Mercurial > repos > iuc > mothur_screen_seqs

comparison screen.seqs.xml @ 9:c1feef4d5e34 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
author iuc
date Tue, 08 Dec 2020 12:46:21 +0000
parents 6202ff80199f
children
comparison
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8:f4d7d5755f01 9:c1feef4d5e34
1 <tool profile="16.07" id="mothur_screen_seqs" name="Screen.seqs" version="@WRAPPER_VERSION@.0"> 1 <tool profile="16.07" id="mothur_screen_seqs" name="Screen.seqs" version="@WRAPPER_VERSION@.1">
2 <description>Screen sequences</description> 2 <description>Screen sequences</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"/>
46 #end if 46 #end if
47 #if int($criteria) > -1: 47 #if int($criteria) > -1:
48 ,criteria=$criteria 48 ,criteria=$criteria
49 #end if 49 #end if
50 #if $optimize: 50 #if $optimize:
51 ,optimize=$optimize 51 ,optimize=#echo str($optimize).replace(',','-') #
52 #end if 52 #end if
53 #if $qfile: 53 #if $qfile:
54 ,qfile=qfile.dat 54 ,qfile=qfile.dat
55 #end if 55 #end if
56 #if $names: 56 #if $names:
174 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/> 174 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
175 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos" ftype="mothur.accnos"/> 175 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos" ftype="mothur.accnos"/>
176 <param name="savelog" value="true"/> 176 <param name="savelog" value="true"/>
177 <expand macro="logfile-test"/> 177 <expand macro="logfile-test"/>
178 </test> 178 </test>
179 <test><!-- test for multiple optimize options minlenght, maxlength, maxhomop -->
180 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
181 <param name="criteria" value="50"/>
182 <param name="optimize" value="minlength,maxlength,maxhomop"/>
183 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.minlength.maxlength.maxhomop.good.fasta" ftype="fasta"/>
184 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.minlength.maxlength.maxhomop.bad.accnos" ftype="mothur.accnos"/>
185 <param name="savelog" value="true"/>
186 <expand macro="logfile-test"/>
187 </test>
188 <test><!-- test for multiple optimize options end, maxambig -->
189 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
190 <param name="criteria" value="50"/>
191 <param name="optimize" value="end,maxambig"/>
192 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.end.maxambig.good.fasta" ftype="fasta"/>
193 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.end.maxambig.bad.accnos" ftype="mothur.accnos"/>
194 <param name="savelog" value="true"/>
195 <expand macro="logfile-test"/>
196 </test>
179 <test><!-- test with count table --> 197 <test><!-- test with count table -->
180 <param name="fasta" value="amazon.fasta" ftype="mothur.align"/> 198 <param name="fasta" value="amazon.fasta" ftype="mothur.align"/>
181 <param name="count" value="amazon1.count_table"/> 199 <param name="count" value="amazon1.count_table"/>
182 <param name="maxambig" value="0"/> 200 <param name="maxambig" value="0"/>
183 <param name="maxlength" value="500"/> 201 <param name="maxlength" value="500"/>