Mercurial > repos > iuc > cat_add_names

annotate cat_add_names.xml @ 0:13192095fd5a 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 16:04:22 -0500
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children acd9fe45eb81
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13192095fd5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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1 <tool id="cat_add_names" name="CAT add_names" version="@VERSION@.0">
13192095fd5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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2 <description>annotate with taxonomic names</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <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 add_names
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10 -i '$input'
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11 @CAT_TAXONOMY@
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12 @ADD_NAMES_OPTIONS@
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13 -o 'output_names.txt'
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14 && @TXT2TSV@ -i 'output_names.txt' -o '$output'
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15 ]]></command>
13192095fd5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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16 <inputs>
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17 <param argument="--input" type="data" format="tabular,txt" label="classification.txt or ORF2LCA.txt from CAT contigs or CAT bins"/>
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18 <expand macro="cat_db" />
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19 <expand macro="add_names_options" />
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20 </inputs>
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21 <outputs>
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22 <data name="output" format="tabular" label="#set name = $input.name.replace('.txt','.names.txt')# $name"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input" ftype="tabular" value="test_contig.contig2classification.txt"/>
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27 <expand macro="test_catdb"/>
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28 <output name="output">
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29 <assert_contents>
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30 <has_text text="Firmicutes" />
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31 </assert_contents>
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32 </output>
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36 **CAT/BAT add_names**
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37
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38 Add taxonomic names to CAT or BAT output files. Names can be added to ORF2LCA.txt, contig2classification.txt, and bin2classification.txt outputs.
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39
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40 @COMMON_HELP@
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41
13192095fd5a "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
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44 Example: contig2classification.txt from CAT conitgs
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45
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46 ::
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47
13192095fd5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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48 # contig classification reason lineage lineage scores
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49 contig_44250 classified based on 1/2 ORFs 1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00
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50 contig_9952 classified based on 1/5 ORFs 1;131567;2;1783272;1239;91061* 1.00;1.00;1.00;1.00;1.00;1.00
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51
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52
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53 **OUTPUT**
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54
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55 ::
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56
13192095fd5a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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57 # contig classification reason lineage lineage scores superkingdom phylum class order family genus species
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58 contig_44250 classified based on 1/2 ORFs 1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 Bacteria: 1.00 Proteobacteria: 1.00 Gammaproteobacteria: 1.00 Vibrionales: 1.00 Vibrionaceae: 1.00 Vibrio: 1.00 Vibrio cholerae: 1.00
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59 contig_9952 classified based on 1/5 ORFs 1;131567;2;1783272;1239;91061* 1.00;1.00;1.00;1.00;1.00;1.00 Bacteria: 1.00 Firmicutes: 1.00 Bacilli*: 1.00 not classified not classified not classified not classified
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60
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61
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62 Required arguments:
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63 -i, --input_file Path to input file. Can be either classification
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64 output file or ORF2LCA output file.
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65 -t, --taxonomy_folder Path to folder that contains taxonomy files.
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66
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67 Optional arguments:
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68 --only_official Only output official level names.
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69 --exclude_scores Do not include bit-score support scores in the
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70 lineage.
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71
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72 ]]></help>
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73 <expand macro="citations" />
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74 </tool>