magicblast: magicblast.xml annotate

annotate magicblast.xml @ 2:34ac212ef95e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit e737cae558b4758afdb6758807b5f19f8b6ea38e

author	iuc
date	Mon, 31 Oct 2022 20:13:18 +0000
parents	aea6702a3cd5
children	ce86aafd8494

rev	line source
0 e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	1 <tool id="magicblast" name="Magic-BLAST: map large RNA or DNA sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	2 <description>against a whole genome or transcriptome</description>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	3 <macros>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	4 <import>macros.xml</import>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	5 </macros>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	6 <expand macro="requirements"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	7 <command detect_errors="exit_code"><![CDATA[
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	8 #import os
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	9
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	10 magicblast
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	11 -num_threads \${GALAXY_SLOTS:-8}
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	12 #if $query.is_of_type('fasta.gz', 'fastqsanger.gz'):
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	13 -query <(gunzip -c '${query}')
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	14 #else:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	15 -query '${query}'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	16 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	17 #if $query_mate:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	18 -paired
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	19 #if $query.is_of_type('fasta.gz', 'fastqsanger.gz'):
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	20 -query_mate <(gunzip -c '${query}')
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	21 #else:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	22 -query_mate '${query}'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	23 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	24 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	25
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	26 #if $query.is_of_type('fastqsanger', 'fastqsanger.gz'):
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	27 -infmt fastq
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	28 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	29
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	30 #if $db_opts.db_opts_selector == "histdb":
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	31 -db '${os.path.join($db_opts.histdb.extra_files_path, "blastdb")}'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	32 #elif $db_opts.db_opts_selector == "db":
1 aea6702a3cd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 03f44b153a1a79a5e7304a2f73e9e9160923ee9b iuc parents: 0 diff changeset	33 -db '${db_opts.database.fields.path}'
0 e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	34 #else:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	35 #if $db_opts.subject.is_of_type('fasta.gz'):
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	36 -subject <(gunzip -c '${$db_opts.subject}')
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	37 #else:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	38 -subject '${db_opts.subject}'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	39 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	40 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	41
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	42 ## General search options
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	43 -word_size $general_search.word_size
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	44 -gapopen $general_search.gapopen
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	45 -gapextend $general_search.gapextend
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	46 -penalty $general_search.penalty
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	47 -max_intron_length $general_search.max_intron_length
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	48
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	49 ## Query filtering options
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	50 $query_filtering.lcase_masking
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	51 -validate_seqs $query_filtering.validate_seqs
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	52 -limit_lookup $query_filtering.limit_lookup
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	53 -max_db_word_count $query_filtering.max_db_word_count
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	54 -lookup_stride $query_filtering.lookup_stride
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	55
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	56 ## Restrict database search
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	57 #if $restrict_search.gilist:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	58 -gilist '$restrict_search.gilist'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	59 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	60 #if $restrict_search.negative_gilist:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	61 -negative_gilist '$restrict_search.negative_gilist'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	62 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	63 #if $restrict_search.seqidlist:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	64 -seqidlist '$restrict_search.seqidlist'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	65 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	66 #if $restrict_search.negative_seqidlist:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	67 -negative_seqidlist '$restrict_search.negative_seqidlist'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	68 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	69 #if str($restrict_search.taxids) != '':
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	70 --taxids '$restrict_search.taxids'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	71 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	72 #if $restrict_search.taxidlist:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	73 -taxidlist '$restrict_search.taxidlist'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	74 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	75 #if str($restrict_search.negative_taxids) != '':
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	76 --negative_taxids '$restrict_search.negative_taxids'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	77 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	78 #if $restrict_search.negative_taxidlist:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	79 -negative_taxidlist '$restrict_search.negative_taxidlist'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	80 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	81
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	82 ## Mapping options
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	83 -score $mapping.score
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	84 #if $mapping.max_edit_dist > 0:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	85 -max_edit_dist $mapping.max_edit_dist
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	86 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	87 -splice '$mapping.splice'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	88 -reftype '$mapping.reftype'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	89
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	90 ## Output unaligned options
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	91 #if str($output_options.report_unaligned_cond.report_unaligned) == 'yes':
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	92 #if str($output_options.report_unaligned_cond.report_unaligned_separately_cond.report_unaligned_separately) == 'yes':
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	93 -out_unaligned 'out_unaligned'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	94 #if str($output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.unaligned_fmt) == 'bam':
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	95 -unaligned_fmt 'sam'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	96 #else:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	97 -unaligned_fmt '$output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.unaligned_fmt'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	98 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	99 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	100 #else:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	101 -no_unaligned
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	102 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	103
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	104 ## Additional output options
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	105 $output_options.no_discordant
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	106 ## Switch default SAM output to be BAM.
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	107 #if str($output_options.outfmt_cond.outfmt) == 'bam':
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	108 $output_options.outfmt_cond.md_tag
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	109 #if $query_mate:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	110 $output_options.outfmt_cond.no_query_id_trim
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	111 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	112 -out 'output.sam'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	113 #if str($output_options.outfmt_cond.output_sort) == 'coordinate':
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	114 && samtools sort -@\${GALAXY_SLOTS:-4} -O bam 'output.sam' > '$output'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	115 #elif str($output_options.outfmt_cond.output_sort) == 'name':
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	116 && samtools sort -n -@\${GALAXY_SLOTS:-4} -O bam -o 'output.sam' > '$output'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	117 #else:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	118 && samtools view -@\${GALAXY_SLOTS:-4} -bS 'output.sam' > '$output'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	119 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	120 #else:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	121 -out '$output'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	122 -outfmt '$output_options.outfmt_cond.outfmt'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	123 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	124
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	125 ## Convert out_unaligned from SAM to BAM if necessary
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	126
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	127 #if str($output_options.report_unaligned_cond.report_unaligned) == 'yes':
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	128 #if str($output_options.report_unaligned_cond.report_unaligned_separately_cond.report_unaligned_separately) == 'yes':
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	129 #if str($output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.unaligned_fmt) == 'bam':
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	130 #if str($output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.output_sort) == 'coordinate':
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	131 && samtools sort -@\${GALAXY_SLOTS:-4} -O bam -o 'out_unaligned' > '$output_unaligned'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	132 #elif str($output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.output_sort) == 'name':
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	133 && samtools sort -n -@\${GALAXY_SLOTS:-4} -O bam -o 'out_unaligned' > '$output_unaligned'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	134 #else:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	135 && samtools view -@\${GALAXY_SLOTS:-4} -bS 'out_unaligned' > '$output_unaligned'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	136 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	137 #else:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	138 && mv 'out_unaligned' '$output_unaligned'
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	139 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	140 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	141 #end if
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	142 ]]></command>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	143 <inputs>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	144 <param argument="-query" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Query file" help="Fasta or fastqsanger, optionally gzipped"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	145 <param argument="-query_mate" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" optional="true" label="Query mate file (optional)" help="Fasta or fastqsanger, optionally gzipped"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	146 <conditional name="db_opts">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	147 <param name="db_opts_selector" type="select" label="Subject database/sequences">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	148 <option value="histdb" selected="true">blast database from your history</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	149 <option value="db">Locally installed blast database</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	150 <option value="file">fasta file from your history (see warning in the tool help section below)</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	151 </param>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	152 <when value="histdb">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	153 <param name="histdb" type="data" format="blastdbn" label="Nucleotide blast database"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	154 </when>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	155 <when value="db">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	156 <param name="database" type="select" multiple="true" optional="false" label="Nucleotide blast database">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	157 <options from_data_table="blastdb"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	158 </param>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	159 </when>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	160 <when value="file">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	161 <param argument="-subject" type="data" format="fasta,fasta.gz" label="Nucleotide fasta subject file to use instead of a database"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	162 </when>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	163 </conditional>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	164 <section name="general_search" title="General search">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	165 <param argument="-word_size" type="integer" value="18" min="12" label="Minimum number of consecutive bases matching exactly"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	166 <param argument="-gapopen" type="integer" value="0" min="0" label="Cost to open a gap"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	167 <param argument="-gapextend" type="integer" value="0" min="0" label="Cost to extend a gap"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	168 <param argument="-penalty" type="integer" value="-4" max="0" label="Penalty for a nucleotide mismatch"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	169 <param argument="-max_intron_length" type="integer" value="500000" min="0" label="Maximum allowed intron length"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	170 </section>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	171 <section name="query_filtering" title="Query filtering">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	172 <param argument="-lcase_masking" type="boolean" truevalue="-lcase_masking" falsevalue="" checked="false" label="Use lower case filtering in subject sequences?"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	173 <param argument="-validate_seqs" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Reject low quality sequences?"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	174 <param argument="-limit_lookup" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove word seeds with high frequency in the searched database?"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	175 <param argument="-max_db_word_count" type="integer" value="30" min="0" label="Words that appear more than this number of times in the database will be masked in the lookup table"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	176 <param argument="-lookup_stride" type="integer" value="0" min="0" label="Number of words to skip after collecting one while creating a lookup table"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	177 </section>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	178 <section name="restrict_search" title="Restrict database search">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	179 <param argument="-gilist" type="data" format="tabular" optional="true" label="Tabular file containing list of GIs to which to restrict database search" help="Available only for database searches"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	180 <param argument="-negative_gilist" type="data" format="tabular" optional="true" label="Tabular file containing list of GIs to restrict database search to everything except the specified GIs" help="Available only for database searches"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	181 <param argument="-seqidlist" type="data" format="tabular" optional="true" label="Tabular file containing list of SeqIDs to which to restrict database search" help="Available only for database searches"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	182 <param argument="-negative_seqidlist" type="data" format="tabular" optional="true" label="Tabular file containing list of SeqIDs to restrict database search to everything except the specified SeqIDs" help="Available only for database searches"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	183 <param argument="-taxids" type="text" optional="true" label="Comma-separated list of taxonomy IDs to which to restrict database search" help="Available only for database searches">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	184 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.digits,string.whitespace,string.punctuation"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	185 </param>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	186 <param argument="-taxidlist" type="data" format="tabular" optional="true" label="Tabular file containing list of taxonomy IDs to which to restrict database search" help="Available only for database searches"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	187 <param argument="-negative_taxids" type="text" optional="true" label="Comma-separated list of taxonomy IDs to restrict database search to everything except the specified taxonomy IDs" help="Available only for database searches">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	188 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.digits,string.whitespace,string.punctuation"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	189 </param>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	190 <param argument="-negative_taxidlist" type="data" format="tabular" optional="true" label="Tabular file containing list of taxonomy IDs to restrict database search to everythin except the specified taxonomy IDs" help="Available only for database searches"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	191 </section>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	192 <section name="mapping" title="Mapping">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	193 <param argument="-score" type="integer" value="0" min="0" label="Cutoff score for accepting alignments" help="Zero value ignores"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	194 <param argument="-max_edit_dist" type="integer" value="0" min="0" label="Cutoff edit distance for accepting an alignment" help="Zero value is unlimited"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	195 <param argument="-splice" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Search for spliced alignments?"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	196 <param argument="-reftype" type="select" label="Type of the reference">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	197 <option value="genome" selected="true">genome</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	198 <option value="transcriptome">transcriptome</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	199 </param>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	200 </section>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	201 <section name="output_options" title="Output options">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	202 <conditional name="report_unaligned_cond">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	203 <param name="report_unaligned" type="select" label="Report unaligned reads?">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	204 <option value="yes" selected="true">Yes</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	205 <option value="no">No</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	206 </param>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	207 <when value="yes">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	208 <conditional name="report_unaligned_separately_cond">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	209 <param name="report_unaligned_separately" type="select" label="Output unaligned reads to a separate file?" help="Select No to output all reads to the same file">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	210 <option value="no" selected="true">No</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	211 <option value="yes">Yes</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	212 </param>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	213 <when value="no"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	214 <when value="yes">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	215 <conditional name="unaligned_fmt_cond">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	216 <param argument="-unaligned_fmt" type="select" label="Output format for unaligned reads">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	217 <option value="bam" selected="true">bam</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	218 <option value="tabular">tabular</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	219 <option value="fasta">fasta</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	220 </param>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	221 <when value="bam">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	222 <expand macro="output_sort_param"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	223 </when>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	224 <when value="tabular"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	225 <when value="fasta"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	226 </conditional>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	227 </when>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	228 </conditional>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	229 </when>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	230 <when value="no"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	231 </conditional>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	232 <conditional name="outfmt_cond">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	233 <param argument="-outfmt" type="select" label="Output format">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	234 <option value="bam" selected="true">bam</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	235 <option value="tabular">tabular</option>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	236 </param>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	237 <when value="bam">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	238 <expand macro="output_sort_param"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	239 <param argument="-md_tag" type="boolean" truevalue="-md_tag" falsevalue="" checked="false" label="Include MD tag in BAM output?"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	240 <param argument="-no_query_id_trim" type="boolean" truevalue="-no_query_id_trim" falsevalue="" checked="false" label="Do not trim '.1', '/1', '.2', or '/2' at the end of read ids in BAM output for paired reads?" help="Ignored if no query mate"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	241 </when>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	242 <when value="tabular"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	243 </conditional>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	244 <param argument="-no_discordant" type="boolean" truevalue="-no_discordant" falsevalue="" checked="false" label="Suppress discordant alignments for paired reads?" help="Ignored if no query mate"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	245 </section>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	246 </inputs>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	247 <outputs>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	248 <data name="output" format="bam" label="${tool.name} on ${on_string}">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	249 <change_format>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	250 <when input="output.outfmt_cond.outfmt" value="tabular" format="tabular"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	251 </change_format>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	252 </data>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	253 <data name="output_unaligned" format="bam" label="${tool.name} on ${on_string}: unaligned reads">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	254 <filter>output_options['report_unaligned_cond']['report_unaligned'] == 'yes' and output_options['report_unaligned_cond']['report_unaligned_separately_cond']['report_unaligned_separately'] == 'yes'</filter>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	255 <change_format>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	256 <when input="output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.unaligned_fmt" value="tabular" format="tabular"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	257 <when input="output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.unaligned_fmt" value="fasta" format="fasta"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	258 </change_format>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	259 </data>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	260 </outputs>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	261 <tests>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	262 <!-- Single fasta.gz input, subject file -->
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	263 <test expect_num_outputs="1">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	264 <param name="query" value="query1.fasta.gz" ftype="fasta.gz"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	265 <param name="db_opts_selector" value="file"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	266 <param name="subject" value="subject1.fasta.gz" ftype="fasta.gz"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	267 <output name="output" ftype="bam">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	268 <assert_contents>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	269 <has_size value="1247" delta="50"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	270 </assert_contents>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	271 </output>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	272 </test>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	273 <!-- Single fasta.gz input, subject file, output unaligned reads separately-->
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	274 <test expect_num_outputs="2">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	275 <param name="query" value="query1.fasta.gz" ftype="fasta.gz"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	276 <param name="db_opts_selector" value="file"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	277 <param name="subject" value="subject1.fasta.gz" ftype="fasta.gz"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	278 <param name="report_unaligned_separately" value="yes"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	279 <param name="unaligned_fmt" value="tabular"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	280 <output name="output" ftype="bam">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	281 <assert_contents>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	282 <has_size value="492" delta="50"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	283 </assert_contents>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	284 </output>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	285 <output name="output_unaligned" ftype="tabular">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	286 <assert_contents>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	287 <has_size value="959"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	288 </assert_contents>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	289 </output>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	290 </test>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	291 <!-- Single fasta.gz input, subject file, gilist file, results in error -->
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	292 <test expect_failure="true">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	293 <param name="query" value="query1.fasta.gz" ftype="fasta.gz"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	294 <param name="db_opts_selector" value="file"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	295 <param name="subject" value="subject1.fasta.gz" ftype="fasta.gz"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	296 <param name="report_unaligned_separately" value="yes"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	297 <param name="gilist" value="gilist1.tabular" ftype="tabular"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	298 <assert_stderr>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	299 <has_text text="Incompatible with argument:"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	300 </assert_stderr>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	301 </test>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	302 <!-- Single fasta.gz input, cached db, taxidlist, results in error -->
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	303 <test expect_failure="true">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	304 <param name="query" value="query1.fasta.gz" ftype="fasta.gz"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	305 <param name="db_opts_selector" value="db"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	306 <param name="database" value="phiX174"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	307 <param name="taxidlist" value="taxids.tabular" ftype="tabular"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	308 <assert_stderr>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	309 <has_text text="Taxonomy filtering is not supported in v4 BLAST dbs"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	310 </assert_stderr>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	311 </test>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	312 <!-- Paired fastqsanger.gz input, subject file -->
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	313 <test expect_num_outputs="1">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	314 <param name="query" value="query_forward1.fastqsanger.gz" ftype="fastqsanger.gz"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	315 <param name="query_mate" value="query_reverse1.fastqsanger.gz" ftype="fastqsanger.gz"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	316 <param name="db_opts_selector" value="file"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	317 <param name="subject" value="subject1.fasta.gz" ftype="fasta.gz"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	318 <output name="output" ftype="bam">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	319 <assert_contents>
2 34ac212ef95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit e737cae558b4758afdb6758807b5f19f8b6ea38e iuc parents: 1 diff changeset	320 <has_size value="61454" delta="50"/>
0 e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	321 </assert_contents>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	322 </output>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	323 </test>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	324 <!-- Paired fastqsanger.gz input, cached blast db -->
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	325 <test expect_num_outputs="1">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	326 <param name="query" value="query_forward1.fastqsanger.gz" ftype="fastqsanger.gz"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	327 <param name="query_mate" value="query_reverse1.fastqsanger.gz" ftype="fastqsanger.gz"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	328 <param name="db_opts_selector" value="db"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	329 <param name="database" value="phiX174"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	330 <output name="output" ftype="bam">
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	331 <assert_contents>
2 34ac212ef95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit e737cae558b4758afdb6758807b5f19f8b6ea38e iuc parents: 1 diff changeset	332 <has_size value="61457" delta="50"/>
0 e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	333 </assert_contents>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	334 </output>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	335 </test>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	336 </tests>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	337 <help><![CDATA[
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	338 What it does
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	339
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	340 .. class:: warningmark
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	341
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	342 In addition to a BLAST database, you can also search against a fasta file of subject (target) sequences. However, this is not
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	343 advised because it is slower (only one CPU is used), but more importantly gives e-values for pairwise searches (very small
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	344 e-values which will look overly signficiant). In most cases you should convert the fasta file into a blast database using
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	345 makeblastdb and search against that.
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	346
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	347 Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	348 Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq,
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	349 locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	350 each exon is scored as a separate hit and read-pairing is ignored.
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	351
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	352 Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	353 extensions by local walk and jump, and recursive clipping of mismatches near the edges of the reads, which avoids accumulating
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	354 artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	355
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	356 The tool accepts a single or paired set of reads in fasta or fastqsanger format and produces bam or tabular output.
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	357
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	358 More information about Magic-BLAST is available in the
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	359 `online documentation <https://ncbi.github.io/magicblast/>`_.
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	360 ]]></help>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	361 <expand macro="citations"/>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08" iuc parents: diff changeset	362 </tool>

Mercurial > repos > iuc > magicblast

annotate magicblast.xml @ 2:34ac212ef95e draft