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annotate cat_summarise.xml @ 0:db1360aae489 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
author iuc
date Tue, 10 Dec 2019 16:04:54 -0500
parents
children 388e6678fa98
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db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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1 <tool id="cat_summarise" name="CAT summarise" version="@VERSION@.0">
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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2 <description>the number of contigs or bins assigned to each taxonomic name</description>
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 CAT summarise
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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10 #if $contigs_fasta
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11 -c '$contigs_fasta'
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12 #end if
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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13 -i '$input'
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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14 -o 'output_names_summary.txt'
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15 && @TXT2TSV@ -i 'output_names_summary.txt' -o '$output'
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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16 ]]></command>
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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17 <inputs>
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18 <param argument="--input" type="data" format="tabular" label="classification.names.txt output from CAT add_names"
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19 help="The classication must be made with --only_official names"/>
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20 <param argument="--contigs_fasta" type="data" format="fasta" optional="true" label="contigs.fasta used for CAT contigs"
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21 help="Required if summarising a contig2classification.names output derived from CAT contigs"/>
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22 </inputs>
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23 <outputs>
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24 <data name="output" format="tabular" label="#set name = $input.name.replace('.txt','.summary.txt')# ${tool.name} on ${on_string} $name"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input" ftype="tabular" value="test_contig.contig2classification.names.txt"/>
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29 <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
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30 <output name="output">
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31 <assert_contents>
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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32 <has_text text="Firmicutes" />
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33 </assert_contents>
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34 </output>
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35 </test>
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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36 </tests>
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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37 <help><![CDATA[
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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38 **CAT summarise**
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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39
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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40 Summarise taxonomic asignemts from a CAT or BAT classification file that has official taxonomic names added by CAT add_names.
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41
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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42 **INPUT**
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43
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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44 ::
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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45
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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46 # bin classification reason lineage lineage scores superkingdom phylum class order family genus species
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47 genome2.fna classified based on 6/17 ORFs 1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;0.89;0.89;0.89;0.89;0.89;0.69 Bacteria: 1.00 Proteobacteria: 0.89 Gammaproteobacteria: 0.89 Vibrionales: 0.89 Vibrionaceae: 0.89 Vibrio: 0.89 Vibrio cholerae: 0.69
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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48 genome3.fna classified based on 4/9 ORFs 1;131567;2;1783272;1239;91061;1385;186820;1637;1639 1.00;1.00;1.00;0.76;0.76;0.76;0.76;0.76;0.76;0.76 Bacteria: 1.00 Firmicutes: 0.76 Bacilli: 0.76 Bacillales: 0.76 Listeriaceae: 0.76 Listeria: 0.76 Listeria monocytogenes: 0.76
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49
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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50
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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51 **OUTPUT**
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52
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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53 ::
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54
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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55 # total number of bins is 2, of which 2 (100.00%) are classified.
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56 #
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57 # rank clade number of bins
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58 superkingdom Bacteria 2
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59 phylum Proteobacteria 1
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60 phylum Firmicutes 1
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61 class Gammaproteobacteria 1
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62 class Bacilli 1
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63 order Vibrionales 1
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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64 order Bacillales 1
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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65 family Vibrionaceae 1
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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66 family Listeriaceae 1
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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67 genus Vibrio 1
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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68 genus Listeria 1
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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69 species Vibrio cholerae 1
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70 species Listeria monocytogenes 1
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71
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72
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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73 Required arguments:
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74 -i, --input_file Path to named CAT contig classification file or BAT
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75 bin classification file. Currently only official ranks
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76 are supported, and only classification files
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77 containing a single classification per contig / bin.
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78
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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79 Optional arguments:
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80 -c, --contigs_fasta
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81 Path to contigs fasta file. This is required if you
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82 want to summarise a contig classification file.
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83
db1360aae489 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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84 @COMMON_HELP@
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85 ]]></help>
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86 <expand macro="citations" />
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87 </tool>