Mercurial > repos > iuc > mothur_align_seqs

comparison align.seqs.xml @ 4:3a0b15089ff6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
author iuc
date Tue, 20 Mar 2018 13:39:00 -0400
parents 4d29fc73525d
children e84817af097b
comparison
equal deleted inserted replaced
3:4d29fc73525d 4:3a0b15089ff6
97 label="threshold - Cutoff (0. - 1.) at which an alignment is deemed 'bad' and the reverse complement may be tried." 97 label="threshold - Cutoff (0. - 1.) at which an alignment is deemed 'bad' and the reverse complement may be tried."
98 help="The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed"/> 98 help="The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed"/>
99 </when> 99 </when>
100 <when value="no"/> 100 <when value="no"/>
101 </conditional> 101 </conditional>
102 <expand macro="param-savelog"/>
102 </inputs> 103 </inputs>
103 <outputs> 104 <outputs>
104 <expand macro="logfile-output"/> 105 <expand macro="logfile-output"/>
105 <data name="out_align" format="mothur.align" from_work_dir="fasta.align" label="${tool.name} on ${on_string}: align"/> 106 <data name="out_align" format="mothur.align" from_work_dir="fasta.align" label="${tool.name} on ${on_string}: align"/>
106 <data name="report" format="mothur.align.report" from_work_dir="fasta.align.report" label="${tool.name} on ${on_string}: align.report"/> 107 <data name="report" format="mothur.align.report" from_work_dir="fasta.align.report" label="${tool.name} on ${on_string}: align.report"/>
117 <assert_contents> 118 <assert_contents>
118 <expand macro="test-align-format"/> 119 <expand macro="test-align-format"/>
119 </assert_contents> 120 </assert_contents>
120 </output> 121 </output>
121 <output name="report" file="Mock_S280_L001_R1_001_small.trim.contigs.good.align.report" ftype="mothur.align.report"/> 122 <output name="report" file="Mock_S280_L001_R1_001_small.trim.contigs.good.align.report" ftype="mothur.align.report"/>
123 <param name="savelog" value="true"/>
122 <expand macro="logfile-test"/> 124 <expand macro="logfile-test"/>
123 </test> 125 </test>
124 <test> 126 <test>
125 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/> 127 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
126 <param name="source" value="history"/> 128 <param name="source" value="history"/>
141 <assert_contents> 143 <assert_contents>
142 <expand macro="test-alignreport-format"/> 144 <expand macro="test-alignreport-format"/>
143 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> 145 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
144 </assert_contents> 146 </assert_contents>
145 </output> 147 </output>
148 <param name="savelog" value="true"/>
146 <expand macro="logfile-test"/> 149 <expand macro="logfile-test"/>
147 </test> 150 </test>
148 <test> 151 <test>
149 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/> 152 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
150 <param name="source" value="history"/> 153 <param name="source" value="history"/>
166 <assert_contents> 169 <assert_contents>
167 <expand macro="test-alignreport-format"/> 170 <expand macro="test-alignreport-format"/>
168 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> 171 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
169 </assert_contents> 172 </assert_contents>
170 </output> 173 </output>
174 <param name="savelog" value="true"/>
171 <expand macro="logfile-test"/> 175 <expand macro="logfile-test"/>
172 </test> 176 </test>
173 <test><!-- test blast --> 177 <test><!-- test blast -->
174 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/> 178 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
175 <param name="source" value="history"/> 179 <param name="source" value="history"/>
188 <assert_contents> 192 <assert_contents>
189 <expand macro="test-alignreport-format"/> 193 <expand macro="test-alignreport-format"/>
190 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> 194 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
191 </assert_contents> 195 </assert_contents>
192 </output> 196 </output>
197 <param name="savelog" value="true"/>
193 <expand macro="logfile-test"/> 198 <expand macro="logfile-test"/>
194 </test> 199 </test>
195 <test><!-- test accno file recovery with flip set to true --> 200 <test><!-- test accno file recovery with flip set to true -->
196 <param name="fasta" value="amazon.fasta"/> 201 <param name="fasta" value="amazon.fasta"/>
197 <param name="source" value="history"/> 202 <param name="source" value="history"/>
214 <assert_contents> 219 <assert_contents>
215 <has_text text="U68621"/> 220 <has_text text="U68621"/>
216 <has_text text="reverse complement"/> 221 <has_text text="reverse complement"/>
217 </assert_contents> 222 </assert_contents>
218 </output> 223 </output>
224 <param name="savelog" value="true"/>
219 <expand macro="logfile-test"/> 225 <expand macro="logfile-test"/>
220 </test> 226 </test>
221 </tests> 227 </tests>
222 <help><![CDATA[ 228 <help><![CDATA[
223 229