hisat: hisat.xml annotate

annotate hisat.xml @ 1:8bb3efa0dae8 draft

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

rev	line source
1 8bb3efa0dae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 8000b1dd0d6b336707cf84867d11f690f6a26f5c devteam parents: 0 diff changeset	1 <tool id="hisat" name="HISAT" version="1.0.2">
0 e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	2 <description>spliced aligner</description>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	3 <macros>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	4 <import>hisat_macros.xml</import>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	5 </macros>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	6 <requirements>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	7 <requirement type="package" version="0.1.6">hisat</requirement>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	8 <requirement type="package" version="1.2">samtools</requirement>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	9 </requirements>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	10 <stdio>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	11 <exit_code range="1:" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	12 </stdio>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	13 <version_command>hisat --version</version_command>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	14 <command><![CDATA[
1 8bb3efa0dae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 8000b1dd0d6b336707cf84867d11f690f6a26f5c devteam parents: 0 diff changeset	15 #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != 'None':
8bb3efa0dae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 8000b1dd0d6b336707cf84867d11f690f6a26f5c devteam parents: 0 diff changeset	16 ln -s "${spliced_options.known_splice_gtf}" splice_sites.gtf &&
8bb3efa0dae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 8000b1dd0d6b336707cf84867d11f690f6a26f5c devteam parents: 0 diff changeset	17 extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&
0 e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	18 #end if
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	19 #if $reference_genome.reference_genome_source == "history":
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	20 ln -s "$reference_genome.history_item" genome.fa &&
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	21 hisat-build genome.fa genome &&
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	22 #set index_path = 'genome'
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	23 #else:
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	24 #set index_path = $reference_genome.index.fields.path
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	25 #end if
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	26 hisat -p \${GALAXY_SLOTS:-1} -x "${index_path}"
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	27 #if str($input_format.paired.paired_selector) == 'paired':
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	28 -1 "${reads_f}" -2 "${reads_r}"
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	29 #else if str($input_format.paired.paired_selector) == 'paired_collection':
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	30 -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}"
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	31 #else if str($input_format.paired.paired_selector) == 'paired_list':
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	32 #set forward_reads = []
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	33 #set reverse_reads = []
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	34 #for read in $input_format.paired.reads:
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	35 $forward_reads.append($read.forward)
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	36 $reverse_reads.append($read.reverse)
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	37 #end for
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	38 -1 "${','.join([str($read) for read in $forward_reads])}"
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	39 -2 "${','.join([str($read) for read in $reverse_reads])}"
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	40 #else:
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	41 -U "${reads}"
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	42 #end if
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	43 #if $input_format.input_format_selector == 'fasta':
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	44 -f
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	45 #end if
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	46 #if str($input_options.input_options_selector) == "advanced":
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	47 -s ${input_options.skip} -u ${input_options.stop_after} -5 ${input_options.trim_five} -3 ${input_options.trim_three}
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	48 #end if
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	49 #if str($scoring_options.scoring_options_selector) == "advanced":
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	50 --ma ${scoring_options.match_bonus} --mp ${scoring_options.max_mismatch},${scoring_options.min_mismatch}
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	51 --np ${scoring_options.ambiguous_penalty} --rdg ${scoring_options.read_open_penalty},${scoring_options.read_extend_penalty}
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	52 --rfg ${scoring_options.ref_open_penalty},${scoring_options.ref_extend_penalty}
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	53 #end if
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	54 #if str($alignment_options.alignment_options_selector) == "advanced":
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	55 --n-ceil ${alignment_options.function_type},${alignment_options.constant_term},${alignment_options.coefficient_term}
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	56 ${alignment_options.skip_forward} ${alignment_options.skip_reverse}
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	57 #end if
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	58 #if str($spliced_options.spliced_options_selector) == "advanced":
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	59 --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty}
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	60 --pen-intronlen ${spliced_options.function_type},${spliced_options.constant_term},${spliced_options.coefficient_term}
1 8bb3efa0dae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 8000b1dd0d6b336707cf84867d11f690f6a26f5c devteam parents: 0 diff changeset	61 #if str($spliced_options.known_splice_gtf) != 'None':
0 e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	62 --known-splicesite-infile splice_sites.txt
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	63 #end if
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	64 #end if
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	65 \| samtools view -bS - \| samtools sort - -o hsbam > "${output_alignments}"
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	66 ]]></command>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	67 <inputs>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	68 <conditional name="input_format">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	69 <param name="input_format_selector" label="Input data format" type="select">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	70 <option value="fastq" selected="selected">FASTQ</option>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	71 <option value="fasta">FASTA</option>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	72 </param>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	73 <when value="fasta">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	74 <conditional name="paired">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	75 <expand macro="single_paired_selector" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	76 <when value="paired_collection">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	77 <param format="fasta" name="reads" type="data_collection" collection_type="paired" label="Paired reads" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	78 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	79 <when value="paired_list">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	80 <param format="fasta" name="reads" type="data_collection" collection_type="list:paired" label="Paired reads" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	81 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	82 <when value="paired">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	83 <param label="Forward reads" type="data" name="reads_f" multiple="true" format="fasta" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	84 <param label="Reverse reads" type="data" name="reads_r" multiple="true" format="fasta" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	85 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	86 <when value="single">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	87 <param label="Reads" type="data" name="reads" multiple="true" format="fasta" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	88 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	89 </conditional>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	90 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	91 <when value="fastq">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	92 <conditional name="paired">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	93 <expand macro="single_paired_selector" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	94 <when value="paired_collection">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	95 <param format="fastq,fastqsanger,fastqsolexa" name="reads" type="data_collection" collection_type="paired" label="Paired reads" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	96 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	97 <when value="paired_list">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	98 <param format="fastq,fastqsanger,fastqsolexa" name="reads" type="data_collection" collection_type="list:paired" label="Paired reads" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	99 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	100 <when value="paired">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	101 <param label="Forward reads" type="data" name="reads_f" multiple="true" format="fastq,fastqsanger,fastqsolexa" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	102 <param label="Reverse reads" type="data" name="reads_r" multiple="true" format="fastq,fastqsanger,fastqsolexa" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	103 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	104 <when value="single">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	105 <param label="Reads" type="data" name="reads" multiple="true" format="fastq,fastqsanger,fastqsolexa" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	106 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	107 </conditional>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	108 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	109 </conditional>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	110 <conditional name="reference_genome">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	111 <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">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	112 <option value="indexed" selected="True">Use a built-in genome</option>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	113 <option value="history">Use a genome from history</option>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	114 </param>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	115 <when value="indexed">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	116 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	117 <options from_data_table="hisat_indexes">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	118 <filter type="sort_by" column="2"/>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	119 <validator type="no_options" message="No genomes are available for the selected input dataset"/>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	120 </options>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	121 </param>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	122 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	123 <when value="history">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	124 <param name="history_item" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	125 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	126 </conditional>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	127 <conditional name="alignment_options">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	128 <param label="Alignment options" name="alignment_options_selector" type="select">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	129 <option value="defaults">Use default values</option>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	130 <option value="advanced">Specify alignment parameters</option>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	131 </param>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	132 <when value="defaults" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	133 <when value="advanced">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	134 <expand macro="function">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	135 <label>Sets a function governing the maximum number of ambiguous characters</label>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	136 </expand>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	137 <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." />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	138 <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." />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	139 <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." />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	140 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	141 </conditional>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	142 <conditional name="input_options">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	143 <param label="Input options" name="input_options_selector" type="select">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	144 <option value="defaults">Use default values</option>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	145 <option value="advanced">Specify input parameters</option>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	146 </param>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	147 <when value="defaults" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	148 <when value="advanced">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	149 <param name="skip" label="Skip the first N reads or pairs in the input" help="-s" type="integer" value="0" default="0" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	150 <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" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	151 <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" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	152 <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" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	153 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	154 </conditional>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	155 <conditional name="scoring_options">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	156 <param label="Scoring options" name="scoring_options_selector" type="select">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	157 <option value="defaults">Use default values</option>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	158 <option value="advanced">Specify scoring parameters</option>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	159 </param>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	160 <when value="defaults" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	161 <when value="advanced">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	162 <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" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	163 <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" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	164 <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" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	165 <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" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	166 <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" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	167 <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" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	168 <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" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	169 <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" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	170 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	171 </conditional>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	172 <conditional name="spliced_options">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	173 <param label="Spliced alignment parameters" name="spliced_options_selector" type="select">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	174 <option value="defaults">Use default values</option>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	175 <option value="advanced">Specify spliced alignment parameters</option>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	176 </param>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	177 <when value="defaults" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	178 <when value="advanced">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	179 <param name="canonical_penalty" label="Penalty for canonical splice sites" type="integer" value="0" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	180 <param name="noncanonical_penalty" label="Penalty for non-canonical splice sites" type="integer" value="3" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	181 <expand macro="function">
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	182 <label>Sets the penalty for long introns so that alignments with shorter introns are preferred to those with longer ones.</label>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	183 </expand>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	184 <param name="min_intron" label="Minimum intron length" type="integer" value="20" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	185 <param name="max_intron" label="Maximum intron length" type="integer" value="500000" />
1 8bb3efa0dae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 8000b1dd0d6b336707cf84867d11f690f6a26f5c devteam parents: 0 diff changeset	186 <param name="known_splice_gtf" label="GTF file with known splice sites" type="data" format="gtf" optional="True" />
0 e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	187 </when>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	188 </conditional>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	189 </inputs>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	190 <tests>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	191 <test>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	192 <param name="input_format_selector" value="fastq" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	193 <param name="paired_selector" value="paired" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	194 <param name="reference_genome_source" value="history" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	195 <param name="history_item" value="phiX.fa" ftype="fasta" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	196 <param name="reads_f" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	197 <param name="reads_r" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	198 <output name="output_alignments" ftype="bam" file="hisat_output_1.bam" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	199 </test>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	200 <test>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	201 <param name="input_format_selector" value="fastq" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	202 <param name="paired_selector" value="paired" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	203 <param name="reference_genome_source" value="history" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	204 <param name="history_item" value="phiX.fa" ftype="fasta" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	205 <param name="input_options_selector" value="advanced" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	206 <param name="trim_three" value="15" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	207 <param name="trim_five" value="15" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	208 <param name="reads_f" ftype="fastqsanger" value="hisat_input_2_forward.fastq" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	209 <param name="reads_r" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	210 <output name="output_alignments" ftype="bam" file="hisat_output_2.bam" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	211 </test>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	212 </tests>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	213 <outputs>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	214 <data name="output_alignments" format="bam" />
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	215 </outputs>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	216 <help><![CDATA[
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	217 Introduction
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	218 ============
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	219
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	220 What is HISAT?
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	221 --------------
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	222
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	223 `HISAT <http://ccb.jhu.edu/software/hisat>`__ is a fast and sensitive
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	224 spliced alignment program. As part of HISAT, we have developed a new
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	225 indexing scheme based on the Burrows-Wheeler transform
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	226 (`BWT <http://en.wikipedia.org/wiki/Burrows-Wheeler_transform>`__) and
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	227 the `FM index <http://en.wikipedia.org/wiki/FM-index>`__, called
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	228 hierarchical indexing, that employs two types of indexes: (1) one global
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	229 FM index representing the whole genome, and (2) many separate local FM
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	230 indexes for small regions collectively covering the genome. Our
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	231 hierarchical index for the human genome (about 3 billion bp) includes
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	232 ~48,000 local FM indexes, each representing a genomic region of
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	233 ~64,000bp. As the basis for non-gapped alignment, the FM index is
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	234 extremely fast with a low memory footprint, as demonstrated by
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	235 `Bowtie <http://bowtie-bio.sf.net>`__. In addition, HISAT provides
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	236 several alignment strategies specifically designed for mapping different
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	237 types of RNA-seq reads. All these together, HISAT enables extremely fast
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	238 and sensitive alignment of reads, in particular those spanning two exons
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	239 or more. As a result, HISAT is much faster >50 times than
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	240 `TopHat2 <http://ccb.jhu.edu/software/tophat>`__ with better alignment
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	241 quality. Although it uses a large number of indexes, the memory
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	242 requirement of HISAT is still modest, approximately 4.3 GB for human.
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	243 HISAT uses the `Bowtie2 <http://bowtie-bio.sf.net/bowtie2>`__
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	244 implementation to handle most of the operations on the FM index. In
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	245 addition to spliced alignment, HISAT handles reads involving indels and
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	246 supports a paired-end alignment mode. Multiple processors can be used
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	247 simultaneously to achieve greater alignment speed. HISAT outputs
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	248 alignments in `SAM <http://samtools.sourceforge.net/SAM1.pdf>`__ format,
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	249 enabling interoperation with a large number of other tools (e.g.
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	250 `SAMtools <http://samtools.sourceforge.net>`__,
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	251 `GATK <http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit>`__)
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	252 that use SAM. HISAT is distributed under the `GPLv3
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	253 license <http://www.gnu.org/licenses/gpl-3.0.html>`__, and it runs on
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	254 the command line under Linux, Mac OS X and Windows.
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	255
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	256 Running HISAT
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	257 =============
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	258
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	259 Reporting
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	260 ---------
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	261
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	262 The reporting mode governs how many alignments HISAT looks for, and how
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	263 to report them.
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	264
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	265 In general, when we say that a read has an alignment, we mean that it
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	266 has a `valid
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	267 alignment <#valid-alignments-meet-or-exceed-the-minimum-score-threshold>`__.
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	268 When we say that a read has multiple alignments, we mean that it has
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	269 multiple alignments that are valid and distinct from one another.
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	270
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	271 Distinct alignments map a read to different places
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	272 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	273
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	274 Two alignments for the same individual read are "distinct" if they map
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	275 the same read to different places. Specifically, we say that two
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	276 alignments are distinct if there are no alignment positions where a
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	277 particular read offset is aligned opposite a particular reference offset
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	278 in both alignments with the same orientation. E.g. if the first
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	279 alignment is in the forward orientation and aligns the read character at
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	280 read offset 10 to the reference character at chromosome 3, offset
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	281 3,445,245, and the second alignment is also in the forward orientation
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	282 and also aligns the read character at read offset 10 to the reference
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	283 character at chromosome 3, offset 3,445,245, they are not distinct
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	284 alignments.
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	285
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	286 Two alignments for the same pair are distinct if either the mate 1s in
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	287 the two paired-end alignments are distinct or the mate 2s in the two
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	288 alignments are distinct or both.
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	289
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	290 Default mode: search for one or more alignments, report each
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	291 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	292
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	293 HISAT searches for up to N distinct, primary alignments for each read,
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	294 where N equals the integer specified with the ``-k`` parameter. Primary
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	295 alignments mean alignments whose alignment score is equal or higher than
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	296 any other alignments. It is possible that multiple distinct alignments
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	297 whave the same score. That is, if ``-k 2`` is specified, HISAT will
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	298 search for at most 2 distinct alignments. The alignment score for a
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	299 paired-end alignment equals the sum of the alignment scores of the
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	300 individual mates. Each reported read or pair alignment beyond the first
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	301 has the SAM 'secondary' bit (which equals 256) set in its FLAGS field.
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	302 See the `SAM specification <http://samtools.sourceforge.net/SAM1.pdf>`__
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	303 for details.
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	304
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	305 HISAT does not "find" alignments in any specific order, so for reads
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	306 that have more than N distinct, valid alignments, HISAT does not
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	307 gaurantee that the N alignments reported are the best possible in terms
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	308 of alignment score. Still, this mode can be effective and fast in
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	309 situations where the user cares more about whether a read aligns (or
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	310 aligns a certain number of times) than where exactly it originated.
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	311
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	312 Alignment summmary
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	313 ------------------
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	314
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	315 When HISAT finishes running, it prints messages summarizing what
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	316 happened. These messages are printed to the "standard error" ("stderr")
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	317 filehandle. For datasets consisting of unpaired reads, the summary might
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	318 look like this:
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	319
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	320 ::
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	321
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	322 20000 reads; of these:
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	323 20000 (100.00%) were unpaired; of these:
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	324 1247 (6.24%) aligned 0 times
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	325 18739 (93.69%) aligned exactly 1 time
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	326 14 (0.07%) aligned >1 times
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	327 93.77% overall alignment rate
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	328
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	329 For datasets consisting of pairs, the summary might look like this:
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	330
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	331 ::
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	332
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	333 10000 reads; of these:
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	334 10000 (100.00%) were paired; of these:
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	335 650 (6.50%) aligned concordantly 0 times
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	336 8823 (88.23%) aligned concordantly exactly 1 time
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	337 527 (5.27%) aligned concordantly >1 times
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	338 ----
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	339 650 pairs aligned concordantly 0 times; of these:
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	340 34 (5.23%) aligned discordantly 1 time
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	341 ----
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	342 616 pairs aligned 0 times concordantly or discordantly; of these:
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	343 1232 mates make up the pairs; of these:
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	344 660 (53.57%) aligned 0 times
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	345 571 (46.35%) aligned exactly 1 time
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	346 1 (0.08%) aligned >1 times
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	347 96.70% overall alignment rate
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	348
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	349 The indentation indicates how subtotals relate to totals.
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	350 ]]></help>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	351 <citations>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	352 <citation type="doi">10.1038/nmeth.3317</citation>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	353 </citations>
e3fe061597ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 5a7365750648c26206f05ac7956936c243c2b980 devteam parents: diff changeset	354 </tool>

Mercurial > repos > devteam > hisat

annotate hisat.xml @ 1:8bb3efa0dae8 draft