diff cmalign.xml @ 20:b10f7688d14c draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e

--- a/cmalign.xml	Thu Sep 23 19:38:15 2021 +0000
+++ b/cmalign.xml	Mon Nov 11 10:26:56 2024 +0000
@@ -3,9 +3,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <expand macro="xrefs"/>
     <command>
 <![CDATA[
 
@@ -33,7 +33,7 @@
                 --mxsize $speed_memory_cont.hmm_banding.mxsize
             #end if
 
-            #if $other_opts.mapali_opt.mapali_cond
+            #if $other_opts.mapali_opt.mapali_cond=="true"
                 --mapali '$other_opts.mapali_opt.mapali'
                 $other_opts.mapali_opt.mapstr
             #end if
@@ -68,26 +68,7 @@
     <inputs>
 
         <param name="seqdb" type="data" format="fasta" label="Sequence database"/>
-
-        <conditional name="cm_opts">
-            <param name="cm_opts_selector" type="select" label="Subject covariance models">
-              <option value="db" selected="True">Locally installed covariance models</option>
-              <option value="histdb">Covariance model from your history</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Covariance models">
-                    <options from_file="infernal.loc">
-                      <column name="value" index="0"/>
-                      <column name="name" index="1"/>
-                      <column name="path" index="2"/>
-                    </options>
-                </param>
-            </when>
-            <when value="histdb">
-                <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
-            </when>
-        </conditional>
-
+        <expand macro="DB" />
         <param argument="-g" truevalue="-g" falsevalue="" checked="False" type="boolean"
             label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/>
 
@@ -105,8 +86,11 @@
                 </when>
             </conditional>
             <conditional name="notrunc_opt">
-                <param argument="--notrunc" truevalue="" falsevalue="--notrunc" checked="true" type="boolean"
-                label="Use truncated alignment algorithm" help=""/>
+                <param argument="--notrunc" type="select"
+                label="Use truncated alignment algorithm">
+                    <option value="">Yes</option>
+                    <option value="--notrunc">No</option>
+                </param>
                 <when value=""></when>
                 <when value="--notrunc">
                     <param argument="--sub" type="boolean" truevalue="--sub" falsevalue="" checked="false"
@@ -143,8 +127,11 @@
 
         <section name="other_opts" title="Other options">
             <conditional name="mapali_opt">
-                <param name="mapali_cond" type="boolean" checked="false"
-                    label="Read the aligment file that used to build the CM" help="The alignment from the file is held fixed. This allows you to align sequences to a model with cmalign and view them in the context of an existing trusted multiple alignment."/>
+                <param name="mapali_cond" type="select"
+                    label="Read the aligment file that used to build the CM" help="The alignment from the file is held fixed. This allows you to align sequences to a model with cmalign and view them in the context of an existing trusted multiple alignment.">
+                    <option value="false">No</option>
+                    <option value="true">Yes</option>
+                </param>
                 <when value="true">
                     <param argument="--mapali" type="data" format="fasta"
                         label="The aligment file that used to build the CM" help=""/>
@@ -189,6 +176,18 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <conditional name="cm_opts">
+                <param name="cm_opts_selector" value="db"/>
+                <param name="database" value="cmalign_input2_tRNA5.c.cm"/>
+            </conditional>
+            <param name="seqdb" value="cmalign_input_mrum_tRNAs10.fa"/>
+            <output name="outfile">
+                <assert_contents>
+                    <has_text text="GGAGCUAUAGCUCAAU..GGC"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[