Mercurial > repos > iuc > mothur_filter_seqs

comparison filter.seqs.xml @ 1:74e541cb0f87 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:36:18 -0400
parents 32f444a36d12
children 3ced7f00e40b
comparison
equal deleted inserted replaced
0:32f444a36d12 1:74e541cb0f87
2 <description>removes columns from alignments</description> 2 <description>removes columns from alignments</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$fasta" fasta.dat && 13 ln -s "$fasta" fasta.dat &&
11 #for $i in $inputs: 14 #for $i in $inputs:
12 ln -s "$i.fasta" fasta${inputs.index($i)}.dat && 15 ln -s "$i.fasta" fasta${inputs.index($i)}.dat &&
13 #end for 16 #end for
24 hard=hard.dat, 27 hard=hard.dat,
25 #end if 28 #end if
26 processors='\${GALAXY_SLOTS:-8}' 29 processors='\${GALAXY_SLOTS:-8}'
27 )' 30 )'
28 | sed 's/ //g' ## mothur trips over whitespace 31 | sed 's/ //g' ## mothur trips over whitespace
29 | mothur && 32 | mothur
33 | tee mothur.out.log &&
30 34
31 ## rename collection files for more transparent element naming 35 ## rename collection files for more transparent element naming
32 mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta && 36 mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta
33 #for i in $inputs: 37 #for i in $inputs:
34 mv fasta${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
35 #end for 39 #end for
36 ]]></command> 40 ]]></command>
37 <inputs> 41 <inputs>
38 <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"/>
39 <repeat name="inputs" title="Additional Alignment File" optional="true"> 43 <repeat name="inputs" title="Additional Alignment File">
40 <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"/>
41 </repeat> 45 </repeat>
42 <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" help="Ignore any column that only contains gap characters (i.e. '-' or '.')"/>
43 <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 <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">
44 <option value="">Off</option> 48 <option value="">Off</option>
52 <outputs> 56 <outputs>
53 <expand macro="logfile-output"/> 57 <expand macro="logfile-output"/>
54 <data name="out_filter" format="mothur.filter" from_work_dir="fasta*.filter" label="${tool.name} on ${on_string}: filter"/> 58 <data name="out_filter" format="mothur.filter" from_work_dir="fasta*.filter" label="${tool.name} on ${on_string}: filter"/>
55 <collection name="filteredfastas" type="list" label="${tool.name} on ${on_string}: filtered fastas"> 59 <collection name="filteredfastas" type="list" label="${tool.name} on ${on_string}: filtered fastas">
56 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.filter\.fasta" format="fasta"/> 60 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.filter\.fasta" format="fasta"/>
61 <filter>inputs</filter> <!-- only output collection if multiple outputs-->
57 </collection> 62 </collection>
63 <data name="filteredfasta" format="fasta" from_work_dir="*.filter.fasta" label="${tool.name} on ${on_string}: filtered fasta">
64 <filter>not inputs</filter>
65 </data>
58 </outputs> 66 </outputs>
59 <tests> 67 <tests>
60 <test> 68 <test><!-- test with multiple inputs and collection output -->
61 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/> 69 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
62 <repeat name="inputs"> 70 <repeat name="inputs">
63 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/> 71 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
64 </repeat> 72 </repeat>
65 <output name="out_filter" md5="3e6c2cfef46baf35d2a8b5cafe53e3a4"/> 73 <output name="out_filter" md5="3e6c2cfef46baf35d2a8b5cafe53e3a4"/>
66 <output_collection name="filteredfastas" count="2"> 74 <output_collection name="filteredfastas" count="2">
67 <element name="HMP_MOCK.v35.align" md5="ef4c6c2d9a882f7a22e5fa3c814af7cc" ftype="fasta"/> 75 <element name="HMP_MOCK.v35.align" md5="ef4c6c2d9a882f7a22e5fa3c814af7cc" ftype="fasta"/>
68 </output_collection> 76 </output_collection>
69 <expand macro="logfile-test"/> 77 <expand macro="logfile-test"/>
70 </test> 78 </test>
79 <test><!-- test with single input and non-collection output -->
80 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
81 <output name="out_filter" md5="3e6c2cfef46baf35d2a8b5cafe53e3a4"/>
82 <output name="filteredfasta" md5="ef4c6c2d9a882f7a22e5fa3c814af7cc"/>
83 <expand macro="logfile-test"/>
84 </test>
71 </tests> 85 </tests>
72 <help> 86 <help>
73 <![CDATA[ 87 <![CDATA[
74 88
75 @MOTHUR_OVERVIEW@ 89 @MOTHUR_OVERVIEW@
76 90
77 **Command Documenation** 91 **Command Documentation**
78 92
79 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. 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.
80 94
81 .. _filter.seqs: http://www.mothur.org/wiki/Filter.seqs 95 .. _filter.seqs: https://www.mothur.org/wiki/Filter.seqs
82 96
83 v.1.20.0: Updated to Mothur 1.33 97 v.1.20.0: Updated to Mothur 1.33
84 98
85 ]]> 99 ]]>
86 </help> 100 </help>