changeset 4:aaeb63501369 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit ec15da3a30507841856303de991cbe80c65128fd-dirty

--- a/cat_bins.xml	Tue Nov 26 15:42:14 2019 -0500
+++ b/cat_bins.xml	Wed Nov 27 10:27:23 2019 -0500
@@ -23,6 +23,7 @@
     @CAT_DB@
     @USE_INTERMEDIATES@
     @CUSTOM_SETTINGS@
+    @DIAMOND_OPTIONS@
     && @TXT2TSV@ *.ORF2LCA.txt *.bin2classification.txt
     #if len($mags) > 1:
         #set pat = '$' + '{i/concatenated./}'
@@ -36,6 +37,7 @@
         <expand macro="cat_db" />
         <expand macro="use_intermediates" />
         <expand macro="custom_settings" />
+        <expand macro="diamond_options" />
         <expand macro="add_names" />
         <expand macro="summarise" />
         <expand macro="select_bat_outputs" />

--- a/cat_contigs.xml	Tue Nov 26 15:42:14 2019 -0500
+++ b/cat_contigs.xml	Wed Nov 27 10:27:23 2019 -0500
@@ -10,6 +10,7 @@
     @CAT_DB@
     @USE_INTERMEDIATES@
     @CUSTOM_SETTINGS@
+    @DIAMOND_OPTIONS@
     && @TXT2TSV@ *.ORF2LCA.txt *.contig2classification.txt
     @ADD_NAMES@
     @SUMMARISE@
@@ -19,6 +20,7 @@
         <expand macro="cat_db" />
         <expand macro="use_intermediates" />
         <expand macro="custom_settings" />
+        <expand macro="diamond_options" />
         <expand macro="add_names" />
         <expand macro="summarise" />
         <expand macro="select_cat_outputs" />

--- a/cat_prepare.xml	Tue Nov 26 15:42:14 2019 -0500
+++ b/cat_prepare.xml	Wed Nov 27 10:27:23 2019 -0500
@@ -23,6 +23,8 @@
 **CAT prepare**
 Prepare CAT reference data for classifying metagomic contigs or genome assemblies.
 
+This requires over a 100GB of RAM, 250GB of disk space, and up to 24 hours.
+
 @COMMON_HELP@
     ]]></help>
     <expand macro="citations" />

--- a/macros.xml	Tue Nov 26 15:42:14 2019 -0500
+++ b/macros.xml	Wed Nov 27 10:27:23 2019 -0500
@@ -56,7 +56,6 @@
             <param name="cat_builtin" value="CAT_prepare_test"/>
         </conditional>
     </xml>
-
     <xml name="use_intermediates">
         <conditional name="previous">
             <param name="use_previous" type="select" label="Use previous gene prediction and diamond alignment">
@@ -85,6 +84,37 @@
       --range $range
       --fraction $fraction
 ]]></token>
+    <xml name="diamond_options">
+        <conditional name="diamond">
+            <param name="set_diamond_opts" type="select" label="Advanced diamond options">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" 
+                    label="Run DIAMOND in sensitive mode (considerably slower)"/>
+                <param argument="--block_size" type="float" value="2.0" min="1" max="10" label="DIAMOND block-size parameter."
+                    help="lower will decrease memory and temporary disk space usage, higher will increase performance."/>
+                <param argument="--index_chunks" type="integer" value="4" min="1" max="10" label="DIAMOND index-chunks parameter" 
+                    help="Set to 1 on high memory machines. The parameter has no effect on temporary disk space usage."/>
+                <param argument="--top" type="integer" value="50" min="1" max="50" label="DIAMOND top parameter" 
+                    help="Governs hits within range of best hit that are written to the alignment file. This implies you know what you are doing."/>
+            </when>
+        </conditional>
+    </xml>
+    <token name="@DIAMOND_OPTIONS@"><![CDATA[
+        #if $diamond.set_diamond_opts == 'yes':
+            $diamond.sensitive
+            --block_size $diamond.block_size
+            --index_chunks $diamond.index_chunks
+            #if $diamond.top < 50:
+                --I_know_what_Im_doing
+                --top $diamond.top
+            #end if
+        #end if
+]]></token>
+
     <xml name="add_names_options">
         <param argument="--only_official" type="boolean" truevalue="--only_official" falsevalue="" checked="true" 
             label="Only output official level names."/>