Merge pull request #11 from jsaintvanne/mp_update

Help section template for Galaxy module

Workflow4Metabolomics Galaxy Documentation/ressources/Help_template.txt

@@ -0,0 +1,163 @@
+<help><![CDATA[
+
+.. class:: infomark
+
+**Credits**
+  | **Original tool code:** Firstname Lastname - affiliation 
+  | **Original tool wrapping:** Firstname Lastname - affiliation 
+  | **Tool maintainer:** Firstname Lastname - affiliation 
+  | **Wrapper maintainer:** Firstname Lastname - affiliation 
+
+.. class:: infomark
+
+**Contact:** Text about contact information
+
+---------------------------------------------------
+
+******************
+Tool name reminder
+******************
+
+===========
+DESCRIPTION
+===========
+
+A description of the tool (objectives, overall functionalities, notes/warnings, widlely spread subcases...).
+
+---------------------------------------------------
+
+==========================
+ALIGNMENT WITH OTHER TOOLS
+==========================
+
+-----------
+INPUT FILES
+-----------
+
+Information about input files (data types, examples of tools generating possible inputs, specificities in format and content...)
+
+------------
+OUTPUT FILES
+------------
+
+Information about possible use of outputs as inputs of other tools.
+*Warnings*: this is different from the 'Outputs description' section following the Parameters section.
+
+----------------------------
+EXAMPLE OF WORKFLOW POSITION
+----------------------------
+
+Ideally a picture positioning the current tool in a workflow of complementary tools. 
+Can also be lists of upstream and downstream tools. 
+
+---------------------------------------------------
+
+===============
+TOOL PARAMETERS
+===============
+
+Usually a list of parameters. 
+Can be one or several of the following:
+
+- a list of all the Galaxy parameters with associated description
+- a list of the key parameters of the Galaxy module with associated description
+- a list of all the parameters for which additionnal information may be needed compared to the message in the help tag of the input XML tag
+- explaination of (key) parameters and how they interconnect
+- a list associating parameters and recommandations (including potential specific subcases)
+
+---------------------------------------------------
+
+==================
+OUTPUT DESCRIPTION
+==================
+
+List of the different possible outputs generated by the Galaxy module, with a content description. 
+
+If information relevant to the users is displayed in the "standard output" when running the module, do not forget to mention it here. 
+
+---------------------------------------------------
+
+==============
+EXAMPLE OF USE
+==============
+
+Can be either the following:
+
+- a working with accessible inputs, the list of parameters to use and the display of expected outputs
+- a step-by-step procedure to illustrate how to set the different parameters and what result should be expected
+- a reference to existing examples or use-cases, for example specific sections of existing GTN materials using the tool
+
+If not mentioned elsewhere, you can also add a subsection regarding known issues (when relevant). 
+
+Example:
+
+------------
+KNOWN ISSUES
+------------
+
+A list of issues users may run into when using the Galaxy module (*e.g.* case-sensitivity issues)
+
+---------------------------------------------------
+
+==========
+CHANGE LOG
+==========
+
+-------------------------------
+Galaxy version number (current)
+-------------------------------
+
+NEW FEATURES
+
+- new feature 1
+- new feature 2
+
+BUG FIXING
+
+- fixed bug 1
+- fixed bug 2
+
+INTERNAL MODIFICATION
+
+- change 1
+- change 2
+
+-----------------------------
+Galaxy version number (older)
+-----------------------------
+
+NEW FEATURES
+
+- new feature 1
+- new feature 2
+
+BUG FIXING
+
+- fixed bug 1
+- fixed bug 2
+
+INTERNAL MODIFICATION
+
+- change 1
+- change 2
+
+-----------------------------
+Galaxy version number (older)
+-----------------------------
+
+NEW FEATURES
+
+- new feature 1
+- new feature 2
+
+BUG FIXING
+
+- fixed bug 1
+- fixed bug 2
+
+INTERNAL MODIFICATION
+
+- change 1
+- change 2
+
+]]></help>