diff toolfactory/ToolFactory.xml @ 6:efefe43f23c8 draft default tip

Uploaded

--- a/toolfactory/ToolFactory.xml	Tue Apr 27 23:33:49 2021 +0000
+++ b/toolfactory/ToolFactory.xml	Fri Apr 30 02:10:32 2021 +0000
@@ -28,24 +28,16 @@
           </repeat>
       </xml>
      <xml name="tool_metadata">
-         <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
+        <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses" type="text" value="0.01"
             help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
-            <param name="tool_desc" label="Tool Synopsis" type="text" value=""
-             help="Supply a brief tool description for the Galaxy tool menu entry" />
-             <param name="install" label="Attempt to install in the host Galaxy"
-                help="This will fail unless running in a very unusual configuration such as a specialised Docker container"
-                type="boolean" checked="True" truevalue="1"  falsevalue="0" />
-         <conditional name="do_test">
-            <param name="run_test" label="Run planemo test on the new archive to add test outputs making a proper tool - takes time"
-                help="Archives must be run and updated using planemo to populate all the test outputs. Will be very quick if no dependencies (eg a bash script). May take a very long time depending on dependencies"
-                type="boolean" checked="False" truevalue="1"  falsevalue="0" />
-                <when value="0">
-                    <param name="tail" type="hidden" value="not_tested"/>
-                </when>
-                <when value="1">
-                    <param name="tail" type="hidden" value="tested"/>
-                </when>
-            </conditional>
+        <param name="tool_desc" label="Tool Synopsis" type="text" value=""
+            help="Supply a brief tool description for the Galaxy tool menu entry" />
+        <param name="install" label="Attempt to install in the host Galaxy"
+            help="This will fail unless running in a very unusual configuration such as a specialised Docker container"
+            type="boolean" checked="False" truevalue="1"  falsevalue="0" />
+         <param name="run_test" label="Finalise new archive with test outputs. Runs externally. Outputs will appear in history when ready"
+                    help="Archives must be run and updated using planemo to populate all the test outputs. May take a long time depending on dependencies"
+                    type="boolean" checked="True" truevalue="1"  falsevalue="0" />
             <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
             value="**What it Does**"
              help="Supply user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
@@ -232,7 +224,7 @@
     #if $install:
        --install
     #end if
-    #if $do_test.run_test:
+    #if $run_test:
        --run_test
     #end if
    #if $io_param.ppass.parampass != '0':
@@ -405,11 +397,7 @@
     <expand macro="tool_metadata" />
   </inputs>
   <outputs>
-    <data format="toolshed.gz" name="new_tool" label="${tool_name}_${do_test.tail}_toolshed.gz" />
-   <collection name="TF_run_report" type="list" label="${tool_name} test run outputs">
-      <filter>do_test['run_test']</filter>
-      <discover_datasets pattern="__name_and_ext__" directory="TF_run_report" />
-  </collection>
+    <data format="toolshed.gz" name="new_tool" label="${tool_name}_not_tested.toolshed.gz" />
   </outputs>
 <tests>
 <test>
@@ -432,7 +420,6 @@
     <param name="choosescript" value="yes" />
     <param name="script_path" value="$runme"/>
     <param name="install" value="0"/>
-    <param name="run_test" value="1"/>
     <output name="new_tool" file="toolfactory_pyrevpos_tgz_sample" compare="sim_size" delta="6000" />
 </test>
 </tests>