Mercurial > repos > galaxyp > blast_plus_remote_blastp

annotate blast_plus_remote_blastp.xml @ 6:e9975de58321 draft

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planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8fd454dc8332fff689a831b57ba50919a55c8277
author galaxyp
date Thu, 27 Jul 2017 17:22:20 -0400
parents 22a767177ac9
children edb3b709e165
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5
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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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
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2 <description>Search protein database with protein query sequence(s)</description>
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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
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4 <!--
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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
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6 -->
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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7 <requirements>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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8 <requirement type="package" version="2.6.0">blast</requirement>
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9 </requirements>
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10 <stdio>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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11 <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
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12 <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
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13 <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
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14 <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
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15 <exit_code range="5:" level="fatal" description="Unknown Error" />
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16 </stdio>
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17 <version_command>blastp -version</version_command>
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18 <command>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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19 ## 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
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20 ## 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
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21 blastp
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22 -query "$query"
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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23 #if $db_opts.db_opts_selector == "db":
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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24 -db "${db_opts.database.fields.path}"
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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25 #elif $db_opts.db_opts_selector == "histdb":
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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26 -db "${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
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27 #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
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28 -db $db_opts.database
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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29 -remote
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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30 #set $txids = []
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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31 #set $ntxids = []
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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32 #for $i, $org in enumerate($db_opts.taxid_repeat):
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33 #if $org.exclude:
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34 #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
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35 #else
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36 #set $txids = $txids + ["txid" + $org.taxid.__str__]
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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37 #end if
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38 #end for
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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39 #if (len($txids) + len($ntxids)) > 0:
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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40 #set $entrez_query = ''
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41 #if len($txids) > 0:
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42 #set $entrez_query = $entrez_query + '(' + ' OR '.join($txids) + ')'
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43 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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44 #if len($ntxids) > 0:
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45 #set $entrez_query = $entrez_query + ' NOT (' + ' OR '.join($ntxids) + ')'
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46 #end if
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47 -entrez_query '$entrez_query'
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48 #end if
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49 #else:
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50 -subject "$db_opts.subject"
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51 #end if
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52 -task $blast_type
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53 -evalue $evalue_cutoff
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54 -out blast_output
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55 ##Set the extended list here so if/when we add things, saved workflows are not affected
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56 #if str($fmt_opt.out_format)=="text":
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57 -outfmt "$fmt_opt.outfmt" $fmt_opt.html $fmt_opt.show_gis
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58 #if $fmt_opt.num_descriptions.__str__.strip() != '':
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59 -num_descriptions $fmt_opt.num_descriptions
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60 #end if
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61 #if $fmt_opt.num_alignments.__str__.strip() != '':
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62 -num_alignments $fmt_opt.num_alignments
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63 #end if
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64 #elif str($fmt_opt.out_format)=="cols":
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65 #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()
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66 -outfmt "6 $cols"
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67 #if $fmt_opt.max_target_seqs.__str__.strip() != '':
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68 -max_target_seqs $fmt_opt.max_target_seqs
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69 #end if
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70 #else:
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71 -outfmt "$fmt_opt.outfmt"
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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72 #if $fmt_opt.max_target_seqs.__str__.strip() != '':
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73 -max_target_seqs $fmt_opt.max_target_seqs
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74 #end if
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75 #end if
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76 #if $db_opts.db_opts_selector != "remote":
6
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77 -num_threads "\${GALAXY_SLOTS:-4}"
5
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78 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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79 #if $adv_opts.adv_opts_selector=="advanced":
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80 $adv_opts.filter_query
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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81 -matrix $adv_opts.scoring.matrix
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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82 $adv_opts.scoring.gap_costs
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83
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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84 #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:
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85 -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:
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86 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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87
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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88 #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
89 -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
90 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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91
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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92 #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:
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93 -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:
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94 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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95
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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96 #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:
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97 -comp_based_stats $adv_opts.comp_based_stats
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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98 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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99
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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100 ##Ungapped disabled for now - see comments below
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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101 ##$adv_opts.ungapped
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
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102 $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
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103 $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:
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104 ## 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:
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105 #end if
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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106 </command>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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107 <inputs>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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108 <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
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109 <conditional name="db_opts">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
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110 <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
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111 <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
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112 <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
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113 <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
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114 <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
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115 </param>
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galaxyp
parents:
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116 <when value="db">
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galaxyp
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117 <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
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118 <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:
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119 <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:
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120 <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:
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121 <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:
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122 </options>
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galaxyp
parents:
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123 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
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124 <param name="subject" type="hidden" value="" />
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125 </when>
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galaxyp
parents:
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126 <when value="histdb">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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127 <param name="database" type="hidden" value="" />
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galaxyp
parents:
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128 <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:
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129 <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:
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130 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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131 <when value="file">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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132 <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:
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133 <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
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parents:
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134 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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135 <when value="remote">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
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136 <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:
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137 <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
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138 <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
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139 <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:
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140 <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:
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141 <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
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142 <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
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143 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
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144 <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
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145 <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
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146 <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
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147 </param>
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148 <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
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149 </repeat>
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150 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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151 </conditional>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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152 <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
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153 <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
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154 <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
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155 <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
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156 </param>
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157 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
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158 <conditional name="fmt_opt">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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159 <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
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160 <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:
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161 <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
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162 <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
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163 <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
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164 </param>
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parents:
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165 <when value="tabular">
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parents:
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166 <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
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parents:
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167 <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:
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168 <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
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parents:
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169 <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
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diff changeset
170 <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
171 </param>
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 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
173 <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
174 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
175 </when>
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 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
177 <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
178 <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
179 <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
180 <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
181 <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
182 <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
183 <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
184 <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
185 <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
186 <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
187 <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
188 <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
189 <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
190 </param>
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 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
192 <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
193 <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
194 <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
195 <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
196 <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
197 <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
198 <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
199 <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
200 <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
201 <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
202 <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
203 <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
204 <option value="salltitles">salltitles = All subject title(s), separated by a '&lt;&gt;'</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 </param>
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 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
207 <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
208 <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
209 <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
210 <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
211 <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
212 <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
213 <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
214 <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
215 <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
216 <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
217 </param>
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 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
219 <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
220 <!-- 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
221 <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
222 <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
223 <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
224 <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
225 </param>
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 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
227 <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
228 <!-- 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
229 <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
230 <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
231 <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
232 <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
233 </param>
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 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
235 <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
236 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
237 </when>
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 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
239 <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
240 <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
241 <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
242 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
243 </when>
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 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
245 <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
246 <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
247 <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
248 <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
249 <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
250 <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
251 </param>
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 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
253 <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
254 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
255 <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
256 <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
257 </param>
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 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
259 <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
260 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
261 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
262 </conditional>
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 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
264 <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
265 <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
266 <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
267 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
268 <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
269 <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
270 <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
271 <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
272 <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
273 <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
274 <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
275 <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
276 <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
277 <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
278 <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
279 <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
280 <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
281 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
282 <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
283 <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
284 <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
285 <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
286 <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
287 <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
288 <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
289 <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
290 <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
291 <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
292 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
293
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
294 </when>
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 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
296 <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
297 <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
298 <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
299 <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
300 <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
301 <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
302 <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
303 <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
304 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
305 </when>
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 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
307 <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
308 <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
309 <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
310 <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
311 <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
312 <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
313 <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
314 <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
315 <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
316 <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
317 <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
318 <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
319 <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
320 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
321
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
322 </when>
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 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
324 <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
325 <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
326 <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
327 <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
328 <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
329 <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
330 <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
331 <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
332 <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
333 <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
334 <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
335 <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
336 <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
337 <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
338 <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
339 <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
340 <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
341 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
342
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
343 </when>
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 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
345 <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
346 <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
347 <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
348 <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
349 <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
350 <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
351 <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
352 <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
353 <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
354 <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
355 <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
356 <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
357 <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
358 <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
359 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
360 </when>
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 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
362 <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
363 <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
364 <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
365 <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
366 <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
367 <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
368 <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
369 <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
370 <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
371 <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
372 <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
373 <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
374 <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
375 <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
376 <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
377 <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
378 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
379
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
380 </when>
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 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
382 <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
383 <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
384 <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
385 <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
386 <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
387 <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
388 <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
389 <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
390 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
391
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
392 </when>
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 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
394 <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
395 <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
396 <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
397 <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
398 <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
399 <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
400 <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
401 <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
402 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
403 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
404 </conditional>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
405
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
406 <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
407 <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
408 </param>
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 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
410 <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
411 </param>
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 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
413 <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
414 </param>
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 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
416 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
417 <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
418 <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
419 <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
420 <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
421 <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
422 </param>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
423
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
424 <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
425
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
426 <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
427 </when>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
428 </conditional>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
429 </inputs>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
430 <outputs>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
431 <data name="output_tabular" format="tabular" label="${blast_type} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
432 <filter>fmt_opt['out_format'] in ("tabular","cols")</filter>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
433 </data>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
434 <data name="output_xml" format="blastxml" label="${blast_type} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
435 <filter>fmt_opt['out_format'] == "blastxml"</filter>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
436 </data>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
437 <data name="output_txt" format="txt" label="${blast_type} on ${db_opts.db_opts_selector} ${db_opts.database}" from_work_dir="blast_output">
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
438 <filter>fmt_opt['out_format'] == "text" and not fmt_opt['html']</filter>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
439 </data>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
440 <data name="output_html" format="html" label="${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
441 <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
442 </data>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
443 </outputs>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
444 <tests>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
445 <test>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
446 <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
447 <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
448 <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
449 <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
450 <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
451 <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
452 <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
453 <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
454 <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
455 <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
456 <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
457 <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
458 <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
459 <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
460 <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
461 <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
462 <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
463 </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
464 </output>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
465 </test>
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 <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
468 <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
469 <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
470 <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
471 <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
472 <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
473 <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
474 <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
475 <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
476 <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
477 <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
478 <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
479 <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
480 <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
481 <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
482 <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
483 <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
484 <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
485 </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
486 </output>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
487 </test>
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 <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
490 <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
491 <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
492 <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
493 <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
494 <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
495 <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
496 <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
497 <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
498 <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
499 <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
500 <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
501 <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
502 <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
503 <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
504 <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
505 <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
506 </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
507 </output>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
508 </test>
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 <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
511 <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
512 <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
513 <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
514 <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
515 <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
516 <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
517 <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
518 <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
519 <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
520 <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
521 <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
522 <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
523 </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
524 </output>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
525 </test>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
526 </tests>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
527 <help>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
528
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
529 .. 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
530
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
531 **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
532 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
533
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 **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
537
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
538 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
539 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
540
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
541 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
542 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
543
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
544 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
545
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 **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
549
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
550 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
551 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
552
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 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
555 ------ --------- --------------------------------------------
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
556 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
557 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
558 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
559 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
560 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
561 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
562 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
563 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
564 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
565 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
566 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
567 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
568 ====== ========= ============================================
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 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
571 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
572 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
573 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
574 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
575 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
576
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 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
579 ------ ------------- -------------------------------------------
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
parents:
diff changeset
580 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
581 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
582 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
583 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
584 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
585 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
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586 19 qframe Query frame
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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587 20 sframe Subject frame
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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588 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
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589 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
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590 23 qlen Query sequence length
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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591 24 slen Subject sequence length
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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592 25 salltitles All subject title(s), separated by a '&lt;&gt;'
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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593 ====== ============= ===========================================
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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594
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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595 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
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596 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
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597
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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598 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
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599 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
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600 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
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601 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
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602 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
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603
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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604 -------
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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605
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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606 **References**
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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607
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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608 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
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609
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610 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.
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611
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612 </help>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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613 <citations>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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614 <citation type="doi">10.1186/1471-2105-10-421</citation>
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615 <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
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616 </citations>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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617 </tool>