Mercurial > repos > iuc > mothur_filter_seqs

annotate filter.seqs.xml @ 4:e71c69acde3f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
author iuc
date Mon, 23 Apr 2018 09:34:35 -0400
parents c799faca02a1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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870f2a438139 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_filter_seqs" name="Filter.seqs" version="@WRAPPER_VERSION@.0">
870f2a438139 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>removes columns from alignments</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
870f2a438139 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11 #import re
0
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12
2
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13 ## create symlinks to input datasets
c799faca02a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$fasta' fasta.dat &&
c799faca02a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 #for $i in $inputs:
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16 ln -s '$i.fasta' fasta${inputs.index($i)}.dat &&
c799faca02a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 #end for
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18 ln -s '$hard' hard.dat &&
0
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19
2
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20 echo 'filter.seqs(
c799faca02a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 fasta=fasta.dat#for $i in $inputs#-fasta${inputs.index($i)}.dat#end for#,
c799faca02a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 vertical=$vertical,
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23 #if $trump:
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24 trump=$trump,
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25 #end if
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26 soft=$soft,
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27 #if $hard:
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28 hard=hard.dat,
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29 #end if
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30 processors='\${GALAXY_SLOTS:-8}'
c799faca02a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 )'
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32 | sed 's/ //g' ## mothur trips over whitespace
c799faca02a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 | mothur
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34 | tee mothur.out.log &&
0
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35
2
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36 ## rename collection files for more transparent element naming
4
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37 #set $identifier=re.sub('[^\w\-\s\.]', '_', str($fasta.element_identifier))
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38 mv fasta.filter.fasta '${identifier}.filter.fasta'
2
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39 #for i in $inputs:
4
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40 #set $identifier=re.sub('[^\w\-\s]', '_', str($i.fasta.element_identifier))
e71c69acde3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
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41 && mv fasta${inputs.index($i)}.filter.fasta '${identifier}.filter.fasta'
2
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42 #end for
0
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43 ]]></command>
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44 <inputs>
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45 <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
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46 <repeat name="inputs" title="Additional Alignment File">
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47 <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
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48 </repeat>
2
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49 <param name="vertical" type="boolean" checked="true" truevalue="true" falsevalue="false" label="vertical - Vertical column"
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50 help="Ignore any column that only contains gap characters (i.e. '-' or '.')"/>
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51 <param name="trump" type="select" label="trump - Trump character"
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52 help="Remove a column if the trump character is found at that position in any sequence of the alignment">
0
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53 <option value="">Off</option>
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54 <option value=".">.</option>
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55 <option value="-">-</option>
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56 <option value="N">N</option>
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57 </param>
2
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58 <param name="soft" type="integer" value="0" min="0" max="100" label="soft - percentage required to retain column. (0-100)"
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59 help="Removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences"/>
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60 <param name="hard" type="data" format="mothur.filter" optional="True" label="hard - Hard Column Filter"
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61 help="A file should only contain one line consisting of 0's and 1's"/>
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62 <expand macro="param-savelog"/>
0
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63 </inputs>
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64 <outputs>
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65 <expand macro="logfile-output"/>
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66 <data name="out_filter" format="mothur.filter" from_work_dir="fasta*.filter" label="${tool.name} on ${on_string}: filter"/>
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67 <collection name="filteredfastas" type="list" label="${tool.name} on ${on_string}: filtered fastas">
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68 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.filter\.fasta" format="fasta"/>
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69 <filter>inputs</filter> <!-- only output collection if multiple outputs-->
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70 </collection>
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71 <data name="filteredfasta" format="fasta" from_work_dir="*.filter.fasta" label="${tool.name} on ${on_string}: filtered fasta">
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72 <filter>not inputs</filter>
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73 </data>
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74 </outputs>
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75 <tests>
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76 <test><!-- test with multiple inputs and collection output -->
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77 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
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78 <repeat name="inputs">
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79 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
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80 </repeat>
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81 <output name="out_filter" md5="3e6c2cfef46baf35d2a8b5cafe53e3a4"/>
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82 <output_collection name="filteredfastas" count="2">
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83 <element name="HMP_MOCK.v35.align" md5="ef4c6c2d9a882f7a22e5fa3c814af7cc" ftype="fasta"/>
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84 </output_collection>
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85 <param name="savelog" value="true"/>
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86 <expand macro="logfile-test"/>
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87 </test>
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88 <test><!-- test with single input and non-collection output -->
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89 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
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90 <output name="out_filter" md5="3e6c2cfef46baf35d2a8b5cafe53e3a4"/>
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91 <output name="filteredfasta" md5="ef4c6c2d9a882f7a22e5fa3c814af7cc"/>
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92 <param name="savelog" value="true"/>
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93 <expand macro="logfile-test"/>
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94 </test>
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95 </tests>
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96 <help><![CDATA[
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97
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98 @MOTHUR_OVERVIEW@
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99
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100 **Command Documentation**
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101
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102 The filter.seqs_ command removes columns from alignments based on a criteria defined by the user. For example, alignments
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103 generated against reference alignments (e.g. from RDP, SILVA, or greengenes) often have columns where every character is
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104 either a '.' or a '-'. These columns are not included in calculating distances because they have no information in them.
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105 By removing these columns, the calculation of a large number of distances is accelerated. Also, people also like to mask
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106 their sequences to remove variable regions using a soft or hard mask (e.g. Lane's mask). This type of masking is only
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107 encouraged for deep-level phylogenetic analysis, not fine level analysis such as that needed with calculating OTUs.
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108
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109 .. _filter.seqs: https://www.mothur.org/wiki/Filter.seqs
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110
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111 v.1.20.0: Updated to Mothur 1.33
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112
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113 ]]></help>
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114 <expand macro="citations"/>
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115 </tool>