blast_plus_remote_blastp: blast_plus_remote

annotate blast_plus_remote_blastp.xml @ 5:22a767177ac9 draft

planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4

author	galaxyp
date	Fri, 20 Jan 2017 16:00:56 -0500
parents
children	e9975de58321

rev	line source
5 22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	1 <tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="2.6.0">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	2 <description>Search protein database with protein query sequence(s)</description>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	3 <!-- If job splitting is enabled, break up the query file into parts -->
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	4 <!--
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	5 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="500" merge_outputs="output1" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	6 -->
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	7 <requirements>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	8 <requirement type="binary">blastp</requirement>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	9 <requirement type="package" version="2.6.0">blast</requirement>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	10 </requirements>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	11 <stdio>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	12 <exit_code range="1" level="fatal" description="Bad input dataset or BLAST options" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	13 <exit_code range="2" level="fatal" description="Error in BLAST database" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	14 <exit_code range="3" level="fatal" description="Error in BLAST engine" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	15 <exit_code range="4" level="fatal" description="Out of Memory" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	16 <exit_code range="5:" level="fatal" description="Unknown Error" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	17 </stdio>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	18 <version_command>blastp -version</version_command>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	19 <command>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	20 ## The command is a Cheetah template which allows some Python based syntax.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	21 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	22 blastp
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	23 -query "$query"
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	24 #if $db_opts.db_opts_selector == "db":
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	25 -db "${db_opts.database.fields.path}"
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	26 #elif $db_opts.db_opts_selector == "histdb":
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	27 -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	28 #elif $db_opts.db_opts_selector == "remote":
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	29 -db $db_opts.database
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	30 -remote
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	31 #set $txids = []
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	32 #set $ntxids = []
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	33 #for $i, $org in enumerate($db_opts.taxid_repeat):
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	34 #if $org.exclude:
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	35 #set $ntxids = $ntxids + ["txid" + $org.taxid.__str__]
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	36 #else
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	37 #set $txids = $txids + ["txid" + $org.taxid.__str__]
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	38 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	39 #end for
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	40 #if (len($txids) + len($ntxids)) > 0:
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	41 #set $entrez_query = ''
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	42 #if len($txids) > 0:
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	43 #set $entrez_query = $entrez_query + '(' + ' OR '.join($txids) + ')'
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	44 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	45 #if len($ntxids) > 0:
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	46 #set $entrez_query = $entrez_query + ' NOT (' + ' OR '.join($ntxids) + ')'
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	47 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	48 -entrez_query '$entrez_query'
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	49 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	50 #else:
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	51 -subject "$db_opts.subject"
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	52 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	53 -task $blast_type
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	54 -evalue $evalue_cutoff
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	55 -out blast_output
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	56 ##Set the extended list here so if/when we add things, saved workflows are not affected
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	57 #if str($fmt_opt.out_format)=="text":
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	58 -outfmt "$fmt_opt.outfmt" $fmt_opt.html $fmt_opt.show_gis
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	59 #if $fmt_opt.num_descriptions.__str__.strip() != '':
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	60 -num_descriptions $fmt_opt.num_descriptions
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	61 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	62 #if $fmt_opt.num_alignments.__str__.strip() != '':
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	63 -num_alignments $fmt_opt.num_alignments
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	64 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	65 #elif str($fmt_opt.out_format)=="cols":
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	66 #set cols = (str($fmt_opt.std_cols)+","+str($fmt_opt.ext_cols)+","+str($fmt_opt.ids_cols)+","+str($fmt_opt.misc_cols)+","+str($fmt_opt.tax_cols)).replace("None", "").replace(",,", ",").replace(",", " ").strip()
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	67 -outfmt "6 $cols"
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	68 #if $fmt_opt.max_target_seqs.__str__.strip() != '':
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	69 -max_target_seqs $fmt_opt.max_target_seqs
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	70 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	71 #else:
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	72 -outfmt "$fmt_opt.outfmt"
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	73 #if $fmt_opt.max_target_seqs.__str__.strip() != '':
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	74 -max_target_seqs $fmt_opt.max_target_seqs
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	75 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	76 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	77 #if $db_opts.db_opts_selector != "remote":
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	78 -num_threads 8
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	79 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	80 #if $adv_opts.adv_opts_selector=="advanced":
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	81 $adv_opts.filter_query
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	82 -matrix $adv_opts.scoring.matrix
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	83 $adv_opts.scoring.gap_costs
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	84
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	85 #if $adv_opts.word_size.__str__.strip() != '':
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	86 -word_size $adv_opts.word_size
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	87 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	88
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	89 #if $adv_opts.window_size.__str__.strip() != '':
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	90 -window_size $adv_opts.window_size
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	91 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	92
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	93 #if $adv_opts.threshold.__str__.strip() != '':
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	94 -threshold $adv_opts.threshold
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	95 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	96
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	97 #if $adv_opts.comp_based_stats.__str__.strip() != '':
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	98 -comp_based_stats $adv_opts.comp_based_stats
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	99 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	100
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	101 ##Ungapped disabled for now - see comments below
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	102 ##$adv_opts.ungapped
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	103 $adv_opts.use_sw_tback
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	104 $adv_opts.parse_deflines
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	105 ## End of advanced options:
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	106 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	107 </command>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	108 <inputs>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	109 <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	110 <conditional name="db_opts">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	111 <param name="db_opts_selector" type="select" label="Subject database/sequences">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	112 <option value="db" selected="True">Local BLAST Database</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	113 <option value="histdb">BLAST database from your history</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	114 <option value="file">Local FASTA file</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	115 <option value="remote">NCBI Remote Database</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	116 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	117 <when value="db">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	118 <param name="database" type="select" label="Protein BLAST database">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	119 <options from_file="blastdb_p.loc">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	120 <column name="value" index="0"/>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	121 <column name="name" index="1"/>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	122 <column name="path" index="2"/>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	123 </options>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	124 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	125 <param name="subject" type="hidden" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	126 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	127 <when value="histdb">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	128 <param name="database" type="hidden" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	129 <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	130 <param name="subject" type="hidden" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	131 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	132 <when value="file">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	133 <param name="database" type="hidden" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	134 <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	135 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	136 <when value="remote">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	137 <param name="database" type="select" label="Protein BLAST database">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	138 <option value="nr" selected="True">Non-redundant protein sequences (nr)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	139 <option value="refseq_protein">Reference proteins (refseq_protein)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	140 <option value="swissprot">UniProtKB/Swiss-Prot(swissprot)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	141 <option value="pat">Patented protein sequences(pat)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	142 <option value="pdb">Protein Data Bank proteins(pdb)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	143 <option value="env_nr">Metagenomic proteins(env_nr)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	144 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	145 <repeat name="taxid_repeat" title="Search Organism Restriction" min="0">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	146 <param name="taxid" type="integer" value="" label="NCBI Taxon ID" help="For example: Human is 9606 (see: http://www.ncbi.nlm.nih.gov/taxonomy ) ">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	147 <validator type="in_range" min="0" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	148 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	149 <param name="exclude" type="boolean" checked="false" label="Exclude this NCBI Taxon ID" help=""/>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	150 </repeat>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	151 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	152 </conditional>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	153 <param name="blast_type" type="select" display="radio" label="Type of BLAST">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	154 <option value="blastp">blastp - Traditional BLASTP to compare a protein query to a protein database</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	155 <option value="blastp-fast">blastp-fast - Use longer words for seeding, faster but less accurate</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	156 <option value="blastp-short">blastp-short - BLASTP optimized for queries shorter than 30 residues</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	157 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	158 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	159 <conditional name="fmt_opt">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	160 <param name="out_format" type="select" label="Output format">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	161 <option value="tabular" selected="True">Tabular</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	162 <option value="cols">Tabular (select which columns)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	163 <option value="blastxml">BLAST XML</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	164 <option value="text">Text Report</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	165 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	166 <when value="tabular">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	167 <param name="outfmt" type="select" label="Tabular columns">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	168 <option value="6" selected="True">Tabular (standard 12 columns)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	169 <option value="7">Tabular (standard 12 columns) with comments</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	170 <option value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen">Tabular (extended 24 columns)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	171 <option value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles">Tabular (extended 25 columns)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	172 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	173 <param name="max_target_seqs" type="integer" value="500" optional="true" label="Maximum hits to show" help="Use zero for default limits">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	174 <validator type="in_range" min="0" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	175 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	176 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	177 <when value="cols">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	178 <param name="std_cols" type="select" multiple="true" display="checkboxes" label="Standard columns">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	179 <option selected="true" value="qseqid">qseqid = Query Seq-id (ID of your sequence)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	180 <option selected="true" value="sseqid">sseqid = Subject Seq-id (ID of the database hit)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	181 <option selected="true" value="pident">pident = Percentage of identical matches</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	182 <option selected="true" value="length">length = Alignment length</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	183 <option selected="true" value="mismatch">mismatch = Number of mismatches</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	184 <option selected="true" value="gapopen">gapopen = Number of gap openings</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	185 <option selected="true" value="qstart">qstart = Start of alignment in query</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	186 <option selected="true" value="qend">qend = End of alignment in query</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	187 <option selected="true" value="sstart">sstart = Start of alignment in subject (database hit)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	188 <option selected="true" value="send">send = End of alignment in subject (database hit)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	189 <option selected="true" value="evalue">evalue = Expectation value (E-value)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	190 <option selected="true" value="bitscore">bitscore = Bit score</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	191 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	192 <param name="ext_cols" type="select" multiple="true" display="checkboxes" label="Extended columns">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	193 <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	194 <option value="score">score = Raw score</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	195 <option value="nident">nident = Number of identical matches</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	196 <option value="positive">positive = Number of positive-scoring matches</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	197 <option value="gaps">gaps = Total number of gaps</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	198 <option value="ppos">ppos = Percentage of positive-scoring matches</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	199 <option value="qframe">qframe = Query frame</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	200 <option value="sframe">sframe = Subject frame</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	201 <option value="qseq">qseq = Aligned part of query sequence</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	202 <option value="sseq">sseq = Aligned part of subject sequence</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	203 <option value="qlen">qlen = Query sequence length</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	204 <option value="slen">slen = Subject sequence length</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	205 <option value="salltitles">salltitles = All subject title(s), separated by a '<>'</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	206 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	207 <param name="ids_cols" type="select" multiple="true" display="checkboxes" label="Other identifier columns">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	208 <option value="qgi">qgi = Query GI</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	209 <option value="qacc">qacc = Query accesion</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	210 <option value="qaccver">qaccver = Query accesion.version</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	211 <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	212 <option value="sgi">sgi = Subject GI</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	213 <option value="sallgi">sallgi = All subject GIs</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	214 <option value="sacc">sacc = Subject accession</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	215 <option value="saccver">saccver = Subject accession.version</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	216 <option value="sallacc">sallacc = All subject accessions</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	217 <option value="stitle">stitle = Subject Title</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	218 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	219 <param name="misc_cols" type="select" multiple="true" display="checkboxes" label="Miscellaneous columns">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	220 <option value="sstrand">sstrand = Subject Strand</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	221 <!-- Is it really worth including 'frames' given have 'qframe' and 'sframe'? -->
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	222 <option value="frames">frames = Query and subject frames separated by a '/'</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	223 <option value="btop">btop = Blast traceback operations (BTOP)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	224 <option value="qcovs">qcovs = Query Coverage Per Subject</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	225 <option value="qcovhsp">qcovhsp = Query Coverage Per HSP</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	226 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	227 <param name="tax_cols" type="select" multiple="true" display="checkboxes" label="Taxonomy columns">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	228 <option value="staxids">staxids = unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	229 <!-- TODO, how to handle the taxonomy data file dependency? If missing these give N/A -->
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	230 <option value="sscinames">sscinames = unique Subject Scientific Name(s), separated by a ';'</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	231 <option value="scomnames">scomnames = unique Subject Common Name(s), separated by a ';'</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	232 <option value="sblastnames">sblastnames = unique Subject Blast Name(s), separated by a ';' (in alphabetical order)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	233 <option value="sskingdoms">sskingdoms = unique Subject Super Kingdom(s), separated by a ';' (in alphabetical order)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	234 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	235 <param name="max_target_seqs" type="integer" value="500" optional="true" label="Maximum hits to show" help="Use zero for default limits">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	236 <validator type="in_range" min="0" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	237 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	238 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	239 <when value="blastxml">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	240 <param name="outfmt" type="hidden" value="5"/>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	241 <param name="max_target_seqs" type="integer" value="500" optional="true" label="Maximum hits to show" help="Use zero for default limits">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	242 <validator type="in_range" min="0" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	243 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	244 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	245 <when value="text">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	246 <param name="outfmt" type="select" label="Text format">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	247 <option value="0">Pairwise text</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	248 <option value="1">Query-anchored text showing identitites</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	249 <option value="2">Query-anchored text</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	250 <option value="3">Flat query-anchored text showing identitites</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	251 <option value="4">Flat query-anchored text</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	252 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	253 <param name="html" type="boolean" label="Html" truevalue="-html" falsevalue="" checked="true" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	254 <param name="show_gis" type="boolean" label="NCBI-gis" truevalue="-show_gis" falsevalue="" checked="false"
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	255 help="Show the NCBI gis in the Subject def lines"/>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	256 <param name="num_descriptions" type="integer" value="500" optional="true" label="Maximum Decriptions to show" help="Show one-line descriptions for this number of database sequences.">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	257 <validator type="in_range" min="0" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	258 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	259 <param name="num_alignments" type="integer" value="250" optional="true" label="Maximum alignments to show" help="Show alignments for this number of database sequences.">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	260 <validator type="in_range" min="0" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	261 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	262 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	263 </conditional>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	264 <conditional name="adv_opts">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	265 <param name="adv_opts_selector" type="select" label="Advanced Options">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	266 <option value="basic" selected="True">Hide Advanced Options</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	267 <option value="advanced">Show Advanced Options</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	268 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	269 <when value="basic" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	270 <when value="advanced">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	271 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	272 <conditional name="scoring">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	273 <param name="matrix" type="select" label="Scoring matrix">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	274 <option value="BLOSUM90">BLOSUM90</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	275 <option value="BLOSUM80">BLOSUM80</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	276 <option value="BLOSUM62" selected="True">BLOSUM62 (default)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	277 <option value="BLOSUM50">BLOSUM50</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	278 <option value="BLOSUM45">BLOSUM45</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	279 <option value="PAM250">PAM250</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	280 <option value="PAM70">PAM70</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	281 <option value="PAM30">PAM30</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	282 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	283 <when value="BLOSUM90">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	284 <param name="gap_costs" type="select" label="Gap Costs">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	285 <option value="">Use Defaults</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	286 <option value="-gapopen 9 -gapextend 2">Existense: 9 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	287 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	288 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	289 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	290 <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	291 <option value="-gapopen 10 -gapextend 1" selected="True">Existense: 10 Extension: 1 (default)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	292 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	293 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	294
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	295 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	296 <when value="BLOSUM80">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	297 <param name="gap_costs" type="select" label="Gap Costs">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	298 <option value="">Use Defaults</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	299 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	300 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	301 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	302 <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	303 <option value="-gapopen 10 -gapextend 1" selected="True">Existense: 10 Extension: 1 (default)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	304 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	305 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	306 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	307 <when value="BLOSUM62">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	308 <param name="gap_costs" type="select" label="Gap Costs">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	309 <option value="">Use Defaults</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	310 <option value="-gapopen 11 -gapextend 2">Existense: 11 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	311 <option value="-gapopen 10 -gapextend 2">Existense: 10 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	312 <option value="-gapopen 9 -gapextend 2">Existense: 9 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	313 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	314 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	315 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	316 <option value="-gapopen 13 -gapextend 1">Existense: 13 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	317 <option value="-gapopen 12 -gapextend 1">Existense: 12 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	318 <option value="-gapopen 11 -gapextend 1" selected="True">Existense: 11 Extension: 1 (default)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	319 <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	320 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	321 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	322
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	323 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	324 <when value="BLOSUM50">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	325 <param name="gap_costs" type="select" label="Gap Costs">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	326 <option value="">Use Defaults</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	327 <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	328 <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	329 <option value="-gapopen 11 -gapextend 3">Existense: 11 Extension: 3</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	330 <option value="-gapopen 10 -gapextend 3">Existense: 10 Extension: 3</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	331 <option value="-gapopen 9 -gapextend 3">Existense: 9 Extension: 3</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	332 <option value="-gapopen 16 -gapextend 2">Existense: 16 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	333 <option value="-gapopen 15 -gapextend 2">Existense: 15 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	334 <option value="-gapopen 14 -gapextend 2">Existense: 14 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	335 <option value="-gapopen 13 -gapextend 2" selected="True">Existense: 13 Extension: 2 (default)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	336 <option value="-gapopen 12 -gapextend 2">Existense: 12 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	337 <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	338 <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	339 <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	340 <option value="-gapopen 16 -gapextend 1">Existense: 16 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	341 <option value="-gapopen 15 -gapextend 1">Existense: 15 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	342 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	343
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	344 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	345 <when value="BLOSUM45">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	346 <param name="gap_costs" type="select" label="Gap Costs">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	347 <option value="">Use Defaults</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	348 <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	349 <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	350 <option value="-gapopen 11 -gapextend 3">Existense: 11 Extension: 3</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	351 <option value="-gapopen 10 -gapextend 3">Existense: 10 Extension: 3</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	352 <option value="-gapopen 15 -gapextend 2" selected="True">Existense: 15 Extension: 2 (default)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	353 <option value="-gapopen 14 -gapextend 2">Existense: 14 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	354 <option value="-gapopen 13 -gapextend 2">Existense: 13 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	355 <option value="-gapopen 12 -gapextend 2">Existense: 12 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	356 <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	357 <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	358 <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	359 <option value="-gapopen 16 -gapextend 1">Existense: 16 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	360 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	361 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	362 <when value="PAM250">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	363 <param name="gap_costs" type="select" label="Gap Costs">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	364 <option value="">Use Defaults</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	365 <option value="-gapopen 15 -gapextend 3">Existense: 15 Extension: 3</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	366 <option value="-gapopen 14 -gapextend 3">Existense: 14 Extension: 3</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	367 <option value="-gapopen 13 -gapextend 3">Existense: 13 Extension: 3</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	368 <option value="-gapopen 12 -gapextend 3">Existense: 12 Extension: 3</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	369 <option value="-gapopen 17 -gapextend 2">Existense: 17 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	370 <option value="-gapopen 16 -gapextend 2">Existense: 16 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	371 <option value="-gapopen 15 -gapextend 2">Existense: 15 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	372 <option value="-gapopen 14 -gapextend 2" selected="True">Existense: 14 Extension: 2 (default)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	373 <option value="-gapopen 13 -gapextend 2">Existense: 13 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	374 <option value="-gapopen 21 -gapextend 1">Existense: 21 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	375 <option value="-gapopen 20 -gapextend 1">Existense: 20 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	376 <option value="-gapopen 19 -gapextend 1">Existense: 19 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	377 <option value="-gapopen 18 -gapextend 1">Existense: 18 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	378 <option value="-gapopen 17 -gapextend 1">Existense: 17 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	379 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	380
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	381 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	382 <when value="PAM70">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	383 <param name="gap_costs" type="select" label="Gap Costs">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	384 <option value="">Use Defaults</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	385 <option value="-gapopen 8 -gapextend 2">Existense: 8 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	386 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	387 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	388 <option value="-gapopen 11 -gapextend 1">Existense: 11 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	389 <option value="-gapopen 10 -gapextend 1" selected="True">Existense: 10 Extension: 1 (default)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	390 <option value="-gapopen 9 -gapextend 1">Existense: 9 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	391 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	392
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	393 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	394 <when value="PAM30">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	395 <param name="gap_costs" type="select" label="Gap Costs">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	396 <option value="">Use Defaults</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	397 <option value="-gapopen 7 -gapextend 2">Existense: 7 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	398 <option value="-gapopen 6 -gapextend 2">Existense: 6 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	399 <option value="-gapopen 5 -gapextend 2">Existense: 5 Extension: 2</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	400 <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	401 <option value="-gapopen 9 -gapextend 1" selected="True">Existense: 9 Extension: 1 (default)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	402 <option value="-gapopen 8 -gapextend 1">Existense: 8 Extension: 1</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	403 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	404 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	405 </conditional>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	406
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	407 <param name="word_size" type="integer" value="" optional="true" label="Word size for wordfinder algorithm" help="Recommended: blastp 3, blastp-short 2">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	408 <validator type="in_range" min="2" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	409 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	410 <param name="window_size" type="integer" value="" optional="true" label="Multiple hits window size, use 0 to specify 1-hit algorithm." help="Recommended: blastp 40, blastp-short 15">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	411 <validator type="in_range" min="0" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	412 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	413 <param name="threshold" type="integer" value="" optional="true" label="Threshold: Minimum score to add a word to the BLAST lookup table." help="Recommended: blastp 11, blastp-short 16">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	414 <validator type="in_range" min="1" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	415 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	416 <param name="comp_based_stats" type="select" optional="true" label="Use composition-based statistics"
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	417 help="Recommended: blastp: 2 blastp-short: 0">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	418 <option value="">Leave Unspecified</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	419 <option value="0">0 or F (No composition-based statistics)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	420 <option value="1">1 (Composition-based statistics as in NAR 29:2994-3005, 2001)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	421 <option value="2">2, T, or D (Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	422 <option value="3">3 (Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally)</option>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	423 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	424
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	425 <param name="use_sw_tback" type="boolean" label="Compute locally optimal Smith-Waterman alignments?" truevalue="-use_sw_tback" falsevalue="" checked="false" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	426
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	427 <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	428 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	429 </conditional>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	430 </inputs>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	431 <outputs>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	432 <data name="output_tabular" format="tabular" label="${blast_type} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	433 <filter>fmt_opt['out_format'] in ("tabular","cols")</filter>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	434 </data>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	435 <data name="output_xml" format="blastxml" label="${blast_type} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	436 <filter>fmt_opt['out_format'] == "blastxml"</filter>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	437 </data>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	438 <data name="output_txt" format="txt" label="${blast_type} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	439 <filter>fmt_opt['out_format'] == "text" and not fmt_opt['html']</filter>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	440 </data>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	441 <data name="output_html" format="html" label="${blast_type} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	442 <filter>fmt_opt['out_format'] == "text" and fmt_opt['html']</filter>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	443 </data>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	444 </outputs>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	445 <tests>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	446 <test>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	447 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	448 <param name="db_opts_selector" value="file" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	449 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	450 <param name="database" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	451 <param name="evalue_cutoff" value="1e-8" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	452 <param name="blast_type" value="blastp" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	453 <param name="out_format" value="blastxml" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	454 <param name="outfmt" value="5" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	455 <param name="adv_opts_selector" value="advanced" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	456 <param name="filter_query" value="False" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	457 <param name="matrix" value="BLOSUM62" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	458 <param name="max_target_seqs" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	459 <param name="word_size" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	460 <param name="parse_deflines" value="False" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	461 <output name="output_xml">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	462 <assert_contents>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	463 <has_text text="sp\|Q9BS26\|ERP44_HUMAN"/>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	464 </assert_contents>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	465 </output>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	466 </test>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	467 <test>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	468 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	469 <param name="db_opts_selector" value="file" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	470 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	471 <param name="database" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	472 <param name="evalue_cutoff" value="1e-8" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	473 <param name="blast_type" value="blastp" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	474 <param name="out_format" value="tabular" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	475 <param name="outfmt" value="6" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	476 <param name="adv_opts_selector" value="advanced" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	477 <param name="filter_query" value="False" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	478 <param name="matrix" value="BLOSUM62" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	479 <param name="max_target_seqs" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	480 <param name="word_size" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	481 <param name="parse_deflines" value="False" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	482 <output name="output_tabular">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	483 <assert_contents>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	484 <has_text_matching expression="sp.P08100.OPSD_HUMAN\tgi.283855846.gb.ADB45242.1.\t\d+.\d+\t\d+\t\d+\t0\t\d+\t\d+\t\d+\t\d+\t\S+\t\s*\d+" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	485 <has_text text="BAB21486.1"/>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	486 </assert_contents>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	487 </output>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	488 </test>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	489 <test>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	490 <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	491 <param name="db_opts_selector" value="file" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	492 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	493 <param name="database" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	494 <param name="evalue_cutoff" value="1e-8" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	495 <param name="blast_type" value="blastp" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	496 <param name="out_format" value="tabular" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	497 <param name="outfmt" value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	498 <param name="adv_opts_selector" value="advanced" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	499 <param name="filter_query" value="False" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	500 <param name="matrix" value="BLOSUM62" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	501 <param name="max_target_seqs" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	502 <param name="word_size" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	503 <param name="parse_deflines" value="False" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	504 <output name="output_tabular">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	505 <assert_contents>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	506 <has_text_matching expression="sp.P08100.OPSD_HUMAN\tgi.283855846.gb.ADB45242.1.\t\d+.\d+\t\d+\t\d+\t\d+\t\d+\t\d+\t\d+\t\d+\t\S+\t\s*\d+\t\S+\t\d+\t\d+\t\d+\t\d+\t\S+\t\d+\t\d+\t\S+\t\S+\t\d+\t\d+" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	507 </assert_contents>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	508 </output>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	509 </test>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	510 <test>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	511 <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	512 <param name="db_opts_selector" value="file" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	513 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	514 <param name="database" value="" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	515 <param name="evalue_cutoff" value="1e-8" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	516 <param name="blast_type" value="blastp" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	517 <param name="out_format" value="tabular" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	518 <param name="outfmt" value="6" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	519 <param name="adv_opts_selector" value="basic" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	520 <output name="output_tabular">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	521 <assert_contents>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	522 <has_text_matching expression="gi.283855846.gb.ADB45242.1.\tsp.P08100.OPSD_HUMAN\t\d+.\d+\t\d+\t\d+\t0\t\d+\t\d+\t\d+\t\d+\t\S+\t\s*\d+" />
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	523 <has_text text="BAB21486.1"/>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	524 </assert_contents>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	525 </output>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	526 </test>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	527 </tests>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	528 <help>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	529
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	530 .. class:: warningmark
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	531
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	532 Note. Database searches may take a substantial amount of time.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	533 For large input datasets it is advisable to allow overnight processing.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	534
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	535 -----
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	536
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	537 What it does
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	538
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	539 Search a protein database using a protein query,
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	540 using the NCBI BLAST+ blastp command line tool.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	541
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	542 The search can be performed using a local database, against a sequence supplied in a fasta file,
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	543 or the blast can be performed remotely at NCBI.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	544
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	545 The remote operation allows searches to be targeted at specific organisms.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	546
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	547 -----
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	548
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	549 Output format
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	550
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	551 Because Galaxy focuses on processing tabular data, the default output of this
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	552 tool is tabular. The standard BLAST+ tabular output contains 12 columns:
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	553
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	554 ====== ========= ============================================
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	555 Column NCBI name Description
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	556 ------ --------- --------------------------------------------
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	557 1 qseqid Query Seq-id (ID of your sequence)
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	558 2 sseqid Subject Seq-id (ID of the database hit)
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	559 3 pident Percentage of identical matches
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	560 4 length Alignment length
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	561 5 mismatch Number of mismatches
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	562 6 gapopen Number of gap openings
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	563 7 qstart Start of alignment in query
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	564 8 qend End of alignment in query
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	565 9 sstart Start of alignment in subject (database hit)
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	566 10 send End of alignment in subject (database hit)
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	567 11 evalue Expectation value (E-value)
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	568 12 bitscore Bit score
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	569 ====== ========= ============================================
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	570
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	571 The BLAST+ tools can optionally output additional columns of information,
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	572 but this takes longer to calculate. Most (but not all) of these columns are
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	573 included by selecting the extended tabular output. The extra columns are
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	574 included after the standard 12 columns. This is so that you can write
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	575 workflow filtering steps that accept either the 12 or 24 column tabular
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	576 BLAST output.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	577
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	578 ====== ============= ===========================================
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	579 Column NCBI name Description
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	580 ------ ------------- -------------------------------------------
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	581 13 sallseqid All subject Seq-id(s), separated by a ';'
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	582 14 score Raw score
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	583 15 nident Number of identical matches
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	584 16 positive Number of positive-scoring matches
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	585 17 gaps Total number of gaps
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	586 18 ppos Percentage of positive-scoring matches
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	587 19 qframe Query frame
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	588 20 sframe Subject frame
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	589 21 qseq Aligned part of query sequence
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	590 22 sseq Aligned part of subject sequence
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	591 23 qlen Query sequence length
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	592 24 slen Subject sequence length
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	593 25 salltitles All subject title(s), separated by a '<>'
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	594 ====== ============= ===========================================
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	595
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	596 The third option is BLAST XML output, which is designed to be parsed by
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	597 another program, and is understood by some Galaxy tools.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	598
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	599 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	600 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	601 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	602 The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	603 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	604
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	605 -------
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	606
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	607 References
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	608
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	609 Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	610
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	611 Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	612
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	613 </help>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	614 <citations>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	615 <citation type="doi">10.1186/1471-2105-10-421</citation>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	616 <citation type="doi">10.1186/s13742-015-0080-7</citation>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	617 </citations>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4 galaxyp parents: diff changeset	618 </tool>

Mercurial > repos > galaxyp > blast_plus_remote_blastp

annotate blast_plus_remote_blastp.xml @ 5:22a767177ac9 draft