Mercurial > repos > iuc > spaln

annotate list_spaln_tables.xml @ 1:37b5e1f0b544 draft

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"planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
author iuc
date Thu, 16 Jul 2020 07:57:10 -0400
parents
children dd0cd2319ae5
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1 <tool id="list_spaln_tables" name="List spaln parameter tables" version="@TOOL_VERSION@+galaxy0">
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2 <description>Given a query species, list the spaln settings tables that exist, from closest related species to most different</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="3.8">python</requirement>
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8 <requirement type="package" version="@TOOL_VERSION@">spaln</requirement>
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9 <requirement type="package" version="1.0.7">rust-ncbitaxonomy</requirement>
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10 </requirements>
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11 <command detect_errors="aggressive"><![CDATA[
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12 #if $gnm2tab.gnm2tab_source == "spaln_tool"
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13 SPALN_LOCATION=\$(dirname \$(dirname \$(which spaln))) &&
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14 GNM2TAB_PATH="\$SPALN_LOCATION/share/spaln/table/gnm2tab" &&
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15 if [[ -f "\$GNM2TAB_PATH" ]] ; then
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16 ln -s "\$GNM2TAB_PATH" gnm2tab ;
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17 else
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18 echo "Cannot find builtin gnm2tab file \$SPALN_LOCATION : \$GNM2TAB_PATH" >&2 ; exit 1 ;
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19 fi &&
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20 #else
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21 ln -s '${gnm2tab.gnm2tab_file}' gnm2tab &&
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22 #end if
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23 #if $taxonomy.taxonomy_source == "cached"
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24 ln -s '${taxonomy.taxonomy_sqlite_table.fields.path}/tax.ncbitaxonomy.sqlite' tax.ncbitaxonomy.sqlite &&
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25 #else
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26 ln -s '${taxonomy.taxonomy_sqlite_file}' tax.ncbitaxonomy.sqlite &&
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27 #end if
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28 python '${__tool_directory__}/list_spaln_tables.py' --taxonomy_db tax.ncbitaxonomy.sqlite --gnm2tab_file gnm2tab '$taxon' | sort -k1n > '${output}'
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29 ]]></command>
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30 <inputs>
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31 <param name="taxon" label="Scientific name" type="text" />
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32 <conditional name="gnm2tab">
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33 <param name="gnm2tab_source" type="select" label="Choose source of gnm2tab file">
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34 <option value="spaln_tool" selected="true">From the spaln tool installation</option>
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35 <option value="history">From dataset in history</option>
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36 </param>
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37 <when value="spaln_tool" />
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38 <when value="history">
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39 <param name="gnm2tab_file" type="data" format="tabular" label="gnm2tab file from spaln" help="The gnm2tab file should be from the table directory of spaln v. @TOOL_VERSION@" />
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40 </when>
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41 </conditional>
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42 <conditional name="taxonomy">
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43 <param type="select" name="taxonomy_source">
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44 <option value="cached" selected="true">Use built-in NCBI Taxonomy SQLite database</option>
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45 <option value="history">Use NCBI Taxonomy SQLite database from history</option>
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46 </param>
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47 <when value="cached">
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48 <param type="select" name="taxonomy_sqlite_table" label="NCBI Taxonomy SQLite database">
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49 <options from_data_table="ncbi_taxonomy_sqlite">
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50 <filter type="sort_by" column="1" />
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51 <validator type="no_options" message="No NCBI Taxonomy SQLite database is available" />
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52 </options>
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53 </param>
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54 </when>
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55 <when value="history">
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56 <param name="taxonomy_sqlite_file" type="data" format="sqlite" label="NCBI Taxonomy SQLite database" />
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57 </when>
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58 </conditional>
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59 </inputs>
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60 <outputs>
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61 <data name="output" format="tabular">
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62 <actions>
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63 <action name="column_names" type="metadata" default="dist_all,dist_canonical,common_ancestor,species_code,settings_group,scientific_name" />
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64 </actions>
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65 </data>
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66 </outputs>
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67
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68 <tests>
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69 <test>
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70 <param name="taxon" value="Lates calcarifer" />
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71 <conditional name="gnm2tab">
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72 <param name="gnm2tab_source" value="spaln_tool" />
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73 </conditional>
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74 <conditional name="taxonomy">
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75 <param name="taxonomy_source" value="history" />
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76 <param name="taxonomy_sqlite_file" ftype="sqlite" value="sqlite_taxdb/tax.ncbitaxonomy.sqlite" />
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77 </conditional>
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78 <output name="output">
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79 <assert_contents>
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80 <has_line_matching expression="5\t4\tActinopteri\tcynosemi\tFish_mdl\tCynoglossus semilaevis" />
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81 <has_line_matching expression="30\t7\tEukaryota\tzea_mays\tMagnolio\tZea mays" />
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82 </assert_contents>
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83 </output>
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84 </test>
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85 <test>
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86 <param name="taxon" value="Lates calcarifer" />
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87 <conditional name="gnm2tab">
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88 <param name="gnm2tab_source" value="spaln_tool" />
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89 </conditional>
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90 <conditional name="taxonomy">
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91 <param name="taxonomy_source" value="cached" />
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92 <param name="taxonomy_sqlite_table" value="sample" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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93 </conditional>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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94 <output name="output">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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95 <assert_contents>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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96 <has_line_matching expression="5\t4\tActinopteri\tcynosemi\tFish_mdl\tCynoglossus semilaevis" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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97 <has_line_matching expression="30\t7\tEukaryota\tzea_mays\tMagnolio\tZea mays" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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98 </assert_contents>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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99 </output>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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100 </test>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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101 <test>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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102 <param name="taxon" value="Lates calcarifer" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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103 <conditional name="gnm2tab">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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104 <param name="gnm2tab_source" value="history" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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105 <param name="gnm2tab_file" ftype="tabular" value="gnm2tab" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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106 </conditional>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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107 <conditional name="taxonomy">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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108 <param name="taxonomy_source" value="cached" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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109 <param name="taxonomy_sqlite_table" value="sample" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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110 </conditional>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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111 <output name="output">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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112 <assert_contents>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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113 <has_line_matching expression="5\t4\tActinopteri\tcynosemi\tFish_mdl\tCynoglossus semilaevis" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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114 <has_line_matching expression="30\t7\tEukaryota\tzea_mays\tMagnolio\tZea mays" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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115 </assert_contents>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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116 </output>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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117 </test>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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118 </tests>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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119 <help><![CDATA[
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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120 Spaln has a number of pre-computed settings files to tune its predictions for different species. These
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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121 are listed in a file named gnm2tab_ in the package. This tool uses the NCBI Taxonomy database to search
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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122 that able for a suitable (i.e. taxonomically close) set of settings for optimising spaln's alignment
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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123 predictions.
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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124
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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125 Input is the scientific name of a species (as reflected in the NCBI Taxonomy DB), output is
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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126 information from the gnm2tab file sorted by taxonomic distance from the query species.
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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127
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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128 .. _gnm2tab: https://github.com/ogotoh/spaln/blob/master/table/gnm2tab
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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129 ]]></help>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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130 <citations>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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131 </citations>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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132 </tool>