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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="truncate_fasta_qual_files" name="truncate_fasta_qual_files" version="1.2.0">
2 <description>Generates filtered fasta and quality score files by truncating at the specified base position.</description>
3 <requirements>
4 <requirement type="binary">truncate_fasta_qual_files.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 truncate_fasta_qual_files.py
10 --fasta_fp=$fasta_fp
11 --qual_fp=$qual_fp
12 --base_pos=$base_pos
13 --output_dir=$__new_file_path__
14 </command>
15 <inputs>
16 <param name="fasta_fp" type="data" format="fasta" label="fasta_fp"
17 help="Fasta file. Needed to test for congruety between the number of nucleotides in the fasta file and quality scores in the qual file. [REQUIRED]"/>
18 <param name="qual_fp" type="data" format="qual" label="qual_fp"
19 help="Quality score file used to generate histogram data. [REQUIRED]"/>
20 <param name="base_pos" type="text" label="base_pos"
21 help="Nucleotide position to truncate the fasta and quality score files at. [REQUIRED]"/>
22 </inputs>
23 <outputs>
24
25 </outputs>
26 <tests>
27 </tests>
28 <help>
29
30 </help>
31 </tool>
32