Mercurial > repos > iuc > mothur_screen_seqs

comparison screen.seqs.xml @ 5:921ff33138df 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 13:46:28 -0400
parents 2159457a4586
children 0b91839225a9
comparison
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4:2159457a4586 5:921ff33138df
139 <param argument="oend" type="integer" value="-1" min="-1" label="oend - Position the overlap must end after (ignored when negative)"/> 139 <param argument="oend" type="integer" value="-1" min="-1" label="oend - Position the overlap must end after (ignored when negative)"/>
140 <param argument="mismatches" type="integer" value="-1" min="-1" label="mismatches - Maximum number of mismatches (ignored when negative)"/> 140 <param argument="mismatches" type="integer" value="-1" min="-1" label="mismatches - Maximum number of mismatches (ignored when negative)"/>
141 </when> 141 </when>
142 <when value="no"/> 142 <when value="no"/>
143 </conditional> 143 </conditional>
144 <expand macro="param-savelog"/>
144 </inputs> 145 </inputs>
145 <outputs> 146 <outputs>
146 <expand macro="logfile-output"/> 147 <expand macro="logfile-output"/>
147 <data name="fasta_out" format_source="fasta" from_work_dir="fasta*.good.dat" label="${tool.name} on ${on_string}: good.${fasta.datatype.file_ext}"/> 148 <data name="fasta_out" format_source="fasta" from_work_dir="fasta*.good.dat" label="${tool.name} on ${on_string}: good.${fasta.datatype.file_ext}"/>
148 <data name="bad_accnos" format="mothur.accnos" from_work_dir="fasta*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos"/> 149 <data name="bad_accnos" format="mothur.accnos" from_work_dir="fasta*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos"/>
170 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/> 171 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
171 <param name="maxambig" value="0"/> 172 <param name="maxambig" value="0"/>
172 <param name="maxlength" value="275"/> 173 <param name="maxlength" value="275"/>
173 <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"/>
174 <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"/>
175 <expand macro="logfile-test"/> 177 <expand macro="logfile-test"/>
176 </test> 178 </test>
177 <test><!-- test with count table --> 179 <test><!-- test with count table -->
178 <param name="fasta" value="amazon.fasta" ftype="mothur.align"/> 180 <param name="fasta" value="amazon.fasta" ftype="mothur.align"/>
179 <param name="count" value="amazon1.count_table"/> 181 <param name="count" value="amazon1.count_table"/>
200 <has_text text="U68589"/> 202 <has_text text="U68589"/>
201 <has_text text="ambig"/> 203 <has_text text="ambig"/>
202 <has_text text="length"/> 204 <has_text text="length"/>
203 </assert_contents> 205 </assert_contents>
204 </output> 206 </output>
207 <param name="savelog" value="true"/>
205 <expand macro="logfile-test"/> 208 <expand macro="logfile-test"/>
206 </test> 209 </test>
207 <test><!-- test screening with contigsreport --> 210 <test><!-- test screening with contigsreport -->
208 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/> 211 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
209 <param name="maxambig" value="0"/> 212 <param name="maxambig" value="0"/>
224 <expand macro="test-contigsreport-format"/> 227 <expand macro="test-contigsreport-format"/>
225 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_22487_4260"/> 228 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_22487_4260"/>
226 <has_text text="M00967_43_000000000-A3JHG_1_1101_15923_3823"/> 229 <has_text text="M00967_43_000000000-A3JHG_1_1101_15923_3823"/>
227 </assert_contents> 230 </assert_contents>
228 </output> 231 </output>
232 <param name="savelog" value="true"/>
229 <expand macro="logfile-test"/> 233 <expand macro="logfile-test"/>
230 </test> 234 </test>
231 <test><!-- test screening with alignment report --> 235 <test><!-- test screening with alignment report -->
232 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/> 236 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
233 <param name="maxambig" value="0"/> 237 <param name="maxambig" value="0"/>
253 <expand macro="test-alignreport-format"/> 257 <expand macro="test-alignreport-format"/>
254 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_14010_4122"/> 258 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_14010_4122"/>
255 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> 259 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
256 </assert_contents> 260 </assert_contents>
257 </output> 261 </output>
262 <param name="savelog" value="true"/>
258 <expand macro="logfile-test"/> 263 <expand macro="logfile-test"/>
259 </test> 264 </test>
260 </tests> 265 </tests>
261 <help><![CDATA[ 266 <help><![CDATA[
262 267