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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="filter_alignment" name="filter_alignment" version="1.2.0">
2 <description>Filter sequence alignment by removing highly variable regions</description>
3 <requirements>
4 <requirement type="binary">filter_alignment.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 ## --galaxy_tmpdir='$__new_file_path__'
9 --galaxy_outputdir='$pfiltered_fasta.extra_files_path'
10 --galaxy_datasets='^\S+_pfiltered\.\S+$:'$pfiltered_fasta
11 filter_alignment.py
12 --input_fasta_file=$input_fasta_file
13 --output_dir='$pfiltered_fasta.extra_files_path'
14 --lane_mask_fp=$lane_mask_fp
15 $suppress_lane_mask_filter
16 --allowed_gap_frac=$allowed_gap_frac
17 $remove_outliers
18 --threshold=$threshold
19 </command>
20 <inputs>
21 <param name="input_fasta_file" type="data" format="align" label="input_fasta_file"
22 help="the input directory [REQUIRED]"/>
23 <param name="lane_mask_fp" type="data" format="filter" label="lane_mask_fp"
24 help="path to lanemask file [default: %default]"/>
25 <param name="suppress_lane_mask_filter" type="boolean" truevalue="--suppress_lane_mask_filter" falsevalue="" checked="false" label="suppress_lane_mask_filter"
26 help="suppress lane mask filtering (necessary to turn off lane-mask-based filtering when a qiime_config default is provided for --lane_mask_fp) [default: False]"/>
27 <param name="allowed_gap_frac" type="float" value="0.999999" label="allowed_gap_frac"
28 help="gap filter threshold, filters positions which are gaps in } allowed_gap_frac of the sequences [default: 0.999999]"/>
29 <param name="remove_outliers" type="boolean" truevalue="--remove_outliers" falsevalue="" checked="false" label="remove_outliers"
30 help="remove seqs very dissimilar to the alignment consensus (see --threshold). [default: False]"/>
31 <param name="threshold" type="float" value="3.0" label="threshold"
32 help="with -r, remove seqs whose dissimilarity to the consensus sequence is approximately } x standard devaitions above the mean of the sequences [default: 3.0]"/>
33 </inputs>
34 <outputs>
35 <data format="align" name="pfiltered_fasta" label="${tool.name} on ${on_string}: pfiltered.fasta"/>
36 </outputs>
37 <tests>
38 </tests>
39 <help>
40
41 </help>
42 </tool>
43