Mercurial > repos > iuc > mothur_make_contigs
comparison make.contigs.xml @ 8:829bb93d3add draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
author | iuc |
---|---|
date | Thu, 26 Nov 2020 04:39:59 +0000 |
parents | bfe5103b1e8f |
children | 7238968f58f7 |
comparison
equal
deleted
inserted
replaced
7:ab12df91b47f | 8:829bb93d3add |
---|---|
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	253	249	2	251	0	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	253	249	2	251	0	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 |