diff lasttrain.xml @ 3:3de2195f32c0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"

--- a/lasttrain.xml	Thu Sep 10 16:08:15 2020 +0000
+++ b/lasttrain.xml	Fri Nov 13 09:05:49 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01">
+<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy2" profile="18.01">
 
     <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>
 
@@ -18,17 +18,16 @@
         last-train
 
         -Q $init_options.Q
-
         -r $init_options.r
         -q $init_options.q
-
         -a $init_options.cost_opt.a
         -b $init_options.cost_opt.b
         -A $init_options.cost_opt.A
         -B $init_options.cost_opt.B
-
         -D $last_train_opt.align_opt.D
-        -E $last_train_opt.align_opt.E
+        #if $last_train_opt.align_opt.E != ""
+            -E $last_train_opt.align_opt.E
+        #end if
         -s $last_train_opt.align_opt.s
         -S $last_train_opt.align_opt.S
         -T $last_train_opt.align_opt.T
@@ -74,7 +73,7 @@
             <!-- Training options missing  -->
             <section name="align_opt" title="Alignment options" expanded="true">
                 <param argument="-D" type="integer" value="1000000" label="Query letters per random alignment"/>
-                <param argument="-E" type="integer" value="10" label="Maximum expected alignments per square giga"/>
+                <param argument="-E" type="integer" value="" optional="true" label="Maximum expected alignments per square giga"/>
                 <param argument="-s" type="select" multiple="false" label="Query strand to use">
                     <option value="0">Reverse</option>
                     <option value="1" selected="true">Forward</option>
@@ -111,6 +110,19 @@
                 <param name="db_opts_input" value="db"/>
                 <param name="database" value="humdb"/>
             </conditional>
+            <section name="last_train_opt">
+                <section name="align_opt">
+                    <param name="E" value="10"/>
+                </section>
+            </section>
+            <param name="query_fasta" value="fuguMito.fa"/>
+            <output name="outfile" file="last_train_E.txt" ftype="txt" lines_diff="22"/>
+        </test>
+        <test>
+            <conditional name="db_opts">
+                <param name="db_opts_input" value="db"/>
+                <param name="database" value="humdb"/>
+            </conditional>
             <param name="query_fasta" value="fuguMito.fa"/>
             <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/>
         </test>