annotate macros.xml @ 1:96c0067106ec draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a

<macros>
    <token name="@TOOL_VERSION@">1.3.5</token>
    <!-- token name="@VERSION_SUFFIX@">0</token -->
    <token name="@PROFILE@">20.09</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">dram</requirement>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <regex match="FileNotFoundError" source="stderr" level="fatal"/>
            <regex match="returned non-zero exit status" source="stdout" level="fatal"/>
            <regex match="returned non-zero exit status" source="stderr" level="fatal"/>
            <regex match="Invalid file path or buffer object type" source="stderr" level="fatal"/>
            <exit_code range="1:" level="fatal"/>
        </stdio>
    </xml>
    <xml name="categories_param">
        <param argument="--categories" type="text" value="" label="Distillate categories" help="Optional, leave blank to ignore">
            <expand macro="sanitizer"/>
        </param>
    </xml>
    <xml name="custom_distillate_param">
        <param argument="--custom_distillate" type="data" format="tabular" optional="true" label="File containing a custom distillate form" help="Optional, leave blank to ignore"/>
    </xml>
    <xml name="genes_param">
        <param argument="--genes" type="text" value="" label="Space-separated list of genes to keep" help="Optional, leave blank to ignore">
            <expand macro="sanitizer"/>
        </param>
    </xml>
    <xml name="identifiers_param">
        <param argument="--identifiers" type="text" value="" label="Database identifiers" help="Optional, leave blank to ignore">
            <expand macro="sanitizer"/>
        </param>
    </xml>
    <xml name="input_file_param">
        <param argument="--input_file" type="data" format="tabular" label="Annotations file" help="Produced by the DRAM annotate tool"/>
    </xml>
    <xml name="sanitizer">
        <sanitizer>
            <valid initial="string.printable">
                <remove value="&apos;"/>
            </valid>
            <mapping initial="none">
                <add source="&apos;" target="__sq__"/>
            </mapping>
        </sanitizer>
    </xml>
    <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>
    <token name="@CUSTOMDISTILLATEFILES@">**Using Custom Distillate files**

The custom distillate sheet must be a tabular file with all the columns specified below.  This sheet is an extension
of the genome_summary_form.tsv file that is installed with the dram databases and which is one of several key data files
that characterizes the distillate.  The genome_summary_form.tsv file is available for viewing here
https://github.com/WrightonLabCSU/DRAM/blob/master/data/genome_summary_form.tsv.  The custom distillate sheet must
contain the following columns.

 * gene_id: the KO ids of the genes in which you are interested
 * gene_description: descriptions of the geans
 * module: the name of your module that you are adding
 * sheet: the name you would like on the excel sheet in which your results appear
 * header: the header that will appear in the dram metabolism summary
 * subheader: the sub-header that will appear in the metabolism summary</token>
    <token name="@WHATITDOESFOOTER@">More information about DRAM can be found here https://github.com/shafferm/DRAM/wiki.</token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/s13104-016-1900-2</citation>
        </citations>
    </xml>
</macros>