Mercurial > repos > bgruening > infernal

diff cmstat.xml @ 9:1d74ed49cf41 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
author bgruening
date Mon, 11 Nov 2024 10:27:19 +0000
parents c9e29ac5d099
children
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line diff
--- a/cmstat.xml	Thu Sep 23 19:38:58 2021 +0000
+++ b/cmstat.xml	Mon Nov 11 10:27:19 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[
         ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
@@ -25,24 +25,7 @@
 ]]>
     </command>
         <inputs>
-            <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" />
         </inputs>
     <outputs>
         <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
@@ -61,6 +44,19 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <conditional name="cm_opts">
+                <param name="cm_opts_selector" value="db"/>
+                <param name="database" value="cmstat_input.cm"/>
+            </conditional>
+            <output name="outfile" >
+                <assert_contents>
+                    <has_text text="idx"/>
+                    <has_text text="accession"/>
+                    <has_text text="nseq"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[