--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mitos/macros.xml	Thu Jun 17 15:27:29 2021 +0000
@@ -0,0 +1,31 @@
+<macros>
+    <token name="@COMMON_HELP@">
+    <![CDATA[
+@MITOS_NAME@ does a de-novo annotation of a given metazoan mitochondrial sequence.
+
+**Inputs**
+
+- A fasta formatted sequence
+
+  - @MITOS_NAME@ processes only FASTA files containing a single sequence. If you have a FASTA file with multiple sequences you may use the tool *Split Fasta files into a collection". The resulting collection can then used as input to @MITOS_NAME@.
+  
+- The correct genetic code needs to be selected
+
+- Reference data needs to be selected (can be provided by an administrator using the MITOS data manager)
+
+**Outputs**
+
+By default the annotation in BED format. Several other outputs can be enabled:
+
+- The annotation can be given as well in GFF, SEQ, or mito (a custom tabular format)
+
+- zipped raw data (all files computed during the run, e.g. BLAST and cmsearch outputs)
+
+- protein and ncRNA prediction plots visualize the predicted genes and their qualities
+
+- ncRNA structure plots (secondary structures of the predicted ncRNAs)
+
+See http://mitos.bioinf.uni-leipzig.de/help.py
+
+  ]]></token>
+</macros>