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annotate lastal.xml @ 1:86206f93fb13 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 67b8e5adffa4015ee60b1b4a0cd220f632ba1082"
author iuc
date Wed, 22 Jul 2020 19:50:13 -0400
parents 9a7e91fc6562
children bf30030e5265
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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86206f93fb13 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 67b8e5adffa4015ee60b1b4a0cd220f632ba1082"
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1 <tool id="last_al" name="LASTal" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01">
0
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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2
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3 <description>finds local alignments between query sequences, and reference sequences.</description>
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4
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5 <macros>
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6 <import>macros_last.xml</import>
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7 </macros>
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8
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9 <requirements>
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10 <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
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11 </requirements>
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12
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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13 <command detect_errors="exit_code"><![CDATA[
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14 #if $db_opts.db_opts_input == 'lastdb'
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15 ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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16 #end if
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17
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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18 lastal
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9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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20 -Q $lastal.Q
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21 -f $lastal.f
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22 -j $lastal.j
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23
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24 -R $lastal.repeats_misc.uppercase_misc$lastal.repeats_misc.simple_repeat_misc
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26 #if $lastal.isprotein.schoring_schemes.score_matrix != 'scoreFile'
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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27 -p $lastal.isprotein.schoring_schemes.score_matrix
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28
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29 -X $lastal.isprotein.schoring_schemes.score_opt.X
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30 -x $lastal.isprotein.schoring_schemes.score_opt.x
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31 -y $lastal.isprotein.schoring_schemes.score_opt.y
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32 -z $lastal.isprotein.schoring_schemes.score_opt.z
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33 -d $lastal.isprotein.schoring_schemes.score_opt.d
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34 -e $lastal.isprotein.schoring_schemes.score_opt.e
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35
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36 -a $lastal.isprotein.schoring_schemes.cost_opt.a
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37 -b $lastal.isprotein.schoring_schemes.cost_opt.b
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38 -A $lastal.isprotein.schoring_schemes.cost_opt.A
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39 -B $lastal.isprotein.schoring_schemes.cost_opt.B
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40
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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41 -s $lastal.isprotein.s
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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42 #else if $lastal.isprotein.schoring_schemes.score_matrix == 'scoreFile'
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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43 -p $lastal.isprotein.schoring_schemes.scoreMatrixFile
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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44 #end if
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45
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46 -D $lastal.evalue_opt.D
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47
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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48 -m $lastal.init_match_opt.m
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49 -l $lastal.init_match_opt.l
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50 -L $lastal.init_match_opt.L
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51 -k $lastal.init_match_opt.k
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52 -W $lastal.init_match_opt.W
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53
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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54 -S $lastal.misc_opt.S
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55 -K $lastal.misc_opt.K
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56 -C $lastal.misc_opt.C
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57 -T $lastal.misc_opt.T
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58 -n $lastal.misc_opt.n
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59 -w $lastal.misc_opt.w
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60 -u $lastal.misc_opt.u
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61 -g $lastal.misc_opt.g
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62
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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63 -P \${GALAXY_SLOTS:-1}
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64
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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65 #if $db_opts.db_opts_input == 'db'
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66 '${"'" "'".join(str($db_opts.database.fields.path).split(","))}'
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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67 #else if $db_opts.db_opts_input == 'lastdb'
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68 'db_files/lastdb'
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69 #end if
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70
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71 '$query_fasta'
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72
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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73 >'$outfile'
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74 ]]></command>
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75
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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76 <inputs>
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77 <expand macro="input_db"/>
1
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78 <param name="query_fasta" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina,tabular" label="Queries FASTA file"/>
0
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79
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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80 <section name="lastal" title="Lastal arguments" expanded="true">
1
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81 <param argument="-Q" type="select" multiple="false" label="Query input format">
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82 <option value="0" selected="true">FASTA</option>
0
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83 <option value="1">fastq-sanger</option>
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84 <option value="2">fastq-solexa</option>
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85 <option value="3">fastq-illumina</option>
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86 <option value="5">PSSM</option>
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87 </param>
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parents:
diff changeset
88 <param argument="-f" type="select" multiple="false" label="Output format">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
89 <option value="MAF" selected="true">MAF</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
90 <option value="TAB">TAB</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
91 <option value="BlastTab">BlastTab</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
92 <option value="BlastTab+">BlastTab+</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
93 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
94 <param argument="-j" type="select" multiple="false" label="Output type">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
95 <option value="0">Match counts</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
96 <option value="1">Gapless</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
97 <option value="2">Redundant gapped</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
98 <option value="3" selected="true">Gapped</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
99 <option value="4">Column ambiguity estimates</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
100 <option value="5">Gamma-centroid</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
101 <option value="6">LAMA</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
102 <option value="7">Expected counts</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
103 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
104
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
105 <conditional name="isprotein">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
106 <param name="lastal_protein" type="select" multiple="false" label="The sequences are :">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
107 <option value="dna" selected="true">DNA</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
108 <option value="prot">Proteins (-p)</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
109 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
110 <when value="dna">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
111 <conditional name="schoring_schemes">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
112 <param name="score_matrix" argument="-p" type="select" multiple="false" label="Match/mismatch score matrix.">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
113 <option value="AT77">AT77</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
114 <option value="ATMAP">ATMAP</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
115 <option value="BISF">BISF</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
116 <option value="BISR">BISR</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
117 <option value="BL62">BLOSUM62</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
118 <option value="BL80" selected="true">BLOSUM80</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
119 <option value="HOXD70">HOXD70</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
120 <option value="MIQS">MIQS</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
121 <option value="PAM10">PAM10</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
122 <option value="PAM30">PAM30</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
123 <option value="scoreFile">Other score matrix</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
124 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
125 <when value="AT77">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
126 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
127 <expand macro="cost_macro" a="15" b="2"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
128 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
129 <when value="ATMAP">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
130 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
131 <expand macro="cost_macro" a="24" b="6"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
132 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
133 <when value="BISF">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
134 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
135 <expand macro="cost_macro" a="21" b="9"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
136 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
137 <when value="BISR">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
138 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
139 <expand macro="cost_macro" a="21" b="9"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
140 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
141 <when value="BL62">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
142 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
143 <expand macro="cost_macro" a="11" b="2"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
144 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
145 <when value="BL80">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
146 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
147 <expand macro="cost_macro" a="7" b="1"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
148 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
149 <when value="HOXD70">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
150 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
151 <expand macro="cost_macro" a="400" b="30"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
152 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
153 <when value="MIQS">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
154 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
155 <expand macro="cost_macro" a="13" b="2"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
156 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
157 <when value="PAM10">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
158 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
159 <expand macro="cost_macro" a="20" b="3"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
160 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
161 <when value="PAM30">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
162 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
163 <expand macro="cost_macro" a="13" b="3"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
164 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
165 <when value="scoreFile">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
166 <param name="scoreMatrixFile" type="data" format="txt" label="Score matrix file" />
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
167 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
168 </conditional>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
169 <param argument="-s" type="select" multiple="false" label="Strand">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
170 <option value="0">Reverse</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
171 <option value="1">Forward</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
172 <option value="2" selected="true">Both</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
173 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
174 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
175 <when value="prot">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
176 <conditional name="schoring_schemes">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
177 <param name="score_matrix" argument="-p" type="select" multiple="false" label="Match/mismatch score matrix.">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
178 <option value="AT77">AT77</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
179 <option value="ATMAP">ATMAP</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
180 <option value="BISF">BISF</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
181 <option value="BISR">BISR</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
182 <option value="BL62" selected="true">BLOSUM62</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
183 <option value="BL80">BLOSUM80</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
184 <option value="HOXD70">HOXD70</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
185 <option value="MIQS">MIQS</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
186 <option value="PAM10">PAM10</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
187 <option value="PAM30">PAM30</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
188 <option value="scoreFile">Other score matrix</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
189 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
190 <when value="AT77">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
191 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
192 <expand macro="cost_macro" a="15" b="2"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
193 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
194 <when value="ATMAP">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
195 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
196 <expand macro="cost_macro" a="24" b="6"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
197 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
198 <when value="BISF">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
199 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
200 <expand macro="cost_macro" a="21" b="9"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
201 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
202 <when value="BISR">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
203 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
204 <expand macro="cost_macro" a="21" b="9"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
205 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
206 <when value="BL62">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
207 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
208 <expand macro="cost_macro" a="11" b="2"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
209 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
210 <when value="BL80">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
211 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
212 <expand macro="cost_macro" a="7" b="1"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
213 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
214 <when value="HOXD70">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
215 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
216 <expand macro="cost_macro" a="400" b="30"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
217 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
218 <when value="MIQS">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
219 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
220 <expand macro="cost_macro" a="13" b="2"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
221 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
222 <when value="PAM10">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
223 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
224 <expand macro="cost_macro" a="20" b="3"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
225 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
226 <when value="PAM30">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
227 <expand macro="score_macro"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
228 <expand macro="cost_macro" a="13" b="3"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
229 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
230 <when value="scoreFile">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
231 <param name="scoreMatrixFile" type="data" format="txt" label="Score matrix file" />
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
232 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
233 </conditional>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
234 <param argument="-s" type="select" multiple="false" label="Strand">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
235 <option value="0">Reverse</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
236 <option value="1" selected="true">Forward</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
237 <option value="2">Both</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
238 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
239 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
240 </conditional>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
241
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
242 <section name="repeats_misc" title="Specify lowercase-marking of repeats. (-R)" expanded="false">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
243 <param name="uppercase_misc" type="select" multiple="false" label="Input sequences to uppercase.">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
244 <option value="0">Convert the input sequences to uppercase while reading them.(0)</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
245 <option value="1" selected="true">Keep any lowercase in the input sequences.(1)</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
246 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
247 <param name="simple_repeat_misc" type="select" multiple="false" label="Check for simple repeats.">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
248 <option value="0" selected="true">Do not check for simple repeats.(0)</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
249 <option value="1">Convert simple repeats to lowercase.(1)</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
250 <option value="2">Convert simple DNA repeats to lowercase.(2)</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
251 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
252 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
253
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
254 <section name="evalue_opt" title="E-value options" expanded="false">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
255 <param argument="-D" type="integer" value="1000000" label="Query letters per random alignment (-D)"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
256 <!--<param argument="-E" type="integer" value="1e+18" label="Maximum expected alignments per square giga"/>-->
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
257 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
258
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
259 <section name="init_match_opt" title="Initial-match options" expanded="false">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
260 <param argument="-m" type="integer" value="10" min="1" label="Maximum initial matches per query position"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
261 <param argument="-l" type="integer" value="1" min="1" label="Minimum length for initial matches"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
262 <!-- Infinity -->
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
263 <param argument="-L" type="integer" value="999999999" min="1" label="Maximum length for initial matches"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
264 <param argument="-k" type="integer" value="1" min="1" label="Use initial matches starting at every k-th position in each query"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
265 <param argument="-W" type="integer" value="1" min="1" label="Use minimum positions in sliding windows of W consecutive positions"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
266 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
267
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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268 <section name="misc_opt" title="Miscellaneous options" expanded="false">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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269 <param argument="-S" type="select" multiple="false" label="Score matrix applies to forward strand of :">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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270 <option value="0" selected="true">Reference</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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271 <option value="1">Query</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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272 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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273 <param argument="-K" type="integer" value="0" min="0" label="Omit alignments whose query range lies in >= K others with > score"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
274 <param argument="-C" type="integer" value="0" min="0" label="Omit gapless alignments in >= C others with > score-per-length"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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diff changeset
275 <!--<param name="omit_gap" argument="-M" type="integer" value="" label="Find minimum-difference alignments (faster but cruder)"/>-->
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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276
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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277 <param argument="-T" type="select" multiple="false" label="Type of alignment">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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278 <option value="0" selected="true">Local</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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279 <option value="1">Overlap</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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280 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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diff changeset
281 <param argument="-n" type="integer" value="10" min="0" label="Maximum gapless alignments per query position" help="Infinity if m=0"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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282 <!--<param name="max_gap_align" argument="-N" type="integer" value="0" label="Stop after the first N alignments per query strand"/>-->
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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283
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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284 <!-- Condition lastdb : 2 if lastdb -c and Q<5 -->
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
285 <param argument="-u" type="select" multiple="false" label="Mask lowercase during extensions.">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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286 <option value="0" selected="true">Never.(0)</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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287 <option value="1">Gapless.(1)</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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288 <option value="2">Gapless+postmask.(2)</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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289 <option value="3">Always.(3)</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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290 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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diff changeset
291 <param argument="-w" type="integer" value="1000" min="0" label="Suppress repeats inside exact matches, offset by less or equal this distance. Use 0 to set this off" help="Use 0 to turn this off"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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292
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
293 <!-- https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi -->
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
294 <!-- Condition if ADN vs prot and -F -->
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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295 <param argument="-G" type="select" multiple="false" label="Genetic code.">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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296 <option value="1" selected="true">Standard Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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297 <option value="2">Vertebrate Mitochondrial Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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298 <option value="3">Yeast Mitochondrial Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
299 <option value="4">Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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300 <option value="5">Invertebrate Mitochondrial Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
301 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
302 <option value="9">Echinoderm and Flatworm Mitochondrial Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
303 <option value="10">Euplotid Nuclear Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
304 <option value="11">Bacterial, Archaeal and Plant Plastid Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
305 <option value="12">Alternative Yeast Nuclear Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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306 <option value="13">Ascidian Mitochondrial Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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307 <option value="14">Alternative Flatworm Mitochondrial Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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308 <option value="16">Chlorophycean Mitochondrial Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
309 <option value="21">Trematode Mitochondrial Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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310 <option value="22">Scenedesmus obliquus Mitochondrial Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
311 <option value="23">Thraustochytrium Mitochondrial Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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312 <option value="24">Pterabranchia Mitochondrial Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
313 <option value="25">Candidate Division SR1 and Gracilibacteria Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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314 <option value="26">Pachysolen tannophilus Nuclear Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
315 <option value="27">Karyorelict Nuclear Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
316 <option value="28">Condylostoma Nuclear Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
317 <option value="29">Mesodinium Nuclear Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
318 <option value="30">Peritrich Nuclear Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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319 <option value="31">Blastocrithidia Nuclear Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
320 <option value="33">Cephalodiscidae Mitochondrial UAA-Tyr Code</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
321 <!-- Add filename option with <repeat> -->
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
322 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
323
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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324 <!--<param name="temperature" argument="-t" type="integer" value="1/lambda" label="Temperature for calculating probabilities"/>-->
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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325 <param argument="-g" type="integer" value="1" min="0" label="Gamma parameter for gamma-centroid and LAMA"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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326 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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327 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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328 </inputs>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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diff changeset
329
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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330 <outputs>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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331 <data name="outfile" format="maf" label="LAST align from ${on_string}" />
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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diff changeset
332 </outputs>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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diff changeset
333
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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334 <tests>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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diff changeset
335 <test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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336 <conditional name="db_opts">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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337 <param name="db_opts_input" value="db"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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diff changeset
338 <param name="database" value="humdb"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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diff changeset
339 </conditional>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
340 <param name="query_fasta" value="fuguMito.fa" ftype="fasta"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
341 <output name="outfile" ftype="maf" file="last_align_gen.maf" lines_diff="2"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
342 </test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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343 <test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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344 <conditional name="db_opts">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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345 <param name="db_opts_input" value="db"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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346 <param name="database" value="hedgdb"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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347 </conditional>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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348 <section name="lastal">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
349 <conditional name="isprotein">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
350 <param name="lastal_protein" value="prot"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
351 </conditional>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
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352 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
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353 <param name="query_fasta" value="hedgehog_prot_drosophila.fa" ftype="fasta"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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354 <output name="outfile" ftype="maf" file="last_align_prot.maf" lines_diff="2"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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355 </test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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356 </tests>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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357
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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358 <help>@LAST_HELP@</help>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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359 <citations><expand macro="citations"/></citations>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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360 </tool>