diff macros.xml @ 5:226949352e31 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit a1c079107b72dc08612fa664897bb9d627624e52-dirty

--- a/macros.xml	Wed Nov 27 10:27:23 2019 -0500
+++ b/macros.xml	Wed Nov 27 12:11:14 2019 -0500
@@ -284,6 +284,50 @@
             </actions>
         </data>
     </xml>
+    <token name="@OPTIONS_HELP@"><![CDATA[
+
+Optional arguments:
+  -r, --range               cut-off range after alignment [0-49] (default: 10).
+  -f, --fraction            fraction of bit-score support for each classification
+                            [0-0.99] (default: 0.5).
+  -p, --proteins_fasta
+                            Path to predicted proteins fasta file. If supplied,
+                            CAT will skip the protein prediction step.
+  -a, --diamond_alignment
+                            Path to DIAMOND alignment table. If supplied, CAT will
+                            skip the DIAMOND alignment step and directly classify
+                            the sequences. A predicted proteins fasta file should
+                            also be supplied with argument [-p / --proteins].
+
+
+DIAMOND specific optional arguments:
+  --sensitive     Run DIAMOND in sensitive mode (default: not enabled).
+
+  --block_size    DIAMOND block-size parameter (default: 2.0). Lower
+                  numbers will decrease memory and temporary disk space
+                  usage.
+
+  --index_chunks
+                  DIAMOND index-chunks parameter (default: 4). Set to 1
+                  on high memory machines. The parameter has no effect
+                  on temporary disk space usage.
+
+  --top
+                  DIAMOND top parameter [0-50] (default: 50). Governs
+                  hits within range of best hit that are written to the
+                  alignment file. This is not the [-r / --range]
+                  parameter!
+
+
+Setting the DIAMOND --top parameter
+
+You can speed up DIAMOND considerably, and at the same time greatly reduce disk usage, by setting the DIAMOND --top parameter to lower values. This will govern hits within range of the best hit that are written to the alignment file.
+
+You have to be very carefull to 1) not confuse this parameter with the r / --range parameter, which does a similar cut-off but after alignment and 2) be aware that if you want to run CAT or BAT again afterwards with different values of the -r / --range parameter, your options will be limited to the range you have chosen with --top earlier, because all hits that fall outside this range will not be included in the alignment file. Importantly, CAT and BAT currently do not warn you if you choose -r / --range in a second run higher than --top in a previous one, so it's up to you to remember this!
+
+If you have understood all this, or you do not plan to tune -r / --range at all afterwards, you can enjoy a huge speedup with much smaller alignment files! For CAT you can for example set --top 11 and for BAT --top 6.
+
+]]></token>
     <token name="@COMMON_HELP@"><![CDATA[
 The CAT/BAT workflow is described at: https://github.com/dutilh/CAT    
 ]]></token>