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annotate dram_distill.xml @ 0:f9a3ea1c618c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
author iuc
date Sat, 10 Dec 2022 21:15:05 +0000
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1 <tool id="dram_distill" name="DRAM distill" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>metagenome-assembled-genomes (MAGs)</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="stdio"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 DRAM.py distill
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10 --input_file '$input_file'
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11 --output_dir 'output_dir'
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12 #if $rrna_path:
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13 --rrna_path '$rrna_path'
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14 #end if
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15 #if $trna_path:
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16 --trna_path '$trna_path'
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17 #end if
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18 --groupby_column '$groupby_column'
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19 #if $custom_distillate:
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20 --custom_distillate '$custom_distillate'
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21 #end if
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22 $distillate_gene_names
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23 --genomes_per_product $genomes_per_product
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24 && test -f 'output_dir/genome_stats.tsv' && mv 'output_dir/genome_stats.tsv' '$output_genome_stats' || echo 'No genome_stats.tsv output produced'
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25 && test -f 'output_dir/metabolism_summary.xlsx' && mv 'output_dir/metabolism_summary.xlsx' '$output_metabolism_summary' || echo 'No metabolism_summary.xlsx output produced'
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26 && test -f 'output_dir/product.html' && mv 'output_dir/product.html' '$output_product_html' || echo 'No product.html output produced'
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27 && test -f 'output_dir/product.tsv' && mv 'output_dir/product.tsv' '$output_product_tsv' || echo 'No product.tsv output produced'
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28 ]]></command>
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29 <inputs>
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30 <expand macro="input_file_param"/>
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31 <param argument="--rrna_path" type="data" format="tabular" optional="true" label="rRNA file" help="Produced by the DRAM annotate tool (optional, leave blank to ignore)"/>
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32 <param argument="--trna_path" type="data" format="tabular" optional="true" label="tRNA file" help="Produced by the DRAM annotate tool (optional, leave blank to ignore)"/>
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33 <param argument="--groupby_column" type="text" value="fasta" label="Column from annotations to group as organism units">
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34 <expand macro="sanitizer"/>
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35 </param>
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36 <expand macro="custom_distillate_param"/>
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37 <param argument="--distillate_gene_names" type="boolean" truevalue="--distillate_gene_names" falsevalue="" checked="false" label="Give names of genes instead of counts in genome metabolism summary?"/>
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38 <param argument="--genomes_per_product" type="integer" value="1000" min="0" label="Number of genomes per product.html output"/>
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39 </inputs>
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40 <outputs>
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41 <data name="output_genome_stats" format="tabular" label="${tool.name} on ${on_string}: genome stats"/>
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42 <data name="output_metabolism_summary" format="xlsx" label="${tool.name} on ${on_string}: metabolism summary"/>
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43 <data name="output_product_html" format="html" label="${tool.name} on ${on_string}: product html"/>
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44 <data name="output_product_tsv" format="tabular" label="${tool.name} on ${on_string}: product_tsv"/>
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45 </outputs>
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46 <tests>
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47 <!--
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48 These tests succeed, but the outputs are empty because the DRAM
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49 database is not available in the test environment. This warning
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50 is displayed in the log...
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51 warnings.warn('Database does not exist at path %s' % self.description_loc)
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52 ...and this exception is raised:
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53 ValueError: Invalid file path or buffer object type: <class 'NoneType'
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54 -->
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55 <test expect_failure="true">
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56 <param name="input_file" ftype="tabular" value="annotated1.tabular"/>
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57 <param name="rrna_path" ftype="tabular" value="input_distill_rrna1.tabular"/>
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58 <param name="trna_path" ftype="tabular" value="input_distill_trna1.tabular"/>
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59 <param name="custom_distillate" ftype="tabular" value="distill_custom.tabular"/>
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60 <assert_stderr>
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61 <has_text text="Traceback"/>
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62 </assert_stderr>
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63 </test>
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64 </tests>
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65 <help>
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66 **What it does**
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67
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68 @WHATITDOESHEADER@
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69
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70 This tool accepts a tabular file with all gene annotations from Pfam, UniProt, dbCAN and MEROPS databases produced by the
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71 DRAM annotate tool and curates them into useful functional categories, creating genome statistics and metabolism summary
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72 files. The genome statistics provides most genome quality information required for MIMAG standards, including GTDB-tk
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73 and checkM information if provided by the user. The summarised metabolism table includes the number of genes with specific
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74 metabolic function identifiers (KO, CAZY ID, etc) for each genome with information obtained from multiple databases.
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75
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76 @CUSTOMDISTILLATEFILES@
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77
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78 This tool produces the following outputs.
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79
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80 * **Distillate**
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81
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82 * **genome stats** - a tabular file with genome statistics for all input genomes including all statistics required by recently defined MIMAG standards
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83 * **metabolism summary** - an Excel file with metabolism summary of all input genomes which gives gene counts of functional and structural genes across a wide variety of metabolisms
f9a3ea1c618c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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84
f9a3ea1c618c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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85 * **Liquor**
f9a3ea1c618c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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86
f9a3ea1c618c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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87 * **product html** - an html file containing an interactive heatmap showing coverage of pathways, the coverage of electron transport chain components and the presence of selected metabolic functions
f9a3ea1c618c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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88 * **product tsv** - a tabular file with corresponding genes for the html heatmap
f9a3ea1c618c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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89
f9a3ea1c618c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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90 @WHATITDOESFOOTER@
f9a3ea1c618c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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91 </help>
f9a3ea1c618c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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92 <expand macro="citations"/>
f9a3ea1c618c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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93 </tool>