From a7e49048e677bbfdf06b5763a34116af643c8a95 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Sat, 3 Aug 2019 18:55:04 +0200
Subject: [PATCH] argument tag: replace dashes by underscores

---
 lib/galaxy/tool_util/xsd/galaxy.xsd  | 19 ++++++++++---------
 lib/galaxy/tools/parameters/basic.py |  9 ++++++++-
 2 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index cea5aa9e6f6..77e9f2a27b8 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -187,7 +187,7 @@ automatically if profile is set to any version newer than ``16.01``, such as
         <xs:annotation>
           <xs:documentation xml:lang="en">This string specifies the minimum Python
 version that is able to fill the Cheetah sections of the tool. If unset defaults
-to 2.7 if the profile is older than 19.01, otherwise defaults to 3.5. Galaxy will 
+to 2.7 if the profile is older than 19.01, otherwise defaults to 3.5. Galaxy will
 attempt to convert Python statements in Cheetah sections using [future](http://python-future.org/)
 if Galaxy is run on Python 3 and ``python_template_version`` is below 3.</xs:documentation>
         </xs:annotation>
@@ -1788,7 +1788,7 @@ statement. A good example tool that demonstrates many conditional parameters is
     </param>
     <when value="tsv">
         <param name="input_table" type="data" format="tabular" label="Tabular File" argument="--input-fp"/>
-        <param name="process_obs_metadata" type="select" label="Process metadata associated with observations when converting" argument="--process-obs-metadata">
+        <param type="select" label="Process metadata associated with observations when converting" argument="--process-obs-metadata">
             <option value="" selected="true">Do Not process metadata</option>
             <option value="taxonomy">taxonomy</option>
             <option value="naive">naive</option>
@@ -2353,9 +2353,10 @@ rendered as a one line text box (if ``false``, the default) or a multi-line text
 
 If the parameter reflects just one command line argument of a certain tool, this
 tag should be set to that particular argument. It is rendered in parenthesis
-after the help section, and it will create the name attribute from the argument
-attribute by stripping the dashes (e.g. if ``argument="--sensitive"`` then
-``name="sensitive"`` is implicit).
+after the help section, and it will create the name attribute (if not given explicitly)
+from the argument attribute by stripping leading dashes and replacing all remaining
+dashes by underscores (e.g. if ``argument="--long-parameter"`` then
+``name="long_parameter"`` is implicit).
 
 ]]></xs:documentation>
           </xs:annotation>
@@ -3217,7 +3218,7 @@ validators is in the ``validator_types`` dictionary in
 [/lib/galaxy/tools/parameters/validation.py](https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/parameters/validation.py).
 Valid values include: ``expression``, ``regex``, ``in_range``, ``length``,
 ``metadata``, ``unspecified_build``, ``no_options``, ``empty_field``,
-``dataset_metadata_in_file``, 
+``dataset_metadata_in_file``,
 ``dataset_metadata_in_data_table``, ``dataset_metadata_not_in_data_table``,
 ``value_in_data_table``, ``value_not_in_data_table``,
 ``dataset_ok_validator``, ``dataset_metadata_in_range``]]></xs:documentation>
@@ -5604,12 +5605,12 @@ A tool can refer multiple reference IDs.
 	
 ```xml
    <!-- Example: this tool is seqtk -->
-   <xrefs>      
+   <xrefs>
 	<xref type="bio.tools">seqtk</xref>
    </xrefs>
    <!-- https://bio.tools/seqtk -->
 ```
-   
+
 ]]></xs:documentation>
     </xs:annotation>
       <xs:sequence>
@@ -5619,7 +5620,7 @@ A tool can refer multiple reference IDs.
   </xs:complexType>
   <xs:complexType name="xref">
     <xs:annotation>
-      <xs:documentation xml:lang="en">The ``xref`` element specifies reference 
+      <xs:documentation xml:lang="en">The ``xref`` element specifies reference
 information according to a catalog.</xs:documentation>
     </xs:annotation>
     <xs:simpleContent>
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index e87c9542b2b..682512d55c6 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -84,6 +84,13 @@ class ToolParameter(Dictifiable):
     Describes a parameter accepted by a tool. This is just a simple stub at the
     moment but in the future should encapsulate more complex parameters (lists
     of valid choices, validation logic, ...)
+
+    >>> from galaxy.util.bunch import Bunch
+    >>> trans = Bunch(app=None)
+    >>> p = TextToolParameter(None, XML('<param argument="--parameter-name" type="text" value="default" />'))
+    >>> print(p.name)
+    parameter_name
+    >>> assert sorted(p.to_dict(trans).items()) == [('area', False), ('argument', '--parameter-name'), ('datalist', []), ('help', ''), ('hidden', False), ('is_dynamic', False), ('label', ''), ('model_class', 'TextToolParameter'), ('name', 'parameter_name'), ('optional', False), ('refresh_on_change', False), ('type', 'text'), ('value', 'default')]
     """
     dict_collection_visible_keys = ['name', 'argument', 'type', 'label', 'help', 'refresh_on_change']
 
@@ -250,7 +257,7 @@ class ToolParameter(Dictifiable):
         if name is None:
             argument = input_source.get('argument')
             if argument:
-                name = argument.lstrip('-')
+                name = argument.lstrip('-').replace("-", "_")
             else:
                 raise ValueError("parameter must specify a name.")
         return name