for small regions collectively covering the genome. Our
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	219 hierarchical index for the human genome (about 3 billion bp) includes
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	220 ~48,000 local FM indexes, each representing a genomic region of
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	221 ~64,000bp. As the basis for non-gapped alignment, the FM index is
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	222 extremely fast with a low memory footprint, as demonstrated by
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	223 `Bowtie <http://bowtie-bio.sf.net>`__. In addition, HISAT provides
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	224 several alignment strategies specifically designed for mapping different
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	225 types of RNA-seq reads. All these together, HISAT enables extremely fast
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	226 and sensitive alignment of reads, in particular those spanning two exons
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	227 or more. As a result, HISAT is much faster >50 times than
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	228 `TopHat2 <http://ccb.jhu.edu/software/tophat>`__ with better alignment
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	229 quality. Although it uses a large number of indexes, the memory
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	230 requirement of HISAT is still modest, approximately 4.3 GB for human.
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	231 HISAT uses the `Bowtie2 <http://bowtie-bio.sf.net/bowtie2>`__
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	232 implementation to handle most of the operations on the FM index. In
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	233 addition to spliced alignment, HISAT handles reads involving indels and
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	234 supports a paired-end alignment mode. Multiple processors can be used
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	235 simultaneously to achieve greater alignment speed. HISAT outputs
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	236 alignments in `SAM <http://samtools.sourceforge.net/SAM1.pdf>`__ format,
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	237 enabling interoperation with a large number of other tools (e.g.
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	238 `SAMtools <http://samtools.sourceforge.net>`__,
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	239 `GATK <http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit>`__)
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	240 that use SAM. HISAT is distributed under the `GPLv3
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	241 license <http://www.gnu.org/licenses/gpl-3.0.html>`__, and it runs on
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	242 the command line under Linux, Mac OS X and Windows.
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	243
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	244 Running HISAT
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	245 =============
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	246
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	247 Reporting
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	248 ---------
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	249
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	250 The reporting mode governs how many alignments HISAT looks for, and how
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	251 to report them.
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	252
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	253 In general, when we say that a read has an alignment, we mean that it
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	254 has a `valid
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	255 alignment <#valid-alignments-meet-or-exceed-the-minimum-score-threshold>`__.
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	256 When we say that a read has multiple alignments, we mean that it has
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	257 multiple alignments that are valid and distinct from one another.
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	258
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	259 Distinct alignments map a read to different places
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	260 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	261
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	262 Two alignments for the same individual read are "distinct" if they map
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	263 the same read to different places. Specifically, we say that two
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	264 alignments are distinct if there are no alignment positions where a
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	265 particular read offset is aligned opposite a particular reference offset
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	266 in both alignments with the same orientation. E.g. if the first
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	267 alignment is in the forward orientation and aligns the read character at
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	268 read offset 10 to the reference character at chromosome 3, offset
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	269 3,445,245, and the second alignment is also in the forward orientation
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	270 and also aligns the read character at read offset 10 to the reference
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	271 character at chromosome 3, offset 3,445,245, they are not distinct
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	272 alignments.
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	273
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	274 Two alignments for the same pair are distinct if either the mate 1s in
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	275 the two paired-end alignments are distinct or the mate 2s in the two
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	276 alignments are distinct or both.
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	277
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	278 Default mode: search for one or more alignments, report each
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	280
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	281 HISAT searches for up to N distinct, primary alignments for each read,
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	282 where N equals the integer specified with the ``-k`` parameter. Primary
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	283 alignments mean alignments whose alignment score is equal or higher than
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	284 any other alignments. It is possible that multiple distinct alignments
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	285 whave the same score. That is, if ``-k 2`` is specified, HISAT will
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	286 search for at most 2 distinct alignments. The alignment score for a
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	287 paired-end alignment equals the sum of the alignment scores of the
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	288 individual mates. Each reported read or pair alignment beyond the first
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	289 has the SAM 'secondary' bit (which equals 256) set in its FLAGS field.
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	290 See the `SAM specification <http://samtools.sourceforge.net/SAM1.pdf>`__
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	291 for details.
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	292
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	293 HISAT does not "find" alignments in any specific order, so for reads
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	294 that have more than N distinct, valid alignments, HISAT does not
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	295 gaurantee that the N alignments reported are the best possible in terms
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	296 of alignment score. Still, this mode can be effective and fast in
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	297 situations where the user cares more about whether a read aligns (or
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	298 aligns a certain number of times) than where exactly it originated.
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	299
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	300 Alignment summmary
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	301 ------------------
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	302
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	303 When HISAT finishes running, it prints messages summarizing what
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	304 happened. These messages are printed to the "standard error" ("stderr")
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	305 filehandle. For datasets consisting of unpaired reads, the summary might
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	306 look like this:
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	307
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	308 ::
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	309
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	310 20000 reads; of these:
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	311 20000 (100.00%) were unpaired; of these:
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	312 1247 (6.24%) aligned 0 times
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	313 18739 (93.69%) aligned exactly 1 time
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	314 14 (0.07%) aligned >1 times
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	315 93.77% overall alignment rate
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	316
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	317 For datasets consisting of pairs, the summary might look like this:
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	318
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	319 ::
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	320
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	321 10000 reads; of these:
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	322 10000 (100.00%) were paired; of these:
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	323 650 (6.50%) aligned concordantly 0 times
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	324 8823 (88.23%) aligned concordantly exactly 1 time
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	325 527 (5.27%) aligned concordantly >1 times
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	326 ----
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	327 650 pairs aligned concordantly 0 times; of these:
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	328 34 (5.23%) aligned discordantly 1 time
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	329 ----
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	330 616 pairs aligned 0 times concordantly or discordantly; of these:
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	331 1232 mates make up the pairs; of these:
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	332 660 (53.57%) aligned 0 times
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	333 571 (46.35%) aligned exactly 1 time
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	334 1 (0.08%) aligned >1 times
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	335 96.70% overall alignment rate
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	336
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	337 The indentation indicates how subtotals relate to totals.
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	338 ]]></help>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	339 <citations>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	340 <citation type="doi">10.1038/nmeth.3317</citation>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	341 </citations>
faed168e996f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	342 </tool>

Mercurial > repos > devteam > hisat

annotate hisat.xml @ 0:faed168e996f draft default tip