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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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1 <tool id="make_qiime_py_file" name="make_qiime_py_file" version="1.2.0">
2 <description>Create python file</description>
3 <requirements>
4 <requirement type="binary">make_qiime_py_file.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 make_qiime_py_file.py
10 --output_fp=$output_fp
11 $script
12 $test
13 --author_name=$author_name
14 --author_email=$author_email
15 --copyright=$copyright
16 </command>
17 <inputs>
18 <param name="script" type="boolean" truevalue="--script" falsevalue="" checked="false" label="script"
19 help="Pass if creating a script to include option parsing framework [default:False]."/>
20 <param name="test" type="boolean" truevalue="--test" falsevalue="" checked="false" label="test"
21 help="Pass if creating a unit test file to include relevant information [default:False]."/>
22 <param name="author_name" type="text" value="AUTHOR_NAME" label="author_name"
23 help="The script author's (probably you) name to be included the header variables. This will typically need to be enclosed in quotes to handle spaces. [default:AUTHOR_NAME]"/>
24 <param name="author_email" type="text" value="AUTHOR_EMAIL" label="author_email"
25 help="The script author's (probably you) e-mail address to be included the header variables. [default:AUTHOR_EMAIL]"/>
26 <param name="copyright" type="text" value="Copyright 2010, The QIIME project" label="copyright"
27 help="The copyright information to be included in the header variables. [default:Copyright 2010, The QIIME project]"/>
28 </inputs>
29 <outputs>
30 <data format="txt" name="output_fp"/>
31 </outputs>
32 <tests>
33 </tests>
34 <help>
35
36 </help>
37 </tool>
38