Mercurial > repos > jjohnson > contig_annotation_tool
annotate macros.xml @ 4:aaeb63501369 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit ec15da3a30507841856303de991cbe80c65128fd-dirty
author | jjohnson |
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date | Wed, 27 Nov 2019 10:27:23 -0500 |
parents | 18ece3d5bcde |
children | 226949352e31 |
rev | line source |
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0
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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1 <macros> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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2 <token name="@VERSION@">5.0.3</token> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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3 <xml name="requirements"> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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4 <requirements> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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5 <requirement type="package" version="@VERSION@">cat</requirement> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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6 <yield/> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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7 </requirements> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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8 </xml> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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9 <xml name="version_command"> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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10 <version_command>CAT --version</version_command> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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11 </xml> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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12 <token name="@DATABASE_FOLDER@">CAT_database</token> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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13 <token name="@TAXONOMY_FOLDER@">taxonomy</token> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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14 <xml name="cat_db"> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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15 <conditional name="db"> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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16 <param name="db_src" type="select" label="CAT database from"> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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17 <option value="cached">local cached database</option> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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18 <option value="history">history</option> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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19 </param> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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20 <when value="cached"> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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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"> |
3
18ece3d5bcde
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 3febcc9ba3d3717877c36bf96742209012a13ac4-dirty
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22 <options from_data_table="cat_database"> |
0
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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23 <filter type="sort_by" column="2" /> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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24 <validator type="no_options" message="No CAT database is available." /> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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25 </options> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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26 </param> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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27 </when> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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28 <when value="history"> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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29 <param name="cat_db" type="data" format="txt" label="A history dataset from CAT prepare tool"/> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
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30 </when> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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31 </conditional> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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32 </xml> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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33 <token name="@CAT_DB@"><![CDATA[ |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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34 #if $db.db_src == 'cached': |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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35 --database_folder $db.cat_builtin.fields.database_folder |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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36 --taxonomy_folder $db.cat_builtin.fields.taxonomy_folder |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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37 #else |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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38 #import os.path |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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39 #set $catdb = $db.cat_db.extra_files_path |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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40 --database_folder '$os.path.join($catdb,"@DATABASE_FOLDER@")' |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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41 --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")' |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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42 #end if |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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43 ]]></token> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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44 <token name="@CAT_TAXONOMY@"><![CDATA[ |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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45 #if $db.db_src == 'cached': |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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46 --taxonomy_folder $db.cat_builtin.fields.taxonomy_folder |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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47 #else |
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48 #import os.path |
ad7507073c3f
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49 #set $catdb = $db.cat_db.extra_files_path |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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50 --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")' |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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51 #end if |
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52 ]]></token> |
ad7507073c3f
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53 <xml name="test_catdb"> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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54 <conditional name="db"> |
ad7507073c3f
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55 <param name="db_src" value="cached"/> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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56 <param name="cat_builtin" value="CAT_prepare_test"/> |
ad7507073c3f
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57 </conditional> |
ad7507073c3f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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58 </xml> |
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59 <xml name="use_intermediates"> |
ad7507073c3f
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60 <conditional name="previous"> |
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61 <param name="use_previous" type="select" label="Use previous gene prediction and diamond alignment"> |
ad7507073c3f
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62 <option value="no">No</option> |
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63 <option value="yes">Yes</option> |
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64 </param> |
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65 <when value="no"/> |
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66 <when value="yes"> |
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67 <param argument="--proteins_fasta" type="data" format="fasta" label="predicted proteins fasta"/> |
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68 <param argument="--diamond_alignment" type="data" format="fasta" label="alignments file"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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69 </when> |
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70 </conditional> |
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71 </xml> |
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72 <token name="@USE_INTERMEDIATES@"><![CDATA[ |
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73 #if $previous.use_previous == 'yes' |
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74 --proteins_fasta '$previous.proteins_fasta' |
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75 --diamond_alignment '$previous.diamond_alignment' |
ad7507073c3f
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76 #end if |
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77 --out_prefix 'cat_output' |
ad7507073c3f
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78 ]]></token> |
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79 <xml name="custom_settings"> |
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80 <param argument="--range" type="integer" value="10" min="0" max="49" label="range"/> |
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81 <param argument="--fraction" type="float" value="0.5" min="0" max="0.99" label="fraction"/> |
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82 </xml> |
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83 <token name="@CUSTOM_SETTINGS@"><![CDATA[ |
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84 --range $range |
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85 --fraction $fraction |
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86 ]]></token> |
4
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87 <xml name="diamond_options"> |
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88 <conditional name="diamond"> |
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89 <param name="set_diamond_opts" type="select" label="Advanced diamond options"> |
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90 <option value="no">No</option> |
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91 <option value="yes">Yes</option> |
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92 </param> |
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93 <when value="no"/> |
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94 <when value="yes"> |
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95 <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" |
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96 label="Run DIAMOND in sensitive mode (considerably slower)"/> |
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97 <param argument="--block_size" type="float" value="2.0" min="1" max="10" label="DIAMOND block-size parameter." |
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98 help="lower will decrease memory and temporary disk space usage, higher will increase performance."/> |
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99 <param argument="--index_chunks" type="integer" value="4" min="1" max="10" label="DIAMOND index-chunks parameter" |
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100 help="Set to 1 on high memory machines. The parameter has no effect on temporary disk space usage."/> |
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101 <param argument="--top" type="integer" value="50" min="1" max="50" label="DIAMOND top parameter" |
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102 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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103 </when> |
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104 </conditional> |
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105 </xml> |
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106 <token name="@DIAMOND_OPTIONS@"><![CDATA[ |
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107 #if $diamond.set_diamond_opts == 'yes': |
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108 $diamond.sensitive |
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109 --block_size $diamond.block_size |
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110 --index_chunks $diamond.index_chunks |
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111 #if $diamond.top < 50: |
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112 --I_know_what_Im_doing |
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113 --top $diamond.top |
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114 #end if |
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115 #end if |
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116 ]]></token> |
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117 |
0
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118 <xml name="add_names_options"> |
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119 <param argument="--only_official" type="boolean" truevalue="--only_official" falsevalue="" checked="true" |
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120 label="Only output official level names."/> |
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121 <param argument="--exclude_scores" type="boolean" truevalue="--exclude_scores" falsevalue="" checked="false" |
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122 label="Exclude bit-score support scores in the lineage."/> |
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123 </xml> |
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124 <token name="@ADD_NAMES_OPTIONS@"><![CDATA[ |
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125 $only_official $exclude_scores |
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126 ]]></token> |
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127 <xml name="add_names"> |
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128 <conditional name="names"> |
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129 <param name="add_names" type="select" label="add_names"> |
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130 <option value="no">No</option> |
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131 <option value="orf2lca">ORF2LCA.txt</option> |
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132 <option value="classification">classification.txt</option> |
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133 <option value="both">ORF2LCA.txt and classification.txt</option> |
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134 </param> |
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135 <when value="no"/> |
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136 <when value="orf2lca"> |
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137 <expand macro="add_names_options"/> |
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138 </when> |
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139 <when value="classification"> |
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140 <expand macro="add_names_options"/> |
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141 </when> |
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142 <when value="both"> |
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143 <expand macro="add_names_options"/> |
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144 </when> |
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145 </conditional> |
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146 </xml> |
3
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147 <token name="@TXT2TSV@">${__tool_directory__}/tabpad.py</token> |
0
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148 <token name="@ADD_NAMES@"><![CDATA[ |
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149 #if $names.add_names in ['classification','both']: |
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150 && CAT add_names $names.only_official $names.exclude_scores |
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151 @CAT_TAXONOMY@ |
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152 #if $bcat == 'CAT' |
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153 -i cat_output.contig2classification.tsv |
0
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154 #else |
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155 -i cat_output.bin2classification.tsv |
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156 #end if |
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157 -o classification_names.txt |
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158 && ${__tool_directory__}/tabpad.py -i classification_names.txt -o $classification_names |
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159 #end if |
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160 #if $names.add_names in ['orf2lca','both']: |
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161 && CAT add_names $names.only_official $names.exclude_scores |
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162 @CAT_TAXONOMY@ |
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163 -i cat_output.ORF2LCA.tsv |
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164 -o orf2lca_names.txt |
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165 && ${__tool_directory__}/tabpad.py -i orf2lca_names.txt -o $orf2lca_names |
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166 #end if |
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167 ]]></token> |
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168 <xml name="summarise"> |
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169 <param name="summarise" type="select" label="summarise"> |
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170 <option value="no">No</option> |
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171 <option value="classification">classification.txt</option> |
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172 </param> |
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173 </xml> |
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174 <token name="@SUMMARISE@"><![CDATA[ |
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175 #if $summarise in ['classification']: |
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176 #if $names.add_names in ['classification','both'] and $names.only_official: |
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177 #set $summary_input = $classification_names |
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178 #else |
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179 #set $summary_input = 'classification_offical_names' |
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180 && CAT add_names --only_official |
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181 @CAT_TAXONOMY@ |
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182 #if $bcat == 'CAT' |
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183 -i cat_output.contig2classification.tsv |
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184 #else |
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185 -i cat_output.bin2classification.tsv |
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186 #end if |
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187 -o $summary_input |
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188 #end if |
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189 && CAT summarise |
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190 #if $bcat == 'CAT' |
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191 -c $contigs_fasta |
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192 #end if |
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193 -i $summary_input |
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194 -o classification_summary.txt |
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195 && ${__tool_directory__}/tabpad.py -i classification_summary.txt -o $classification_summary |
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196 #end if |
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197 ]]></token> |
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198 |
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199 <xml name="select_outputs"> |
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200 <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs"> |
2
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201 <option value="log" selected="true">log</option> |
0
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202 <option value="predicted_proteins_faa" selected="true">predicted_proteins.faa</option> |
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203 <option value="predicted_proteins_gff">predicted_proteins.gff</option> |
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204 <option value="alignment_diamond">alignment.diamond</option> |
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205 <option value="orf2lca" selected="true">ORF2LCA.txt</option> |
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206 <yield/> |
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207 </param> |
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208 </xml> |
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209 <xml name="select_cat_outputs"> |
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210 <param name="bcat" type="hidden" value="CAT"/> |
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211 <param name="seqtype" type="hidden" value="contig"/> |
2
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212 <param name="sum_titles" type="hidden" value="contigs,number of ORFs,number of positions"/> |
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213 <param name="bin_col" type="hidden" value=""/> |
0
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214 <expand macro="select_outputs"> |
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215 <option value="contig2classification" selected="true">contig2classification.txt</option> |
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216 </expand> |
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217 </xml> |
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218 <xml name="select_bat_outputs"> |
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219 <param name="bcat" type="hidden" value="BAT"/> |
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220 <param name="seqtype" type="hidden" value="bin"/> |
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221 <param name="sum_titles" type="hidden" value="bins"/> |
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222 <param name="bin_col" type="hidden" value="bin,"/> |
0
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223 <expand macro="select_outputs"> |
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224 <option value="bin2classification" selected="true">bin2classification.txt</option> |
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225 </expand> |
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226 </xml> |
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227 <xml name="outputs"> |
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228 <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log"> |
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229 <filter>'log' in select_outputs or not select_outputs</filter> |
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230 </data> |
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231 <data name="predicted_proteins_faa" format="fasta" label="${bcat}.predicted_proteins.faa" from_work_dir="cat_output.predicted_proteins.faa"> |
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232 <filter>'predicted_proteins_faa' in select_outputs</filter> |
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233 </data> |
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234 <data name="predicted_proteins_gff" format="gff" label="${bcat}.predicted_proteins.gff" from_work_dir="cat_output.predicted_proteins.gff"> |
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235 <filter>'predicted_proteins_gff' in select_outputs</filter> |
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236 </data> |
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237 <data name="alignment_diamond" format="tabular" label="${bcat}.alignment.diamond" from_work_dir="cat_output.alignment.diamond"> |
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238 <filter>'alignment_diamond' in select_outputs</filter> |
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239 <actions> |
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240 <action name="comment_lines" type="metadata" default="1" /> |
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241 <action name="column_names" type="metadata" default="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" /> |
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242 </actions> |
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243 </data> |
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244 <data name="orf2lca" format="tabular" label="${bcat}.ORF2LCA.txt" from_work_dir="cat_output.ORF2LCA.tsv"> |
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245 <filter>'orf2lca' in select_outputs</filter> |
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246 <actions> |
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247 <action name="comment_lines" type="metadata" default="1" /> |
2
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248 <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score" /> |
0
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249 </actions> |
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250 </data> |
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251 <data name="contig2classification" format="tabular" label="${bcat}.contig2classification.txt" from_work_dir="cat_output.contig2classification.tsv"> |
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252 <filter>'contig2classification' in select_outputs</filter> |
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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="contig,classification,reason,lineage,lineage scores" /> |
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256 </actions> |
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257 </data> |
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258 <data name="bin2classification" format="tabular" label="${bcat}.bin2classification.txt" from_work_dir="cat_output.bin2classification.tsv"> |
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259 <filter>'bin2classification' in select_outputs</filter> |
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260 <actions> |
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261 <action name="comment_lines" type="metadata" default="1" /> |
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262 <action name="column_names" type="metadata" default="bin,classification,reason,lineage,lineage scores" /> |
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263 </actions> |
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264 </data> |
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265 <data name="orf2lca_names" format="tabular" label="${bcat}.ORF2LCA.names.txt"> |
2
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266 <filter>names['add_names'] in ['both','orf2lca']</filter> |
0
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267 <actions> |
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268 <action name="comment_lines" type="metadata" default="1" /> |
2
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269 <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score,superkingdom,phylum,class,order,family,genus,species" /> |
0
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270 </actions> |
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271 </data> |
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272 <data name="classification_names" format="tabular" label="${bcat}.${seqtype}2classification.names.txt"> |
2
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273 <filter>names['add_names'] in ['both','classification']</filter> |
0
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274 <actions> |
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275 <action name="comment_lines" type="metadata" default="1" /> |
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276 <action name="column_names" type="metadata" default="${seqtype},classification,reason,lineage,lineage scores,superkingdom,phylum,class,order,family,genus,species" /> |
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277 </actions> |
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278 </data> |
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279 <data name="classification_summary" format="tabular" label="${bcat}.${seqtype}2classification.summary.txt"> |
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280 <filter>'classification' in summarise</filter> |
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281 <actions> |
2
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282 <action name="comment_lines" type="metadata" default="4" /> |
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283 <action name="column_names" type="metadata" default="rank,clade,number of ${sum_titles}" /> |
0
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284 </actions> |
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285 </data> |
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286 </xml> |
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287 <token name="@COMMON_HELP@"><![CDATA[ |
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288 The CAT/BAT workflow is described at: https://github.com/dutilh/CAT |
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289 ]]></token> |
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290 <xml name="citations"> |
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291 <citations> |
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292 <citation type="doi">https://doi.org/10.1101/072868</citation> |
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293 <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation> |
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294 <citation type="doi">https://doi.org/10.1038/nmeth.3176</citation> |
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295 <citation type="doi">https://doi.org/10.1186/1471-2105-11-119</citation> |
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296 <yield /> |
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297 </citations> |
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298 </xml> |
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299 </macros> |