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comparison filter_alignment.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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1 <tool id="qiime_filter_alignment" name="filter alignment" version="1.9.1galaxy1">
2 <description>Filter sequence alignment by removing highly variable
3 regions</description>
4
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8
9 <expand macro="requirements" />
10
11 <command><![CDATA[
12 filter_alignment.py -i $input_fasta_file -o filter_alignment_output
13 #if str($lane_mask_fp) != 'None':
14 -m $lane_mask_fp
15 #end if
16
17 #if $suppress_lane_mask_filter:
18 -s
19 #end if
20
21 #if $allowed_gap_frac:
22 -g $allowed_gap_frac
23 #end if
24
25 #if $remove_outliers:
26 -r
27 #end if
28
29 #if $threshold:
30 -t $threshold
31 #end if
32
33 #if $entropy_threshold:
34 -e $entropy_threshold
35 #end if
36 ]]>
37 </command>
38
39 <inputs>
40 <param label="-i/--input_fasta_file: the input fasta file containing the
41 alignment" name="input_fasta_file" optional="False" type="data"/>
42 <param default="None" label="-m/--lane_mask_fp: path to lane mask file
43 [default: 16S alignment lane mask (Lane, D.J. 1991)]"
44 name="lane_mask_fp" optional="True" type="data"/>
45 <param label="-s/--suppress_lane_mask_filter: suppress lane mask filtering
46 [default: False]" name="suppress_lane_mask_filter" selected="False"
47 type="boolean"/>
48 <param default="0.999999" label="-g/--allowed_gap_frac: gap filter threshold,
49 filters positions which are gaps in &gt; allowed_gap_frac of the
50 sequences [default: 0.999999]" name="allowed_gap_frac" optional="True"
51 type="float"/>
52 <param label="-r/--remove_outliers: remove seqs very dissimilar to the
53 alignment consensus (see --threshold). [default: False]"
54 name="remove_outliers" selected="False" type="boolean"/>
55 <param default="3.0" label="-t/--threshold: with -r, remove seqs whose
56 dissimilarity to the consensus sequence is approximately &gt; x standard
57 deviations above the mean of the sequences [default: 3.0]" name="threshold"
58 optional="True" type="float"/>
59 <param default="None" label="-e/--entropy_threshold: Percent threshold for
60 removing base positions with the highest entropy, expressed as a
61 fraction between 0 and 1. For example, if 0.10 were specified, the
62 top 10% most entropic base positions would be filtered. If this
63 value is used, any lane mask supplied will be ignored. Entropy filtering
64 occurs after gap filtering. [default: None]" name="entropy_threshold"
65 optional="True" type="float"/>
66 </inputs>
67
68 <outputs>
69 <data format="fasta" name="pfiltered.fasta"
70 from_work_dir="filter_alignment_output/*pfiltered.fasta"
71 label="filtered_alignement.fasta"/>
72 </outputs>
73
74 <tests>
75 <test>
76 </test>
77 </tests>
78
79 <help><![CDATA[
80 **What it does**
81
82 This script should be applied to generate a useful tree when aligning against a
83 template alignment (e.g., with PyNAST). This script will remove positions which
84 are gaps in every sequence (common for PyNAST, as typical sequences cover only
85 200-400 bases, and they are being aligned against the full 16S gene). Additionally,
86 the user can supply a lanemask file, that defines which positions should included
87 when building the tree, and which should be ignored. Typically, this will differentiate
88 between non-conserved positions, which are uninformative for tree building, and
89 conserved positions which are informative for tree building. FILTERING ALIGNMENTS
90 WHICH WERE BUILT WITH PYNAST AGAINST THE GREENGENES CORE SET ALIGNMENT SHOULD BE
91 CONSIDERED AN ESSENTIAL STEP.
92
93 The output of filter_alignment.py consists of a single FASTA file, which ends with
94 &quot;pfiltered.fasta&quot;, where the &quot;p&quot; stands for positional
95 filtering of the columns.
96 ]]>
97 </help>
98
99 <citations>
100 <expand macro="citations" />
101 </citations>
102 </tool>