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annotate filter_alignment.xml @ 0:c1bd0c560018 draft default tip

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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">
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2 <description>Filter sequence alignment by removing highly variable
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3 regions</description>
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4
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements" />
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10
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11 <command><![CDATA[
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12 filter_alignment.py -i $input_fasta_file -o filter_alignment_output
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13 #if str($lane_mask_fp) != 'None':
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14 -m $lane_mask_fp
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15 #end if
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16
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17 #if $suppress_lane_mask_filter:
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18 -s
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19 #end if
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20
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21 #if $allowed_gap_frac:
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22 -g $allowed_gap_frac
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23 #end if
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24
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25 #if $remove_outliers:
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26 -r
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27 #end if
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28
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29 #if $threshold:
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30 -t $threshold
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31 #end if
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32
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33 #if $entropy_threshold:
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34 -e $entropy_threshold
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35 #end if
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36 ]]>
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37 </command>
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38
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39 <inputs>
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40 <param label="-i/--input_fasta_file: the input fasta file containing the
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41 alignment" name="input_fasta_file" optional="False" type="data"/>
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42 <param default="None" label="-m/--lane_mask_fp: path to lane mask file
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43 [default: 16S alignment lane mask (Lane, D.J. 1991)]"
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44 name="lane_mask_fp" optional="True" type="data"/>
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45 <param label="-s/--suppress_lane_mask_filter: suppress lane mask filtering
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46 [default: False]" name="suppress_lane_mask_filter" selected="False"
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47 type="boolean"/>
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48 <param default="0.999999" label="-g/--allowed_gap_frac: gap filter threshold,
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49 filters positions which are gaps in &gt; allowed_gap_frac of the
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50 sequences [default: 0.999999]" name="allowed_gap_frac" optional="True"
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51 type="float"/>
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52 <param label="-r/--remove_outliers: remove seqs very dissimilar to the
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53 alignment consensus (see --threshold). [default: False]"
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54 name="remove_outliers" selected="False" type="boolean"/>
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55 <param default="3.0" label="-t/--threshold: with -r, remove seqs whose
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56 dissimilarity to the consensus sequence is approximately &gt; x standard
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57 deviations above the mean of the sequences [default: 3.0]" name="threshold"
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58 optional="True" type="float"/>
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59 <param default="None" label="-e/--entropy_threshold: Percent threshold for
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60 removing base positions with the highest entropy, expressed as a
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61 fraction between 0 and 1. For example, if 0.10 were specified, the
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62 top 10% most entropic base positions would be filtered. If this
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63 value is used, any lane mask supplied will be ignored. Entropy filtering
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64 occurs after gap filtering. [default: None]" name="entropy_threshold"
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65 optional="True" type="float"/>
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66 </inputs>
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67
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68 <outputs>
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69 <data format="fasta" name="pfiltered.fasta"
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70 from_work_dir="filter_alignment_output/*pfiltered.fasta"
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71 label="filtered_alignement.fasta"/>
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72 </outputs>
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73
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74 <tests>
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75 <test>
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76 </test>
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77 </tests>
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78
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79 <help><![CDATA[
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80 **What it does**
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81
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82 This script should be applied to generate a useful tree when aligning against a
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83 template alignment (e.g., with PyNAST). This script will remove positions which
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84 are gaps in every sequence (common for PyNAST, as typical sequences cover only
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85 200-400 bases, and they are being aligned against the full 16S gene). Additionally,
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86 the user can supply a lanemask file, that defines which positions should included
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87 when building the tree, and which should be ignored. Typically, this will differentiate
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88 between non-conserved positions, which are uninformative for tree building, and
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89 conserved positions which are informative for tree building. FILTERING ALIGNMENTS
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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90 WHICH WERE BUILT WITH PYNAST AGAINST THE GREENGENES CORE SET ALIGNMENT SHOULD BE
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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91 CONSIDERED AN ESSENTIAL STEP.
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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92
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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93 The output of filter_alignment.py consists of a single FASTA file, which ends with
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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94 &quot;pfiltered.fasta&quot;, where the &quot;p&quot; stands for positional
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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95 filtering of the columns.
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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96 ]]>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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97 </help>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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98
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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99 <citations>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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100 <expand macro="citations" />
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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101 </citations>
c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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102 </tool>