diff align-it.xml @ 2:06d9381593a4 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit 00844534f9a2ffdf41fb9d5186d9a1e574c302d2"

--- a/align-it.xml	Tue May 07 13:41:07 2019 -0400
+++ b/align-it.xml	Fri Sep 10 08:09:03 2021 +0000
@@ -1,7 +1,11 @@
-<tool id="ctb_alignit" name="Pharmacophore alignment" version="1.0.3.1">
+<tool id="ctb_alignit" name="Pharmacophore alignment" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
     <description>and optimization (Align-it)</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.4</token>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.0.3">align_it</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">align_it</requirement>
     </requirements>
     <command detect_errors="aggressive">
 <![CDATA[
@@ -53,8 +57,8 @@
 ]]>
     </command>
     <inputs>
-        <param name="database" type="data" format='mol,mol2,sdf,smi,txt' label="Defines the database of molecules that will be used to screen"/>
-        <param name="reference" type="data" format='mol,mol2,sdf,smi,txt' label="Reference molecule"/>
+        <param name="database" type="data" format='mol,mol2,sdf,smi,phar' label="Defines the database of molecules that will be used to screen"/>
+        <param name="reference" type="data" format='mol,mol2,sdf,smi,phar' label="Reference molecule"/>
 
         <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups to be used in the alignment">
             <option value='AROM' selected="true">aromatic rings</option>
@@ -107,7 +111,7 @@
 
     </inputs>
     <outputs>
-        <data name="aligned_pharmacophores" format="txt" label="${tool.name} on ${on_string} (aligned pharmacophores)"/>
+        <data name="aligned_pharmacophores" format="phar" label="${tool.name} on ${on_string} (aligned pharmacophores)"/>
         <data name="aligned_structures" format="smi" label="${tool.name} on ${on_string} (aligned structures)">
             <change_format>
                 <when input="oformat" value="inchi" format="inchi"/>
@@ -121,7 +125,7 @@
             <param name="database" ftype="sdf" value="CID_2244.sdf"/>
             <param name="reference" ftype="sdf" value="CID_2244.sdf"/>
             <param name="oformat" value="sdf"/>
-            <output name="aligned_pharmacophores" file="align-it_Search_on_CID2244.phar" />
+            <output name="aligned_pharmacophores" file="align-it_Search_on_CID2244.phar" ftype="phar" />
             <output name="aligned_structures" file="align-it_Search_on_CID2244.sdf" lines_diff="2" />
             <output name="score_result_file" file="aliginit_scores.tabular.tabular" />
         </test>