Mercurial > repos > iuc > cat_contigs

annotate cat_contigs.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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f5d2f8a27477 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit b6c674376eade4fdf9ffb31380f6689ede84a091"
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1 <tool id="cat_contigs" name="CAT contigs" version="@VERSION@.1">
0
2feaf3d2805b "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 classification</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 contigs
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10 -c '$contigs_fasta'
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11 @CAT_DB@
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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12 @USE_INTERMEDIATES@
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13 @CUSTOM_SETTINGS@
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14 @DIAMOND_OPTIONS@
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15 && @TXT2TSV@ *.ORF2LCA.txt *.contig2classification.txt
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16 @ADD_NAMES@
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17 @SUMMARISE@
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18 ]]></command>
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19 <inputs>
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20 <param name="contigs_fasta" type="data" format="fasta" label="Contigs fasta"/>
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21 <expand macro="cat_db" />
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22 <expand macro="use_intermediates" />
1
f5d2f8a27477 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit b6c674376eade4fdf9ffb31380f6689ede84a091"
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23 <expand macro="custom_settings_contigs" />
0
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24 <expand macro="diamond_options" />
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25 <expand macro="add_names" />
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26 <expand macro="summarise" />
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27 <expand macro="select_cat_outputs" />
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28 </inputs>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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29 <outputs>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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30 <expand macro="outputs" />
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31 </outputs>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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32 <tests>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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33 <test>
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34 <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
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35 <expand macro="test_catdb"/>
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36 <param name="select_outputs" value="contig2classification"/>
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37 <output name="contig2classification">
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38 <assert_contents>
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39 <has_text text="contig_38063" />
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40 </assert_contents>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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41 </output>
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42 </test>
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43 <test>
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44 <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
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45 <expand macro="test_catdb"/>
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46 <param name="select_outputs" value="predicted_proteins_faa"/>
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47 <conditional name="names">
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48 <param name="add_names" value="both"/>
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49 </conditional>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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50 <param name="summarise" value="classification"/>
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51 <output name="predicted_proteins_faa">
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52 <assert_contents>
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53 <has_text text=">contig_9952" />
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54 </assert_contents>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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55 </output>
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56 <output name="orf2lca_names">
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57 <assert_contents>
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58 <has_text text="Listeria" />
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59 </assert_contents>
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60 </output>
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61 <output name="classification_summary">
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62 <assert_contents>
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63 <has_text text="Listeria" />
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64 </assert_contents>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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65 </output>
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66 </test>
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67 </tests>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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68 <help><![CDATA[
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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69 **CAT contigs**
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70
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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71 Classifiy metagenomics contigs.
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72
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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73 @COMMON_HELP@
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74
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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75 @OUTPUTS_HELP@
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76
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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77
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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78 **CAT contigs**
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79
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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80 Run Contig Annotation Tool (CAT).
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81
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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82 Required arguments:
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83 -c, --contigs_fasta Path to contigs fasta file.
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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84 -d, --database_folder Path to folder that contains database files.
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85 -t, --taxonomy_folder Path to folder that contains taxonomy files.
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86
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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87
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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88 @OPTIONS_HELP@
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89
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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90 ]]></help>
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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91 <expand macro="citations" />
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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92 </tool>