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Introduction

Tool wrapping is quite challenging. Most tools will require the use of a trick or established pattern to solve problems related to running programs on galaxy. We need a place to store tricky situations alongside the patterns which solve those situations.

This file is intended to be the reference which stores tool xml patterns and workarounds for tricky situations.


Contents


Variables

Setting and accessing variables

cheetah and environment variables

cheetah

#set myvar = 1
echo $myvar

environment

export MYVAR=1 (note there is no whitespace around '=')
echo \$MYVAR   (note the dollar is escaped)

embedded commands

cheetah

#set date='`date +"%Y-%m-%d"`'  (note the extra pair of quotes around the backticks)
echo $date

environment

export DATE=`date +"%Y-%m-%d"`
echo \$DATE

Filetypes

Getting filetype from object

Simplest approach:

$input.is_of_type('fastq')

example: sorting list of history inputs by file type

#def sort_fastq_fasta(files):
    #set fastqs = [f for f in $files if f.is_of_type('fastq')]
    #set fastas = [f for f in $files if f.is_of_type('fasta')]
    #set out = $fastqs + $fastas
    #return $out
#end def

Imports

Import a local Python module

Sometimes it is useful to export complex logic to a Python file.

But you can't do this:

import mymodule

Or this:

from . import mymodule

...because who knows where the Python interpreter is at runtime?

Sometimes it may be cleaner to call a Python script with bash in the <command> section, but this is not an option if you are writing a <configfile>.

Solution

This seems to work reliably:

## Import render module from ./subdir/render.py to template some app code
## -----------------------------------------------------------------------------
#import os
#import importlib.util
#set modpath = $os.path.join($__tool_directory__, "subdir/render.py")
#set spec = $importlib.util.spec_from_file_location("render", $modpath)
#set render = $importlib.util.module_from_spec(spec)
#$spec.loader.exec_module(render)

## render.app() should return and insert templated code as a string
$render.app($input1, $input2, $input3)

Static files

Sometimes you'll see tools with a static folder in the tool root. Static assets in this folder can be accessed in the tool help section.

Note: This won't work in development. These static files are collected and served from the Toolshed, so will only work if the tool have been installed from the Toolshed. On Galaxy, static assets will be given a path like this:

Example: Bandage tool

Image URL rendered: https://usegalaxy.org.au/shed_tool_static/toolshed.g2.bx.psu.edu/iuc/bandage/bandage_image/0.8.1+galaxy3/bandage_graph.png

Take this tool directory:

test-data/
static/
  - images/
    - logo.png
mytool.xml

In the <help> section of mytool.xml you can reference the image logo.png like so:

<help><![CDATA[

Help text blah blah blah

.. image:: $PATH_TO_IMAGES/logo.png
:height: 500
:alt: Tool logo

Blah blah blah

]]></help>