Mercurial > repos > iuc > dram_annotate

comparison macros.xml @ 0:cf3f6929b52c 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 21:14:46 +0000
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children 4058af4457c0
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-1:000000000000 0:cf3f6929b52c
1 <macros>
2 <token name="@TOOL_VERSION@">1.3.5</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">20.09</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">dram</requirement>
8 </requirements>
9 </xml>
10 <xml name="stdio">
11 <stdio>
12 <regex match="FileNotFoundError" source="stderr" level="fatal"/>
13 <regex match="returned non-zero exit status" source="stdout" level="fatal"/>
14 <regex match="returned non-zero exit status" source="stderr" level="fatal"/>
15 <regex match="Invalid file path or buffer object type" source="stderr" level="fatal"/>
16 <exit_code range="1:" level="fatal"/>
17 </stdio>
18 </xml>
19 <xml name="categories_param">
20 <param argument="--categories" type="text" value="" label="Distillate categories" help="Optional, leave blank to ignore">
21 <expand macro="sanitizer"/>
22 </param>
23 </xml>
24 <xml name="custom_distillate_param">
25 <param argument="--custom_distillate" type="data" format="tabular" optional="true" label="File containing a custom distillate form" help="Optional, leave blank to ignore"/>
26 </xml>
27 <xml name="genes_param">
28 <param argument="--genes" type="text" value="" label="Space-separated list of genes to keep" help="Optional, leave blank to ignore">
29 <expand macro="sanitizer"/>
30 </param>
31 </xml>
32 <xml name="identifiers_param">
33 <param argument="--identifiers" type="text" value="" label="Database identifiers" help="Optional, leave blank to ignore">
34 <expand macro="sanitizer"/>
35 </param>
36 </xml>
37 <xml name="input_file_param">
38 <param argument="--input_file" type="data" format="tabular" label="Annotations file" help="Produced by the DRAM annotate tool"/>
39 </xml>
40 <xml name="sanitizer">
41 <sanitizer>
42 <valid initial="string.printable">
43 <remove value="&apos;"/>
44 </valid>
45 <mapping initial="none">
46 <add source="&apos;" target="__sq__"/>
47 </mapping>
48 </sanitizer>
49 </xml>
50 <token name="@WHATITDOESHEADER@">DRAM (Distilled and Refined Annotation of Metabolism) is a tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs. DRAM annotates MAGs and viral contigs using UniRef90, PFAM, dbCAN, RefSeq viral, VOGDB and the MEROPS peptidase database.</token>
51 <token name="@CUSTOMDISTILLATEFILES@">**Using Custom Distillate files**
52
53 The custom distillate sheet must be a tabular file with all the columns specified below. This sheet is an extension
54 of the genome_summary_form.tsv file that is installed with the dram databases and which is one of several key data files
55 that characterizes the distillate. The genome_summary_form.tsv file is available for viewing here
56 https://github.com/WrightonLabCSU/DRAM/blob/master/data/genome_summary_form.tsv. The custom distillate sheet must
57 contain the following columns.
58
59 * gene_id: the KO ids of the genes in which you are interested
60 * gene_description: descriptions of the geans
61 * module: the name of your module that you are adding
62 * sheet: the name you would like on the excel sheet in which your results appear
63 * header: the header that will appear in the dram metabolism summary
64 * subheader: the sub-header that will appear in the metabolism summary</token>
65 <token name="@WHATITDOESFOOTER@">More information about DRAM can be found here https://github.com/shafferm/DRAM/wiki.</token>
66 <xml name="citations">
67 <citations>
68 <citation type="doi">10.1186/s13104-016-1900-2</citation>
69 </citations>
70 </xml>
71 </macros>
72