Mercurial > repos > tduigou > cloning_simulation

diff cloning_similation.xml @ 2:3171db614963 draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Fri, 16 May 2025 11:32:06 +0000
parents 32e44a646b68
children 044d36066cb3
line wrap: on
line diff
--- a/cloning_similation.xml	Fri May 16 09:41:19 2025 +0000
+++ b/cloning_similation.xml	Fri May 16 11:32:06 2025 +0000
@@ -24,7 +24,7 @@
             #set domesticated_input_paths = ""
             #set file_name_mapping_dom = ""
         #end if
-        mkdir 'outdir_zip' &&
+        mkdir 'outdir_zip' && mkdir 'outdir_gb' &&
         python '$__tool_directory__/cloning_simulation.py'
             --parts_files '$genbank_file_paths'
             --domesticated_seq '$domesticated_input_paths'
@@ -34,6 +34,7 @@
             --file_name_mapping_dom '$file_name_mapping_dom'
             --use_file_names_as_id '$adv.use_file_names_as_ids'
             --outdir_simulation 'outdir_zip'
+            --outdir_gb 'outdir_gb'
             --output_simulation 'output_zip.zip'
             --enzyme '$adv.enzyme' 
             --topology '$topology'&&
@@ -61,6 +62,9 @@
     </inputs>   
     <outputs>
         <data format="zip" name="output_zip" label="simulation results"/>
+        <collection name="construct_gb" type="list" label="All constrauct GenBank">
+                <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" />
+        </collection>
     </outputs>
     <tests>
         <!--test type2s_assembly class-->
@@ -93,6 +97,28 @@
                     </has_archive_member>
                 </assert_contents>
             </output>
+            <output_collection name="outdir_gb" type="list" count="4">
+                <element name="construct_1">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+                <element name="construct_2">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+                <element name="construct_3">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+                 <element name="construct_4">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+            </output_collection>
         </test>
         <!--test gibson_assembly class-->
         <test> 
@@ -113,6 +139,23 @@
                     </has_archive_member>
                 </assert_contents>
             </output>
+            <output_collection name="outdir_gb" type="list" count="4">
+                <element name="construct_1">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+                <element name="construct_2">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+                <element name="construct_3">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+            </output_collection>
         </test>
         <!--test lcr_assembly class-->
         <test> 
@@ -134,6 +177,8 @@
                     </has_archive_member>
                 </assert_contents>
             </output>
+            <output_collection name="outdir_gb" type="list" count="0">
+            </output_collection>
         </test>
         <!--test BASIC_assembly class-->
         <test> 
@@ -158,6 +203,8 @@
                     </has_archive_member>
                 </assert_contents>
             </output>
+            <output_collection name="outdir_gb" type="list" count="0">
+            </output_collection>
         </test>
         <!--test biobrick_assembly class-->
         <test> 
@@ -182,6 +229,8 @@
                     </has_archive_member>
                 </assert_contents>
             </output>
+            <output_collection name="outdir_gb" type="list" count="0">
+            </output_collection>
         </test>
         <!--test type2s_assembly with domesticated files-->
         <test> 
@@ -217,6 +266,28 @@
                     </has_archive_member>
                 </assert_contents>
             </output>
+            <output_collection name="outdir_gb" type="list" count="4">
+                <element name="construct_1">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+                <element name="construct_2">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+                <element name="construct_3">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+                 <element name="construct_4">
+                    <assert_contents>
+                     <has_n_lines min="20" />
+                    </assert_contents>
+                </element>
+            </output_collection>
         </test>
     </tests>