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annotate macros.xml @ 1:f5d2f8a27477 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit b6c674376eade4fdf9ffb31380f6689ede84a091"
author iuc
date Wed, 08 Jan 2020 18:01:18 +0000
parents 2feaf3d2805b
children 3b5e95687bd2
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2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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1 <macros>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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2 <token name="@VERSION@">5.0.3</token>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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3 <xml name="requirements">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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4 <requirements>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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5 <requirement type="package" version="@VERSION@">cat</requirement>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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6 <yield/>
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7 </requirements>
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8 </xml>
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9 <xml name="version_command">
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10 <version_command><![CDATA[CAT --version]]></version_command>
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11 </xml>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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12 <token name="@DATABASE_FOLDER@">CAT_database</token>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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13 <token name="@TAXONOMY_FOLDER@">taxonomy</token>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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14 <xml name="cat_db">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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15 <conditional name="db">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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16 <param name="db_src" type="select" label="CAT database (--database_folder,--taxonomy_folder) from">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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17 <option value="cached">local cached database</option>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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18 <option value="history">history</option>
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19 </param>
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20 <when value="cached">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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21 <param name="cat_builtin" type="select" label="Use a built-in CAT database" help="If the CAT database of interest is not listed, contact your Galaxy administrator">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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22 <options from_data_table="cat_database">
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23 <filter type="sort_by" column="2" />
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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24 <validator type="no_options" message="No CAT database is available." />
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25 </options>
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26 </param>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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27 </when>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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28 <when value="history">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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29 <param name="cat_db" type="data" format="txt" label="A history dataset from CAT prepare tool"/>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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30 </when>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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31 </conditional>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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32 </xml>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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33 <token name="@CAT_DB@"><![CDATA[
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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34 #if $db.db_src == 'cached':
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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35 --database_folder '$db.cat_builtin.fields.database_folder'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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36 --taxonomy_folder '$db.cat_builtin.fields.taxonomy_folder'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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37 #else
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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38 #import os.path
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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39 #set $catdb = $db.cat_db.extra_files_path
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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40 --database_folder '$os.path.join($catdb,"@DATABASE_FOLDER@")'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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41 --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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42 #end if
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43 ]]></token>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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44 <token name="@CAT_TAXONOMY@"><![CDATA[
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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45 #if $db.db_src == 'cached':
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46 --taxonomy_folder '$db.cat_builtin.fields.taxonomy_folder'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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47 #else
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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48 #import os.path
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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49 #set $catdb = $db.cat_db.extra_files_path
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50 --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")'
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51 #end if
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52 ]]></token>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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53 <xml name="test_catdb">
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54 <conditional name="db">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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55 <param name="db_src" value="cached"/>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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56 <param name="cat_builtin" value="CAT_prepare_test"/>
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57 </conditional>
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58 </xml>
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59 <xml name="use_intermediates">
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60 <conditional name="previous">
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61 <param name="use_previous" type="select" label="Use previous prodigal gene prediction and diamond alignment">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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62 <help>predicted_proteins.faa and alignment.diamond from previous CAT run.</help>
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63 <option value="yes">Yes</option>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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64 <option value="no" selected="true">No</option>
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65 </param>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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66 <when value="yes">
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67 <param argument="--proteins_fasta" type="data" format="fasta" label="prodigal predicted proteins fasta"/>
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68 <param argument="--diamond_alignment" type="data" format="tabular" label="alignment.diamond file"/>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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69 </when>
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70 <when value="no"/>
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71 </conditional>
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72 </xml>
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73 <token name="@USE_INTERMEDIATES@"><![CDATA[
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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74 #if $previous.use_previous == 'yes'
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75 --proteins_fasta '$previous.proteins_fasta'
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76 --diamond_alignment '$previous.diamond_alignment'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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77 #end if
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78 --out_prefix 'cat_output'
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79 ]]></token>
1
f5d2f8a27477 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit b6c674376eade4fdf9ffb31380f6689ede84a091"
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80 <xml name="custom_settings_bins">
f5d2f8a27477 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit b6c674376eade4fdf9ffb31380f6689ede84a091"
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81 <param argument="--range" type="integer" value="5" min="0" max="49" label="range"/>
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82 <param argument="--fraction" type="float" value="0.3" min="0" max="0.99" label="fraction"/>
f5d2f8a27477 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit b6c674376eade4fdf9ffb31380f6689ede84a091"
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83 </xml>
f5d2f8a27477 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit b6c674376eade4fdf9ffb31380f6689ede84a091"
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84 <xml name="custom_settings_contigs">
0
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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85 <param argument="--range" type="integer" value="10" min="0" max="49" label="range"/>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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86 <param argument="--fraction" type="float" value="0.5" min="0" max="0.99" label="fraction"/>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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87 </xml>
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88 <token name="@CUSTOM_SETTINGS@"><![CDATA[
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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89 --range '$range'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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90 --fraction '$fraction'
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91 ]]></token>
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92 <xml name="diamond_options">
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93 <conditional name="diamond">
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94 <param name="set_diamond_opts" type="select" label="Set advanced diamond options">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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95 <option value="yes">Yes</option>
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96 <option value="no" selected="true">No</option>
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97 </param>
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98 <when value="yes">
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99 <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false"
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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100 label="Run DIAMOND in sensitive mode (considerably slower)"/>
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101 <param argument="--block_size" type="float" value="2.0" min="1" max="10" label="DIAMOND block-size parameter."
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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102 help="lower will decrease memory and temporary disk space usage, higher will increase performance."/>
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103 <param argument="--index_chunks" type="integer" value="4" min="1" max="10" label="DIAMOND index-chunks parameter"
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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104 help="Set to 1 on high memory machines. The parameter has no effect on temporary disk space usage."/>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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105 <param argument="--top" type="integer" value="50" min="1" max="50" label="DIAMOND top parameter"
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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106 help="Governs hits within range of best hit that are written to the alignment file. This implies you know what you are doing."/>
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107 </when>
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108 <when value="no"/>
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109 </conditional>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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110 </xml>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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111 <token name="@DIAMOND_OPTIONS@"><![CDATA[
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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112 #if $diamond.set_diamond_opts == 'yes':
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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113 $diamond.sensitive
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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114 --block_size '$diamond.block_size'
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115 --index_chunks '$diamond.index_chunks'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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116 #if $diamond.top < 50:
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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117 --I_know_what_Im_doing
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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118 --top '$diamond.top'
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119 #end if
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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120 #end if
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121 ]]></token>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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122
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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123 <xml name="add_names_options">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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124 <param argument="--only_official" type="boolean" truevalue="--only_official" falsevalue="" checked="true"
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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125 label="Only output official level names."/>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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126 <param argument="--exclude_scores" type="boolean" truevalue="--exclude_scores" falsevalue="" checked="false"
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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127 label="Exclude bit-score support scores in the lineage."/>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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128 </xml>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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129 <token name="@ADD_NAMES_OPTIONS@"><![CDATA[
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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130 $only_official $exclude_scores
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131 ]]></token>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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132 <xml name="add_names">
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133 <conditional name="names">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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134 <param name="add_names" type="select" label="CAT add_names for"
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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135 help="annotate with taxonomic names.">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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136 <option value="no">No</option>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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137 <option value="orf2lca">ORF2LCA.names.txt</option>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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138 <option value="classification">classification.names.txt</option>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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139 <option value="both">ORF2LCA.names.txt and classification.names.txt</option>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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140 </param>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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141 <when value="no"/>
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142 <when value="orf2lca">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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143 <expand macro="add_names_options"/>
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144 </when>
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145 <when value="classification">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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146 <expand macro="add_names_options"/>
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147 </when>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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148 <when value="both">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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149 <expand macro="add_names_options"/>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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150 </when>
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151 </conditional>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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152 </xml>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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153 <token name="@TXT2TSV@">${__tool_directory__}/tabpad.py</token>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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154 <token name="@ADD_NAMES@"><![CDATA[
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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155 #if $names.add_names in ['classification','both']:
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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156 && CAT add_names $names.only_official $names.exclude_scores
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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157 @CAT_TAXONOMY@
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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158 #if $bcat == 'CAT'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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159 -i 'cat_output.contig2classification.tsv'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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160 #else
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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161 -i 'cat_output.bin2classification.tsv'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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162 #end if
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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163 -o 'classification_names.txt'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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164 && ${__tool_directory__}/tabpad.py -i 'classification_names.txt' -o '$classification_names'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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165 #end if
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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166 #if $names.add_names in ['orf2lca','both']:
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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167 && CAT add_names $names.only_official $names.exclude_scores
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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168 @CAT_TAXONOMY@
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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169 -i 'cat_output.ORF2LCA.tsv'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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170 -o 'orf2lca_names.txt'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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171 && ${__tool_directory__}/tabpad.py -i 'orf2lca_names.txt' -o '$orf2lca_names'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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172 #end if
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173 ]]></token>
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174 <xml name="summarise">
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175 <param name="summarise" type="select" label="CAT summarise report"
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176 help="Report the number of assignments to each taxonomic name">
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177 <option value="no">No</option>
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178 <option value="classification">classification.summary.txt</option>
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179 </param>
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180 </xml>
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181 <token name="@SUMMARISE@"><![CDATA[
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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182 #if $summarise in ['classification']:
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183 #if $names.add_names in ['classification','both'] and $names.only_official:
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184 #set $summary_input = $classification_names
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185 #else
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186 #set $summary_input = 'classification_offical_names'
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187 && CAT add_names --only_official
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188 @CAT_TAXONOMY@
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189 #if $bcat == 'CAT'
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190 -i 'cat_output.contig2classification.tsv'
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191 #else
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192 -i 'cat_output.bin2classification.tsv'
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193 #end if
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194 -o '$summary_input'
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195 #end if
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196 && CAT summarise
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197 #if $bcat == 'CAT'
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198 -c '$contigs_fasta'
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199 #end if
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200 -i '$summary_input'
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201 -o 'classification_summary.txt'
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202 && ${__tool_directory__}/tabpad.py -i 'classification_summary.txt' -o '$classification_summary'
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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203 #end if
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204 ]]></token>
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205
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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206 <xml name="select_outputs">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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207 <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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208 <option value="log" selected="true">log</option>
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209 <option value="predicted_proteins_faa" selected="true">Prodigal predicted_proteins.faa</option>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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210 <option value="predicted_proteins_gff">Prodigal predicted_proteins.gff</option>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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211 <option value="alignment_diamond">Diamond blastp alignment.diamond</option>
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212 <option value="orf2lca" selected="true">ORF2LCA.txt (taxonomic assignment per predicted ORF)</option>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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213 <yield/>
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214 </param>
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215 </xml>
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216 <xml name="select_cat_outputs">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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217 <param name="bcat" type="hidden" value="CAT"/>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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218 <param name="seqtype" type="hidden" value="contig"/>
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219 <param name="sum_titles" type="hidden" value="contigs,number of ORFs,number of positions"/>
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220 <param name="bin_col" type="hidden" value=""/>
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221 <expand macro="select_outputs">
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222 <option value="contig2classification" selected="true">contig2classification.txt (taxonomic assignment per contig)</option>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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223 </expand>
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224 </xml>
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225 <xml name="select_bat_outputs">
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226 <param name="bcat" type="hidden" value="BAT"/>
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227 <param name="seqtype" type="hidden" value="bin"/>
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228 <param name="sum_titles" type="hidden" value="bins"/>
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229 <param name="bin_col" type="hidden" value="bin,"/>
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230 <expand macro="select_outputs">
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231 <option value="bin2classification" selected="true">bin2classification.txt (taxonomic assignment per metagenome assembly)</option>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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232 </expand>
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233 </xml>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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234 <xml name="outputs">
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235 <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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236 <filter>'log' in select_outputs or not select_outputs</filter>
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237 </data>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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238 <data name="predicted_proteins_faa" format="fasta" label="${bcat}.predicted_proteins.faa" from_work_dir="cat_output.predicted_proteins.faa">
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239 <filter>'predicted_proteins_faa' in select_outputs and previous['use_previous'] == 'no'</filter>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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240 </data>
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241 <data name="predicted_proteins_gff" format="gff" label="${bcat}.predicted_proteins.gff" from_work_dir="cat_output.predicted_proteins.gff">
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242 <filter>'predicted_proteins_gff' in select_outputs and previous['use_previous'] == 'no'</filter>
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243 </data>
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244 <data name="alignment_diamond" format="tabular" label="${bcat}.alignment.diamond" from_work_dir="cat_output.alignment.diamond">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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245 <filter>'alignment_diamond' in select_outputs and previous['use_previous'] == 'no'</filter>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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246 <actions>
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247 <action name="comment_lines" type="metadata" default="1" />
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248 <action name="column_names" type="metadata" default="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" />
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249 </actions>
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250 </data>
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251 <data name="orf2lca" format="tabular" label="${bcat}.ORF2LCA.txt" from_work_dir="cat_output.ORF2LCA.tsv">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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252 <filter>'orf2lca' in select_outputs</filter>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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253 <actions>
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254 <action name="comment_lines" type="metadata" default="1" />
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255 <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score" />
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256 </actions>
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257 </data>
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258 <data name="contig2classification" format="tabular" label="${bcat}.contig2classification.txt" from_work_dir="cat_output.contig2classification.tsv">
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259 <filter>'contig2classification' in select_outputs</filter>
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260 <actions>
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261 <action name="comment_lines" type="metadata" default="1" />
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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262 <action name="column_names" type="metadata" default="contig,classification,reason,lineage,lineage scores" />
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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263 </actions>
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264 </data>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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265 <data name="bin2classification" format="tabular" label="${bcat}.bin2classification.txt" from_work_dir="cat_output.bin2classification.tsv">
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266 <filter>'bin2classification' in select_outputs</filter>
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267 <actions>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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268 <action name="comment_lines" type="metadata" default="1" />
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269 <action name="column_names" type="metadata" default="bin,classification,reason,lineage,lineage scores" />
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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270 </actions>
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271 </data>
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272 <data name="orf2lca_names" format="tabular" label="${bcat}.ORF2LCA.names.txt">
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273 <filter>names['add_names'] in ['both','orf2lca']</filter>
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274 <actions>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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275 <action name="comment_lines" type="metadata" default="1" />
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276 <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score,superkingdom,phylum,class,order,family,genus,species" />
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277 </actions>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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278 </data>
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279 <data name="classification_names" format="tabular" label="${bcat}.${seqtype}2classification.names.txt">
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280 <filter>names['add_names'] in ['both','classification']</filter>
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281 <actions>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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282 <action name="comment_lines" type="metadata" default="1" />
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283 <action name="column_names" type="metadata" default="${seqtype},classification,reason,lineage,lineage scores,superkingdom,phylum,class,order,family,genus,species" />
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284 </actions>
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285 </data>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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286 <data name="classification_summary" format="tabular" label="${bcat}.${seqtype}2classification.summary.txt">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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287 <filter>'classification' in summarise</filter>
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288 <actions>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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289 <action name="comment_lines" type="metadata" default="4" />
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290 <action name="column_names" type="metadata" default="rank,clade,number of ${sum_titles}" />
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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291 </actions>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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292 </data>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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293 </xml>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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294 <token name="@COMMON_HELP@"><![CDATA[
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295 The Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) workflows are described at: https://github.com/dutilh/CAT
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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296
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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297 - CAT contigs/CAT bins - runs Prodigal_ prokaryotic protein prediction on the fasta input.
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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298 - CAT contigs/CAT bins - runs Diamond_ to align predicted proteins to the reference proteins in the CAT database.
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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299 - CAT contigs/CAT bins - assigns taxonomic classification to fasta entries and ORFs based on alignments.
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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300 - CAT add_names - annotates outputs with taxonomic names.
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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301 - CAT summerise - reports number of assignments to each taxonomic name.
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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302
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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303 A CAT database can either be installed by data_manager_cat or in the local history by CAT prepare tool.
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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304
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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305 .. _Prodigal: https://github.com/hyattpd/Prodigal
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306 .. _Diamond: https://github.com/bbuchfink/diamond
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307
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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308 ]]></token>
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309 <token name="@OUTPUTS_HELP@"><![CDATA[
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310
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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311 **OUTPUTS**
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312
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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313 Any of the files produced by the CAT workflow are available as outputs
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314 - Prodigal
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315
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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316 - predicted_proteins.faa
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317 - predicted_proteins.gff
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318
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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319 - Diamond
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320
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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321 - alignment.diamond
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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322
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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323 - CAT contigs/bins
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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324
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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325 - contigs/bin2classification.txt
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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326 - ORF2LCA.txt
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327
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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328 - CAT add_names (optional)
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329
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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330 - contigs/bin2classification.names.txt
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331 - ORF2LCA.names.txt
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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332
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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333 - CAT summarise (optional)
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334
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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335 - contigs/bin2classification.summary.txt
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336
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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337
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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338 ]]></token>
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339
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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340 <token name="@OPTIONS_HELP@"><![CDATA[
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341
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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342 Optional arguments:
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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343 -r, --range cut-off range after alignment [0-49] (default: 10).
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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344 -f, --fraction fraction of bit-score support for each classification
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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345 [0-0.99] (default: 0.5).
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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346 -p, --proteins_fasta
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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347 Path to predicted proteins fasta file. If supplied,
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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348 CAT will skip the protein prediction step.
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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349 -a, --diamond_alignment
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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350 Path to DIAMOND alignment table. If supplied, CAT will
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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351 skip the DIAMOND alignment step and directly classify
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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352 the sequences. A predicted proteins fasta file should
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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353 also be supplied with argument [-p / --proteins].
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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354
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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355
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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356 DIAMOND specific optional arguments:
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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357 --sensitive Run DIAMOND in sensitive mode (default: not enabled).
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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358
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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359 --block_size DIAMOND block-size parameter (default: 2.0). Lower
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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360 numbers will decrease memory and temporary disk space
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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361 usage.
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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362
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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363 --index_chunks
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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364 DIAMOND index-chunks parameter (default: 4). Set to 1
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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365 on high memory machines. The parameter has no effect
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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366 on temporary disk space usage.
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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367
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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368 --top
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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369 DIAMOND top parameter [0-50] (default: 50). Governs
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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370 hits within range of best hit that are written to the
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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371 alignment file. This is not the [-r / --range]
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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372 parameter!
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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373
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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374
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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375 Setting the DIAMOND --top parameter
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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376
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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377 You can speed up DIAMOND considerably, and at the same time greatly reduce disk usage, by setting the DIAMOND --top parameter to lower values. This will govern hits within range of the best hit that are written to the alignment file.
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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378
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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379 You have to be very carefull to 1) not confuse this parameter with the r / --range parameter, which does a similar cut-off but after alignment and 2) be aware that if you want to run CAT or BAT again afterwards with different values of the -r / --range parameter, your options will be limited to the range you have chosen with --top earlier, because all hits that fall outside this range will not be included in the alignment file. Importantly, CAT and BAT currently do not warn you if you choose -r / --range in a second run higher than --top in a previous one, so it's up to you to remember this!
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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380
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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381 If you have understood all this, or you do not plan to tune -r / --range at all afterwards, you can enjoy a huge speedup with much smaller alignment files! For CAT you can for example set --top 11 and for BAT --top 6.
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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382
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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383 ]]></token>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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384 <xml name="citations">
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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385 <citations>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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386 <citation type="doi">https://doi.org/10.1101/072868</citation>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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387 <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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388 <citation type="doi">https://doi.org/10.1038/nmeth.3176</citation>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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389 <citation type="doi">https://doi.org/10.1186/1471-2105-11-119</citation>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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390 <yield />
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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391 </citations>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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392 </xml>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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393 </macros>