# New Tool Review Guide

This document describes a checklist suitable as a guide for reviewers of pull requests against the IUC's tools repo. It is a guide only and reviewer discretion is still advised.

**This document is a work in progress!**

The comprehensive list is aimed at new tools. Obviously for tool updates just use the appropriate section of the checklist on the PR diffs.

This checklist is based on the IUC's [Best Practices](https://galaxy-iuc-standards.readthedocs.io/en/latest/index.html) document.

## Repository

* [ ] Is this tool appropriate for the IUC repo (see [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md))
* [ ] Does the tool already exist in the toolshed?
    * [ ] Is this tool warranted?
    * [ ] Does the `iuc` user have write access to the current repo in both Test and Main ToolSheds? (Under "Grant authority to make changes", select `iuc` and click "Grant access")
    * [ ] Does the IUC group have admin access to the current repo in both Test and Main ToolSheds? (Under "Repository Actions" -> "Manager repository administrators": "Intergalactic Utilities Commission" should be present in the "Groups associated with ..." box)
* [ ] If the repository contains more than one tool, should it be separated or made a tool collection?
* [ ] Is there a `.shed.yml` file?
* [ ] Is there a tool `.xml` file?
* [ ] No `tool_dependencies.xml` file. (Has been deprecated and is no longer "Best Practice")


## Files

### .shed.yml

* [ ] Is there a correctly-formatted `.shed.yml` file?
* [ ] Are the categories appropriate?
* [ ] Does the `name` match the folder name and, in the case of a single tool, the tool `.xml` file name?
    - [ ] Alphanumeric and underscore `_` only, no `-`
* [ ] Is the owner set to `iuc`? If this is an existing tool being migrated to tools-iuc, the previous `owner` can be maintained in order to preserve the tool lineage, but the owner need to grant authority to make changes to `iuc` in the main Tool Shed repository page and add `Intergalactic Utilities Commission` to the admin groups in "Manager repository administrators" **before** the PR is merged.
* [ ] Is there a `description`?
* [ ] Are there `homepage_url` and `remote_repository_url` fields? Do they point somewhere sensible?

### tool.xml

**Linting**

* [ ] Does the tool pass planemo/travis lint with no warnings or errors?
* [ ] 4 spaces indentation?

**Order of XML Elements**

* [ ] Are the XML elements in the order suggested in the [Best Practices Coding Style](http://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#coding-style)?

**<tool> (name and id etc.)**

* [ ] Are the `id` and `name` sensible and not previously used?
* [ ] Does the `version` follow [PEP 440](https://www.python.org/dev/peps/pep-0440/) with `+galaxyN`?
* [ ] Is there a `@TOOL_VERSION@` macro token used? (Should there be?)
* [ ] If there is a `profile` attribute, is it appropriate?

**<description>**

* [ ] Is there a description tag?
* [ ] Is the description of suitable length?

**<macros>**

* [ ] If there is more than one tool present (tool collection), is there a `macros.xml` file?
* [ ] Is it appropriate?

**<edam_topics> & <edam_operations>**

* Link to the [EDAM browser](https://bioportal.bioontology.org/ontologies/EDAM?p=classes)

**<[parallelism]>**

**<requirements>**

* [ ] Are there corresponding conda packages in the best practice channels?
* [ ] Are they versioned correctly with `@TOOL_VERSION@`? (or multiple packages/docker containers with correctly described versions)

**<~~code~~>**

* [ ] this element has been deprecated and should not be used (xref. [galaxyproject/galaxy#2712](https://github.com/galaxyproject/galaxy/issues/2712) )

**Error detection**

* [ ] Is there a `<stdio />` element, or does `<command />` have a `detect_errors` attribute, or does the tool specify a `profile` attribute?

**&lt;version_command&gt;**

* [ ] Is there a version command?
* [ ] Is it book-ended with `<![CDATA[ ... ]]>` tags?

**&lt;command&gt;**

* [ ] Is it book-ended with `<![CDATA[ ... ]]>` tags?
* [ ] No `interpreter` attribute for the `<command />` element - This is deprecated.
* [ ] Text parameters, input and output paths `'single quoted'`?
* [ ] Is the Cheetah left-aligned, indented and readable?
* [ ] Are multiple commands joined with `&&`?
* [ ] Are any extra temporary files (such as indices etc.) created in the current working directory?
* [ ] Are parameters of type `text` or having `optional="true"` attribute checked with `if str($param)` before being used?

**&lt;environment_variables&gt;**

**&lt;configfiles&gt;**

**&lt;inputs&gt; and &lt;parameters&gt;**

*General*
* [ ] Do data parameters have a `format` attribute containing datatypes recognised by Galaxy?
* [ ] Are the parameter attributes in the order suggested in the [Best Practices Coding Style](http://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#coding-style)
* [ ] Do the `argument` attributes include the long form of the underlying tool parameters?

*Boolean*
* [ ] Are the `truevalue` and `falsevalue` set with the underlying tool parameter?

*Dynamic Options*
* [ ] Do conditional parameters use a `select` and not a `boolean`
* [ ] Are the advanced parameters of the tool hidden with appropriate `<section>` tags?

**&lt;request_param_translation&gt;**

**&lt;outputs&gt;**

* [ ] Are optional output files selected using `<filter>` tags (with corresponding `<select>` tags in the `<inputs>` section)

**&lt;tests&gt;**

* [ ] Is most of the functionality of the tool tested?
* [ ] Are the test datasets included in the `test-data` directory?
* [ ] Is the test data of suitable size? (i.e. small, ideally <1MB per file)
* [ ] Do the tests pass?
* [ ] Is the output filtering tested using the `expect_num_outputs` attribute?
* [ ] Are there unused files in `test-data/`
* [ ] In the case where the tool uses built in reference data, is there a `tool-data/tool_data_table_conf.xml.test` file?

**&lt;help&gt;**

* [ ] Is it book-ended with `<![CDATA[ ... ]]>` tags?
* [ ] Is it correctly formatted in [restructuredText](http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html)?
* [ ] Are images in the `./static/images` directory?

**&lt;citations&gt;**

* [ ] Is there a citation
    - [ ] Is it in `bibtex` or `doi` format? (`doi` preferred)

### Data Tables

For tools that use the built in reference data and indices:

* [ ] Is there a `tool-data/*.loc.sample` file?
* [ ] Is there a `tool-data/tool_data_table_conf.xml.sample` file?