Mercurial > repos > iuc > mothur_make_contigs

comparison make.contigs.xml @ 10:80fcd4bf633a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
author iuc
date Thu, 26 Nov 2020 02:09:17 +0000
parents b1b4240133f5
children
comparison
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9:4fc844fea7d0 10:80fcd4bf633a
1 <tool profile="16.07" id="mothur_make_contigs" name="Make.contigs" version="@WRAPPER_VERSION@.0"> 1 <tool profile="16.07" id="mothur_make_contigs" name="Make.contigs" version="@WRAPPER_VERSION@.1">
2 <description>Aligns paired forward and reverse fastq files to contigs as fasta and quality</description> 2 <description>Aligns paired forward and reverse fastq files to contigs as fasta and 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"/>
52 #end if 52 #end if
53 match=$match, 53 match=$match,
54 mismatch=$mismatch, 54 mismatch=$mismatch,
55 gapopen=$gapopen, 55 gapopen=$gapopen,
56 gapextend=$gapextend, 56 gapextend=$gapextend,
57 rename=$rename 57 rename=$rename,
58 processors='\${GALAXY_SLOTS:-8}' 58 processors='\${GALAXY_SLOTS:-8}'
59 )' 59 )'
60 | sed 's/ //g' ## mothur trips over whitespace 60 | sed 's/ //g' ## mothur trips over whitespace
61 | mothur 61 | mothur
62 | tee mothur.out.log 62 | tee mothur.out.log
130 </conditional> 130 </conditional>
131 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/> 131 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
132 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/> 132 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/>
133 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/> 133 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
134 <param name="savelog" value="true"/> 134 <param name="savelog" value="true"/>
135 <param name="rename" value="false"/>
135 <expand macro="logfile-test"/> 136 <expand macro="logfile-test"/>
136 </test> 137 </test>
137 <!-- Test with a simple paired collection as input --> 138 <!-- Test with a simple paired collection as input -->
138 <test> 139 <test>
139 <conditional name="input_type"> 140 <conditional name="input_type">
147 </conditional> 148 </conditional>
148 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/> 149 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
149 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/> 150 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/>
150 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/> 151 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
151 <param name="savelog" value="true"/> 152 <param name="savelog" value="true"/>
153 <param name="rename" value="false"/>
152 <expand macro="logfile-test"/> 154 <expand macro="logfile-test"/>
153 </test> 155 </test>
154 <!-- Test with a simple paired collection as input + extra parameters specified --> 156 <!-- Test with a simple paired collection as input + extra parameters specified -->
155 <test> 157 <test>
156 <conditional name="input_type"> 158 <conditional name="input_type">
165 <param name="align" value="gotoh"/> 167 <param name="align" value="gotoh"/>
166 <param name="match" value="2"/> 168 <param name="match" value="2"/>
167 <param name="mismatch" value="-2"/> 169 <param name="mismatch" value="-2"/>
168 <param name="gapopen" value="-3"/> 170 <param name="gapopen" value="-3"/>
169 <param name="gapextend" value="-2"/> 171 <param name="gapextend" value="-2"/>
170 <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta"/> 172 <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta">
171 <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual"/> 173 <assert_contents>
172 <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt"/> 174 <has_text text=">M00967_43_000000000-A3JHG_1_1101_19936_3208" />
173 <param name="savelog" value="true"/> 175 </assert_contents>
176 </output>
177 <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual">
178 <assert_contents>
179 <has_text text=">M00967_43_000000000-A3JHG_1_1101_19936_3208" />
180 </assert_contents>
181 </output>
182 <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt">
183 <assert_contents>
184 <has_line line="M00967_43_000000000-A3JHG_1_1101_19936_3208&#009;253&#009;249&#009;2&#009;251&#009;0&#009;0" />
185 </assert_contents>
186 </output>
187 <param name="savelog" value="true"/>
188 <param name="rename" value="false"/>
189 <expand macro="logfile-test"/>
190 </test>
191 <!-- Test with a simple paired collection as input + rename sequences -->
192 <test>
193 <conditional name="input_type">
194 <param name="type" value="simple_collection"/>
195 <param name="paired_collection">
196 <collection type="paired">
197 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
198 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
199 </collection>
200 </param>
201 </conditional>
202 <output name="fasta" md5="addcc2f4233df75ab9e5feacadb6850f" ftype="fasta">
203 <assert_contents>
204 <has_text text=">1" />
205 </assert_contents>
206 </output>
207 <output name="qual" md5="476932c0236a672c0c99cada2b114fe7" ftype="qual">
208 <assert_contents>
209 <has_text text=">1" />
210 </assert_contents>
211 </output>
212 <output name="report" md5="7634bcab8db8907f80087da03259012a" ftype="txt">
213 <assert_contents>
214 <has_line line="1&#009;253&#009;249&#009;2&#009;251&#009;0&#009;0" />
215 </assert_contents>
216 </output>
217 <param name="savelog" value="true"/>
218 <param name="rename" value="true"/>
174 <expand macro="logfile-test"/> 219 <expand macro="logfile-test"/>
175 </test> 220 </test>
176 <!-- Test with a list:paired collection as input --> 221 <!-- Test with a list:paired collection as input -->
177 <test> 222 <test>
178 <conditional name="input_type"> 223 <conditional name="input_type">
197 <output name="fasta" md5="91bd3b91adc6559182ad118b767f0a07" ftype="fasta"/> 242 <output name="fasta" md5="91bd3b91adc6559182ad118b767f0a07" ftype="fasta"/>
198 <output name="qual" md5="7094d1ac82a40e9f89cc6cdf5e214da7" ftype="qual"/> 243 <output name="qual" md5="7094d1ac82a40e9f89cc6cdf5e214da7" ftype="qual"/>
199 <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/> 244 <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/>
200 <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/> 245 <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/>
201 <param name="savelog" value="true"/> 246 <param name="savelog" value="true"/>
247 <param name="rename" value="false"/>
202 <expand macro="logfile-test"/> 248 <expand macro="logfile-test"/>
203 </test> 249 </test>
204 </tests> 250 </tests>
205 <help><![CDATA[ 251 <help><![CDATA[
206 252