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comparison trim.seqs.xml @ 1:08692ab7170c 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 18:38:04 -0400
parents 47923befeb9a
children e695fda56931
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0:47923befeb9a 1:08692ab7170c
2 <description>Trim sequences - primers, barcodes, quality</description> 2 <description>Trim sequences - primers, barcodes, quality</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 ln -s "$names" names.dat && 14 ln -s "$names" names.dat &&
12 ln -s "$count" count.dat && 15 ln -s "$count" count.dat &&
13 #if $oligo.add == "yes": 16 #if $oligo.add == "yes":
56 #end if 59 #end if
57 processors='\${GALAXY_SLOTS:-8}' 60 processors='\${GALAXY_SLOTS:-8}'
58 )' 61 )'
59 | sed 's/ //g' ## mothur trips over whitespace 62 | sed 's/ //g' ## mothur trips over whitespace
60 | mothur 63 | mothur
64 | tee mothur.out.log
61 ## prevent these two files from being gathered into collection 65 ## prevent these two files from being gathered into collection
62 && mv fasta.trim.fasta fasta.trim 66 && mv fasta.trim.fasta fasta.trim
63 && mv fasta.scrap.fasta fasta.scrap 67 && mv fasta.scrap.fasta fasta.scrap
64 ]]></command> 68 ]]></command>
65 <inputs> 69 <inputs>
155 <output name="scrap_names" md5="80f9252837e4b189f06ec00469b88e85" ftype="mothur.names"/> 159 <output name="scrap_names" md5="80f9252837e4b189f06ec00469b88e85" ftype="mothur.names"/>
156 <expand macro="logfile-test"/> 160 <expand macro="logfile-test"/>
157 </test> 161 </test>
158 <test><!-- test with count table --> 162 <test><!-- test with count table -->
159 <param name="fasta" value="amazon.fasta" ftype="fasta"/> 163 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
160 <param name="count" value="amazon.count_table" ftype="mothur.count_table"/> 164 <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
161 <param name="maxhomop" value="4"/> 165 <param name="maxhomop" value="4"/>
162 <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/> 166 <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
163 <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/> 167 <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
164 <output name="trim_count" md5="2024cbb895f79346606ab196dd130639" ftype="mothur.count_table"/> 168 <output name="trim_count" md5="836b4d72a8cda3741ef435741783b384" ftype="mothur.count_table"/>
165 <output name="scrap_count" md5="04ae9f50c1b6f0d8d7e1ac28f845dd4c" ftype="mothur.count_table"/> 169 <output name="scrap_count" md5="04ae9f50c1b6f0d8d7e1ac28f845dd4c" ftype="mothur.count_table"/>
166 <expand macro="logfile-test"/> 170 <expand macro="logfile-test"/>
167 </test> 171 </test>
168 <test><!-- test with oligos --> 172 <test><!-- test with oligos -->
169 <param name="fasta" value="amazon.fasta" ftype="fasta"/> 173 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
208 <help> 212 <help>
209 <![CDATA[ 213 <![CDATA[
210 214
211 @MOTHUR_OVERVIEW@ 215 @MOTHUR_OVERVIEW@
212 216
213 **Command Documenation** 217 **Command Documentation**
214 218
215 The trim.seqs_ command provides the preprocessing features needed to screen and sort pyrosequences. The command will enable you to trim off primer sequences and barcodes, use the barcode information to generate a group file and split a fasta file into sub-files, screen sequences based on the qual file that comes from 454 sequencers, cull sequences based on sequence length and the presence of ambiguous bases and get the reverse complement of your sequences. While this analysis is clearly geared towards pyrosequencing collections, it can also be used with traditional Sanger sequences. 219 The trim.seqs_ command provides the preprocessing features needed to screen and sort pyrosequences. The command will enable you to trim off primer sequences and barcodes, use the barcode information to generate a group file and split a fasta file into sub-files, screen sequences based on the qual file that comes from 454 sequencers, cull sequences based on sequence length and the presence of ambiguous bases and get the reverse complement of your sequences. While this analysis is clearly geared towards pyrosequencing collections, it can also be used with traditional Sanger sequences.
216 220
217 .. _trim.seqs: http://www.mothur.org/wiki/Trim.seqs 221 .. _trim.seqs: https://www.mothur.org/wiki/Trim.seqs
218 222
219 ]]> 223 ]]>
220 </help> 224 </help>
221 <expand macro="citations"/> 225 <expand macro="citations"/>
222 </tool> 226 </tool>