--- a/dbkit_create.xml	Thu Nov 26 11:05:51 2020 +0000
+++ b/dbkit_create.xml	Wed Dec 16 12:02:48 2020 +0000
@@ -1,14 +1,29 @@
 <tool id="dbkit_create" name="DBKit Create" version="0.1.1" python_template_version="3.5" license="MIT">
     <description>database generator</description>
     <command detect_errors="exit_code"><![CDATA[
-        mkdir temp &&
-        python3 '$__tool_directory__/dbkit_create.py' -l '$input' -u '$url' -o '$index' -d '$database' -g '$log' -il '$advanced.idlength' -ic '$advanced.idcase' -ie '$advanced.idextension'
+        #if str($source.type) == "false":
+            mkdir -p inputs &&
+            #for item in $source.inputs
+                cp '${str(item)}' 'inputs/${item.element_identifier}' &&
+            #end for
+        #end if
+        python3 '$__tool_directory__/dbkit_create.py' -l '$input' -u '$source.url' -p 'inputs' -o '$index' -d '$database' -g '$log' -il '$advanced.idlength' -ic '$advanced.idcase' -ie '$advanced.idextension'
     ]]></command>
     <inputs>
-        <param format="tabular" name="input" type="data" label="List of Identifiers" help="Specify a list containing all entry identifiers to be downloaded."/>
-        <param name="url" type="text" label="URL to External Source" help="Specify the URL to the external database source.">
-            <option value="https://files.rcsb.org/download/">https://files.rcsb.org/download/</option>
-        </param>
+        <param format="tabular" name="input" type="data" label="List of Identifiers" help="Specify a list containing all entry identifiers to be downloaded."/>    
+        <conditional name="source">
+            <param name="type" type="boolean" label="Download from URL"/>
+            <when value="true">
+                <param name="url" type="text" label="URL to External Source" help="Specify the URL to the external database source.">
+                    <option value="https://files.rcsb.org/download/">https://files.rcsb.org/download/</option>
+                </param>
+                <param name="inputs" type="hidden"/>
+            </when>
+            <when value="false">
+                <param name="url" type="hidden"/>
+                <param name="inputs" type="data_collection" collection_type="list" label="Collection" help="Specify a collection containing the datasets."/>
+            </when>
+        </conditional>
         <conditional name="advanced">
             <param name="type" type="boolean" label="Identifier Formatting Options" />
             <when value="true">        
@@ -35,7 +50,10 @@
     <tests>
         <test>
             <param name="input" value="create/chains.tabular" />
-            <param name="url" value="https://files.rcsb.org/download/" />
+            <conditional name="source">
+                <param name="type" value="true"/>
+                <param name="url" value="https://files.rcsb.org/download/" />
+            </conditional>
             <conditional name="advanced">
                 <param name="type" value="true" />
                 <param name="idextension" value="pdb" />
@@ -43,12 +61,31 @@
                 <param name="idcase" value="lower" />
             </conditional>
             <param format="tabular" name="database" value="roc/biogrid_fret.txt" />
-            <output name="index" file="create/index.ffindex" />
-            <output name="database" file="create/data.ffdata" />
+            <output name="index" file="create/first.ffindex" />
+            <output name="database" file="create/first.ffdata" />
+        </test>
+        <test>
+            <param name="input" value="create/sequences.tabular" />
+            <conditional name="source">
+                <param name="type" value="false"/>
+                <param name="inputs">
+                    <collection type="list">
+                        <element name="NP_000282.1.hhr" value="create/NP_000282.1.hhr" />
+                        <element name="NP_000290.2.hhr" value="create/NP_000290.2.hhr" />
+                        <element name="NP_000548.2.hhr" value="create/NP_000548.2.hhr" />
+                        <element name="NP_000836.2.hhr" value="create/NP_000836.2.hhr" />
+                    </collection>
+                </param>
+            </conditional>
+            <conditional name="advanced">
+                <param name="type" value="false" />
+            </conditional>
+            <output name="index" file="create/sequences.ffindex" />
+            <output name="database" file="create/sequences.ffdata" />
         </test>
     </tests>
     <help><![CDATA[
 This database creation tool downloads entries from an external resource and creates a datasets with all its contents. Additionally an index file is
-generated indicating the start and end of every entry within the database file.
+generated indicating the start and size of every entry within the database file. The tool can also operate on collections.
     ]]></help>
 </tool>
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