diff macros.xml @ 0:2675f8d7b2a5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sat Dec 10 21:14:28 2022 +0000
@@ -0,0 +1,72 @@
+<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>
+