Mercurial > repos > iuc > mothur_filter_seqs

comparison filter.seqs.xml @ 3:3ced7f00e40b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:40:41 -0500
parents 74e541cb0f87
children ff039df26c3f
comparison
equal deleted inserted replaced
2:410d665a16a0 3:3ced7f00e40b
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 #for $i in $inputs: 14 #for $i in $inputs:
15 ln -s "$i.fasta" fasta${inputs.index($i)}.dat && 15 ln -s '$i.fasta' fasta${inputs.index($i)}.dat &&
16 #end for 16 #end for
17 ln -s "$hard" hard.dat && 17 ln -s '$hard' hard.dat &&
18 18
19 echo 'filter.seqs( 19 echo 'filter.seqs(
20 fasta=fasta.dat#for $i in $inputs#-fasta${inputs.index($i)}.dat#end for#, 20 fasta=fasta.dat#for $i in $inputs#-fasta${inputs.index($i)}.dat#end for#,
21 vertical=$vertical, 21 vertical=$vertical,
22 #if $trump: 22 #if $trump:
23 trump=$trump, 23 trump=$trump,
24 #end if 24 #end if
25 soft=$soft, 25 soft=$soft,
26 #if $hard: 26 #if $hard:
27 hard=hard.dat, 27 hard=hard.dat,
28 #end if 28 #end if
29 processors='\${GALAXY_SLOTS:-8}' 29 processors='\${GALAXY_SLOTS:-8}'
30 )' 30 )'
31 | sed 's/ //g' ## mothur trips over whitespace 31 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur 32 | mothur
33 | tee mothur.out.log && 33 | tee mothur.out.log &&
34 34
35 ## rename collection files for more transparent element naming 35 ## rename collection files for more transparent element naming
36 mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta 36 mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta
37 #for i in $inputs: 37 #for i in $inputs:
38 && mv fasta${inputs.index($i)}.filter.fasta "${i.fasta.element_identifier}".filter.fasta 38 && mv fasta${inputs.index($i)}.filter.fasta "${i.fasta.element_identifier}".filter.fasta
39 #end for 39 #end for
40 ]]></command> 40 ]]></command>
41 <inputs> 41 <inputs>
42 <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/> 42 <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
43 <repeat name="inputs" title="Additional Alignment File"> 43 <repeat name="inputs" title="Additional Alignment File">
44 <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/> 44 <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
45 </repeat> 45 </repeat>
46 <param name="vertical" type="boolean" checked="true" truevalue="true" falsevalue="false" label="vertical - Vertical column" help="Ignore any column that only contains gap characters (i.e. '-' or '.')"/> 46 <param name="vertical" type="boolean" checked="true" truevalue="true" falsevalue="false" label="vertical - Vertical column"
47 <param name="trump" type="select" label="trump - Trump character" help="Remove a column if the trump character is found at that position in any sequence of the alignment"> 47 help="Ignore any column that only contains gap characters (i.e. '-' or '.')"/>
48 <param name="trump" type="select" label="trump - Trump character"
49 help="Remove a column if the trump character is found at that position in any sequence of the alignment">
48 <option value="">Off</option> 50 <option value="">Off</option>
49 <option value=".">.</option> 51 <option value=".">.</option>
50 <option value="-">-</option> 52 <option value="-">-</option>
51 <option value="N">N</option> 53 <option value="N">N</option>
52 </param> 54 </param>
53 <param name="soft" type="integer" value="0" min="0" max="100" label="soft - percentage required to retain column. (0-100)" 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"/> 55 <param name="soft" type="integer" value="0" min="0" max="100" label="soft - percentage required to retain column. (0-100)"
54 <param name="hard" type="data" format="mothur.filter" optional="True" label="hard - Hard Column Filter" help="A file should only contain one line consisting of 0's and 1's"/> 56 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"/>
57 <param name="hard" type="data" format="mothur.filter" optional="True" label="hard - Hard Column Filter"
58 help="A file should only contain one line consisting of 0's and 1's"/>
55 </inputs> 59 </inputs>
56 <outputs> 60 <outputs>
57 <expand macro="logfile-output"/> 61 <expand macro="logfile-output"/>
58 <data name="out_filter" format="mothur.filter" from_work_dir="fasta*.filter" label="${tool.name} on ${on_string}: filter"/> 62 <data name="out_filter" format="mothur.filter" from_work_dir="fasta*.filter" label="${tool.name} on ${on_string}: filter"/>
59 <collection name="filteredfastas" type="list" label="${tool.name} on ${on_string}: filtered fastas"> 63 <collection name="filteredfastas" type="list" label="${tool.name} on ${on_string}: filtered fastas">
81 <output name="out_filter" md5="3e6c2cfef46baf35d2a8b5cafe53e3a4"/> 85 <output name="out_filter" md5="3e6c2cfef46baf35d2a8b5cafe53e3a4"/>
82 <output name="filteredfasta" md5="ef4c6c2d9a882f7a22e5fa3c814af7cc"/> 86 <output name="filteredfasta" md5="ef4c6c2d9a882f7a22e5fa3c814af7cc"/>
83 <expand macro="logfile-test"/> 87 <expand macro="logfile-test"/>
84 </test> 88 </test>
85 </tests> 89 </tests>
86 <help> 90 <help><![CDATA[
87 <![CDATA[
88 91
89 @MOTHUR_OVERVIEW@ 92 @MOTHUR_OVERVIEW@
90 93
91 **Command Documentation** 94 **Command Documentation**
92 95
93 The filter.seqs_ command removes columns from alignments based on a criteria defined by the user. For example, alignments generated against reference alignments (e.g. from RDP, SILVA, or greengenes) often have columns where every character is either a '.' or a '-'. These columns are not included in calculating distances because they have no information in them. By removing these columns, the calculation of a large number of distances is accelerated. Also, people also like to mask their sequences to remove variable regions using a soft or hard mask (e.g. Lane's mask). This type of masking is only encouraged for deep-level phylogenetic analysis, not fine level analysis such as that needed with calculating OTUs. 96 The filter.seqs_ command removes columns from alignments based on a criteria defined by the user. For example, alignments
97 generated against reference alignments (e.g. from RDP, SILVA, or greengenes) often have columns where every character is
98 either a '.' or a '-'. These columns are not included in calculating distances because they have no information in them.
99 By removing these columns, the calculation of a large number of distances is accelerated. Also, people also like to mask
100 their sequences to remove variable regions using a soft or hard mask (e.g. Lane's mask). This type of masking is only
101 encouraged for deep-level phylogenetic analysis, not fine level analysis such as that needed with calculating OTUs.
94 102
95 .. _filter.seqs: https://www.mothur.org/wiki/Filter.seqs 103 .. _filter.seqs: https://www.mothur.org/wiki/Filter.seqs
96 104
97 v.1.20.0: Updated to Mothur 1.33 105 v.1.20.0: Updated to Mothur 1.33
98 106
99 ]]> 107 ]]></help>
100 </help>
101 <expand macro="citations"/> 108 <expand macro="citations"/>
102 </tool> 109 </tool>