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comparison align.seqs.xml @ 1:16083fc07186 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:01:07 -0400
parents 5c0b829902eb
children 4d29fc73525d
comparison
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0:5c0b829902eb 1:16083fc07186
2 <description>Align sequences to a template alignment</description> 2 <description>Align sequences to a template alignment</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 ## enable mothur to find blast 12 ## enable mothur to find blast
10 loc=`which mothur` && ln -s "\${loc%/mothur}"/* . && 13 loc=`which mothur` && ln -s "\${loc%/mothur}"/* . &&
11 14
12 ## create symlinks to input datasets 15 ## create symlinks to input datasets
13 ln -s "$candidate" candidate.dat && 16 ln -s "$candidate" candidate.dat &&
34 #end if 37 #end if
35 processors='\${GALAXY_SLOTS:-8}' 38 processors='\${GALAXY_SLOTS:-8}'
36 )' 39 )'
37 | sed 's/ //g' ## mothur trips over whitespace 40 | sed 's/ //g' ## mothur trips over whitespace
38 | ./mothur 41 | ./mothur
42 | tee mothur.out.log
39 ]]></command> 43 ]]></command>
40 <inputs> 44 <inputs>
41 <param name="candidate" type="data" format="fasta" label="fasta - Candiate Sequences"/> 45 <param name="candidate" type="data" format="fasta" label="fasta - Candiate Sequences"/>
42 <conditional name="alignment"> 46 <conditional name="alignment">
43 <param name="source" type="select" label="Select Reference Template from" help=""> 47 <param name="source" type="select" label="Select Reference Template from" help="">
96 </inputs> 100 </inputs>
97 <outputs> 101 <outputs>
98 <expand macro="logfile-output"/> 102 <expand macro="logfile-output"/>
99 <data name="out_file" format="mothur.align" from_work_dir="candidate.align" label="${tool.name} on ${on_string}: align"/> 103 <data name="out_file" format="mothur.align" from_work_dir="candidate.align" label="${tool.name} on ${on_string}: align"/>
100 <data name="report" format="mothur.align.report" from_work_dir="candidate.align.report" label="${tool.name} on ${on_string}: align.report"/> 104 <data name="report" format="mothur.align.report" from_work_dir="candidate.align.report" label="${tool.name} on ${on_string}: align.report"/>
105 <data name="flip_accnos" format="mothur.accnos" from_work_dir="candidate.flip.accnos" label="${tool.name} on ${on_string}: flip.accnos">
106 <filter>reverse['flip'] == 'yes'</filter>
107 </data>
101 </outputs> 108 </outputs>
102 <tests> 109 <tests>
103 <test> 110 <test>
104 <param name="candidate" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/> 111 <param name="candidate" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
105 <param name="source" value="history"/> 112 <param name="source" value="history"/>
147 <param name="threshold" value="0.5"/> 154 <param name="threshold" value="0.5"/>
148 <output name="out_file" md5="3b89c0afbec5f46e9c0c2974a234bc6e" ftype="mothur.align"/> 155 <output name="out_file" md5="3b89c0afbec5f46e9c0c2974a234bc6e" ftype="mothur.align"/>
149 <output name="report" md5="9ec830c9a278e20d8499ba55fef6f501" ftype="mothur.align.report"/> 156 <output name="report" md5="9ec830c9a278e20d8499ba55fef6f501" ftype="mothur.align.report"/>
150 <expand macro="logfile-test"/> 157 <expand macro="logfile-test"/>
151 </test> 158 </test>
159 <test><!-- test accno file recovery with flip set to true -->
160 <param name="candidate" value="amazon.fasta"/>
161 <param name="source" value="history"/>
162 <param name="template" value="HMP_MOCK.v35.align"/>
163 <param name="flip" value="yes"/>
164 <param name="threshold" value="0.5"/>
165 <output name="out_file" md5="73b3b1d0c1176ed9731eedbda70b5957" ftype="mothur.align"/>
166 <output name="report" md5="e502a984ffb97026f1d84c9aee616003" ftype="mothur.align.report"/>
167 <output name="flip_accnos" md5="afd8e7629be76baa74451b91423aaa2f" ftype="mothur.accnos"/>
168 <expand macro="logfile-test"/>
169 </test>
152 </tests> 170 </tests>
153 <help> 171 <help>
154 <![CDATA[ 172 <![CDATA[
155 173
156 @MOTHUR_OVERVIEW@ 174 @MOTHUR_OVERVIEW@
157 175
158 **Command Documenation** 176 **Command Documentation**
159 177
160 The align.seqs_ command aligns a user-supplied fasta-formatted candidate sequence file to a user-supplied fasta-formatted template_alignment_. 178 The align.seqs_ command aligns a user-supplied fasta-formatted candidate sequence file to a user-supplied fasta-formatted template_alignment_.
161 179
162 The general approach is to 180 The general approach is to
163 i) find the closest template for each candidate using kmer searching, blastn, or suffix tree searching; 181 i) find the closest template for each candidate using kmer searching, blastn, or suffix tree searching;
164 ii) to make a pairwise alignment between the candidate and de-gapped template sequences using the Needleman-Wunsch, Gotoh, or blastn algorithms; and 182 ii) to make a pairwise alignment between the candidate and de-gapped template sequences using the Needleman-Wunsch, Gotoh, or blastn algorithms; and
165 iii) to re-insert gaps to the candidate and template pairwise alignments using the NAST algorithm so that the candidate sequence alignment is compatible with the original template alignment. 183 iii) to re-insert gaps to the candidate and template pairwise alignments using the NAST algorithm so that the candidate sequence alignment is compatible with the original template alignment.
166 184
167 In general the alignment is very fast - we are able to align over 186,000 full-length sequences to the SILVA alignment in less than 3 hrs with a quality as good as the SINA aligner. Furthermore, this rate can be accelerated using multiple processors. While the aligner doesn't explicitly take into account the secondary structure of the 16S rRNA gene, if the template database is based on the secondary structure, then the resulting alignment will at least be implicitly based on the secondary structure. 185 In general the alignment is very fast - we are able to align over 186,000 full-length sequences to the SILVA alignment in less than 3 hrs with a quality as good as the SINA aligner. Furthermore, this rate can be accelerated using multiple processors. While the aligner doesn't explicitly take into account the secondary structure of the 16S rRNA gene, if the template database is based on the secondary structure, then the resulting alignment will at least be implicitly based on the secondary structure.
168 186
169 .. _template_alignment: http://www.mothur.org/wiki/Alignment_database 187 .. _template_alignment: https://www.mothur.org/wiki/Alignment_database
170 .. _align.seqs: http://www.mothur.org/wiki/Align.seqs 188 .. _align.seqs: https://www.mothur.org/wiki/Align.seqs
171 189
172 ]]> 190 ]]>
173 </help> 191 </help>
174 <expand macro="citations"/> 192 <expand macro="citations"/>
175 </tool> 193 </tool>