Mercurial > repos > iuc > dram_distill

annotate macros.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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f9a3ea1c618c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.3.5</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@PROFILE@">20.09</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">dram</requirement>
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8 </requirements>
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9 </xml>
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10 <xml name="stdio">
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11 <stdio>
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12 <regex match="FileNotFoundError" source="stderr" level="fatal"/>
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13 <regex match="returned non-zero exit status" source="stdout" level="fatal"/>
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14 <regex match="returned non-zero exit status" source="stderr" level="fatal"/>
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15 <regex match="Invalid file path or buffer object type" source="stderr" level="fatal"/>
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16 <exit_code range="1:" level="fatal"/>
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17 </stdio>
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18 </xml>
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19 <xml name="categories_param">
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20 <param argument="--categories" type="text" value="" label="Distillate categories" help="Optional, leave blank to ignore">
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21 <expand macro="sanitizer"/>
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22 </param>
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23 </xml>
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24 <xml name="custom_distillate_param">
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25 <param argument="--custom_distillate" type="data" format="tabular" optional="true" label="File containing a custom distillate form" help="Optional, leave blank to ignore"/>
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26 </xml>
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27 <xml name="genes_param">
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28 <param argument="--genes" type="text" value="" label="Space-separated list of genes to keep" help="Optional, leave blank to ignore">
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29 <expand macro="sanitizer"/>
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30 </param>
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31 </xml>
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32 <xml name="identifiers_param">
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33 <param argument="--identifiers" type="text" value="" label="Database identifiers" help="Optional, leave blank to ignore">
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34 <expand macro="sanitizer"/>
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35 </param>
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36 </xml>
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37 <xml name="input_file_param">
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38 <param argument="--input_file" type="data" format="tabular" label="Annotations file" help="Produced by the DRAM annotate tool"/>
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39 </xml>
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40 <xml name="sanitizer">
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41 <sanitizer>
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42 <valid initial="string.printable">
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43 <remove value="&apos;"/>
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44 </valid>
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45 <mapping initial="none">
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46 <add source="&apos;" target="__sq__"/>
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47 </mapping>
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48 </sanitizer>
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49 </xml>
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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>
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51 <token name="@CUSTOMDISTILLATEFILES@">**Using Custom Distillate files**
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52
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53 The custom distillate sheet must be a tabular file with all the columns specified below. This sheet is an extension
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54 of the genome_summary_form.tsv file that is installed with the dram databases and which is one of several key data files
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55 that characterizes the distillate. The genome_summary_form.tsv file is available for viewing here
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56 https://github.com/WrightonLabCSU/DRAM/blob/master/data/genome_summary_form.tsv. The custom distillate sheet must
f9a3ea1c618c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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57 contain the following columns.
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58
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59 * gene_id: the KO ids of the genes in which you are interested
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60 * gene_description: descriptions of the geans
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61 * module: the name of your module that you are adding
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62 * sheet: the name you would like on the excel sheet in which your results appear
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63 * header: the header that will appear in the dram metabolism summary
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64 * subheader: the sub-header that will appear in the metabolism summary</token>
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65 <token name="@WHATITDOESFOOTER@">More information about DRAM can be found here https://github.com/shafferm/DRAM/wiki.</token>
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66 <xml name="citations">
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67 <citations>
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68 <citation type="doi">10.1186/s13104-016-1900-2</citation>
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69 </citations>
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70 </xml>
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71 </macros>
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72