Mercurial > repos > iuc > last

annotate lastdb.xml @ 5:f5a5a2b39ff2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
author iuc
date Thu, 25 Mar 2021 20:53:27 +0000
parents 8705e0d74a0f
children 19c265784f35
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1 <tool id="last_db" name="LASTdb" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">
0
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3 <description>prepares sequences for subsequent comparison and alignment using lastal.</description>
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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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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 set -e -o pipefail;
2
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16 #if $input_files.ext.endswith('.gz')
8705e0d74a0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
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17 zcat
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18 #else
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19 cat
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20 #end if
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21 '$input_files' | lastdb
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8705e0d74a0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
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23 #if $input_files.ext.startswith('fasta')
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24 -Q 0
4
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25 #else if $input_files.ext.startswith('fastqsanger')
2
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26 -Q 1
4
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27 #else if $input_files.ext.startswith('fastqsolexa')
2
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28 -Q 2
4
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29 #else if $input_files.ext.startswith('fastqillumina')
2
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30 -Q 3
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31 #end if
0
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32 $lastdb.sequences_type.protein
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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33 -a $lastdb.sequences_type.a
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34 -R $lastdb.repeats.uppercase$lastdb.repeats.simple_repeat
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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35 $lastdb.repeats.sm_lower
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36 -S $lastdb.lastdb_advanced.S
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37 #if $lastdb.lastdb_advanced.seeds.u != ''
f5a5a2b39ff2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
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38 -u $lastdb.lastdb_advanced.seeds.u
f5a5a2b39ff2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
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39 #end if
0
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40 -w $lastdb.lastdb_advanced.seeds.w
4
8705e0d74a0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
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41 #if $lastdb.lastdb_advanced.seeds.W
8705e0d74a0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
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42 -W $lastdb.lastdb_advanced.seeds.W
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43 #end if
0
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44 -m $lastdb.lastdb_advanced.seeds.m
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45 -i $lastdb.lastdb_advanced.i
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46 -C $lastdb.lastdb_advanced.C
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47 -s \${GALAXY_MEMORY_MB:-2G}
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48 -P \${GALAXY_SLOTS:-1}
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49 'lastdb'
4
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50
0
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51
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52 &&
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53
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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54 mkdir '$outfile.files_path' &&
2
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55 mv lastdb* '$outfile.files_path'
0
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56 ]]></command>
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57
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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58 <inputs>
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59 <param name="input_files" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Reference(s) input files" />
0
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60 <section name="lastdb" title="Lastdb arguments" expanded="true">
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61 <conditional name="sequences_type">
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62 <param name="protein" type="select" multiple="false" label="The sequences are :">
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63 <option value="" selected="true">DNA</option>
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64 <option value="-p">Proteins (-p)</option>
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65 </param>
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66 <when value="">
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67 <param argument="-a" type="text" value="ACGT" label="User-defined alphabet."/>
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68 </when>
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69 <when value="-p">
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70 <param argument="-a" type="text" value="ACDEFGHIKLMNPQRSTVWY" label="User-defined alphabet."/>
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71 </when>
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72 </conditional>
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73
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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74 <section name="repeats" title="Specify lowercase-marking of repeats. (-R)" expanded="false">
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75 <param name="uppercase" type="select" multiple="false" label="Convert the input sequences to uppercase while reading them.">
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76 <option value="0">Convert the input sequences to uppercase while reading them. (0)</option>
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77 <option value="1" selected="true">Keep any lowercase in the input sequences. (1)</option>
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78 </param>
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79 <param name="simple_repeat" type="select" multiple="false" label="Check for simple repeats.">
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80 <option value="0" selected="true">Do not check for simple repeats.(0)</option>
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81 <option value="1">Convert simple repeats to lowercase.(1)</option>
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82 <option value="2">Convert simple DNA repeats to lowercase.(2)</option>
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83 </param>
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84 <param name="sm_lower" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="true" label="Soft-mask lowercase letters." help="This means that, when we compare these sequences to some other sequences using lastal, lowercase letters will be excluded from initial matches. This will apply to lowercase letters in both sets of sequences."/>
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85 </section>
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86
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
87 <section name="lastdb_advanced" title="Advanced options" expanded="false">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
88 <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
89 <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
90 <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
91 <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
92 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
93
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
94 <conditional name="seeds">
5
f5a5a2b39ff2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
iuc
parents: 4
diff changeset
95 <param argument="-u" type="select" multiple="false" label="Specify a seeding scheme.">
f5a5a2b39ff2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
iuc
parents: 4
diff changeset
96 <option value="">Do not apply seeding scheme</option>
0
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
97 <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
98 <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
99 <option value="MAM4">MAM4</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="MAM8">MAM8</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="MURPHY10">MURPHY10</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="NEAR">NEAR</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
103 <option value="YASS" selected="true">YASS</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
104 <!-- Add filename option -->
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
105 </param>
5
f5a5a2b39ff2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
iuc
parents: 4
diff changeset
106 <when value=""/>
0
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
107 <when value="BISF">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
108 <expand macro="step_macro" step="2"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
109 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
110 <when value="BISR">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
111 <expand macro="step_macro" step="2"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
112 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
113 <when value="MAM4">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
114 <expand macro="step_macro" step="1"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
115 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
116 <when value="MAM8">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
117 <expand macro="step_macro" step="1"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
118 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
119 <when value="MURPHY10">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
120 <expand macro="step_macro" step="1"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
121 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
122 <when value="NEAR">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
123 <expand macro="step_macro" step="1"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
124 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
125 <when value="YASS">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
126 <expand macro="step_macro" step="1"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
127 </when>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
128 </conditional>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
129
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
130 <param argument="-i" type="integer" value="0" label="Minimum limit on 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
131
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
132 <param argument="-C" type="select" multiple="false" label="Child table type">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
133 <option value="0" selected="true">None</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
134 <option value="1">Byte-size</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
135 <option value="2">Short-syze</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
136 <option value="3">Full</option>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
137 </param>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
138 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
139 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
140 </inputs>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
141
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
142 <outputs>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
143 <data name="outfile" format="lastdb">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
144 <discover_datasets pattern="__designation__" directory="ref_genome"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
145 </data>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
146 </outputs>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
147
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
148 <tests>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
149 <test>
4
8705e0d74a0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 2
diff changeset
150 <param name="input_files" value="humanMito.fa.gz" ftype="fasta.gz"/>
0
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
151 <section name="lastdb">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
152 <section name="repeats">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
153 <param name="uppercase" value="0"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
154 <param name="simple_repeat" value="1"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
155 <param name="sm_lower" value="true"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
156 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
157 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
158 <output name="outfile" compare="contains" file="humdb.lastdb" ftype="lastdb">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
159 <extra_files type="file" value="humdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
160 <extra_files type="file" value="humdb.des" name="lastdb.des"/>
4
8705e0d74a0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 2
diff changeset
161 <extra_files type="file" value="humdb.prj" name="lastdb.prj" compare="sim_size" delta="2"/>
0
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
162 <extra_files type="file" value="humdb.sds" name="lastdb.sds"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
163 <extra_files type="file" value="humdb.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
164 <extra_files type="file" value="humdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
165 <extra_files type="file" value="humdb.tis" name="lastdb.tis" compare="sim_size" delta="1"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
166 </output>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
167 </test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
168 <test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
169 <param name="input_files" value="hedgehog_prot_human.fa" ftype="fasta"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
170 <section name="lastdb">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
171 <conditional name="sequences_type">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
172 <param name="protein" value="-p"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
173 </conditional>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
iuc
parents:
diff changeset
174 </section>
4
8705e0d74a0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 2
diff changeset
175 <section name="lastdb_advanced">
8705e0d74a0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
iuc
parents: 2
diff changeset
176 <conditional name="seeds">
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177 <param name="u" value="MURPHY10"/>
5
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178 </conditional>
4
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179 </section>
0
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180 <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb">
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181 <extra_files type="file" value="hedgdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
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182 <extra_files type="file" value="hedgdb.des" name="lastdb.des"/>
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183 <extra_files type="file" value="hedgdb.prj" name="lastdb.prj"/>
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184 <extra_files type="file" value="hedgdb.sds" name="lastdb.sds"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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185 <extra_files type="file" value="hedgdb.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/>
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186 <extra_files type="file" value="hedgdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/>
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187 <extra_files type="file" value="hedgdb.tis" name="lastdb.tis" compare="sim_size" delta="1"/>
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188 </output>
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189 </test>
2
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190 <test>
4
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191 <param name="input_files" value="humanMito.fq.gz" ftype="fastqsanger.gz"/>
2
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192 <section name="lastdb">
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193 <param name="Q" value="1"/>
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194 <section name="repeats">
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195 <param name="uppercase" value="0"/>
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196 <param name="simple_repeat" value="1"/>
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197 <param name="sm_lower" value="true"/>
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198 </section>
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199 </section>
5
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200 <output name="outfile" compare="contains" file="humdb-sanger.lastdb" ftype="lastdb">
2
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201 <extra_files type="file" value="humdb-sanger.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
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202 <extra_files type="file" value="humdb-sanger.des" name="lastdb.des"/>
4
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203 <extra_files type="file" value="humdb-sanger.prj" name="lastdb.prj" lines_diff="2"/>
2
bf30030e5265 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db"
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204 <extra_files type="file" value="humdb-sanger.sds" name="lastdb.sds"/>
bf30030e5265 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db"
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205 <extra_files type="file" value="humdb-sanger.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/>
bf30030e5265 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db"
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206 <extra_files type="file" value="humdb-sanger.suf" name="lastdb.suf" compare="sim_size" delta="1"/>
bf30030e5265 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db"
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207 <extra_files type="file" value="humdb-sanger.tis" name="lastdb.tis" compare="sim_size" delta="1"/>
bf30030e5265 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db"
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208 </output>
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209 </test>
0
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210 </tests>
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211
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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212 <help>@LAST_HELP@</help>
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213 <citations><expand macro="citations"/></citations>
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214 </tool>