Mercurial > repos > iuc > mothur_remove_seqs

comparison remove.seqs.xml @ 4:d71c95ed484d 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 13:56:11 -0400
parents cfab052e5e8a
children
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3:cfab052e5e8a 4:d71c95ed484d
99 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/> 99 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/>
100 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> 100 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
101 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> 101 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
102 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 102 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
103 <param name="dups" type="boolean" truevalue="" falsevalue=",dups=false" checked="true" label="dups - Apply to duplicates"/> 103 <param name="dups" type="boolean" truevalue="" falsevalue=",dups=false" checked="true" label="dups - Apply to duplicates"/>
104 <expand macro="param-savelog"/>
104 </inputs> 105 </inputs>
105 <outputs> 106 <outputs>
106 <expand macro="logfile-output"/> 107 <expand macro="logfile-output"/>
107 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in.pick.dat" label="${tool.name} on ${on_string}: pick.fasta"> 108 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in.pick.dat" label="${tool.name} on ${on_string}: pick.fasta">
108 <filter>fasta_in</filter> 109 <filter>fasta_in</filter>
135 <tests> 136 <tests>
136 <test> 137 <test>
137 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> 138 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
138 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> 139 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
139 <param name="dups" value=""/> 140 <param name="dups" value=""/>
141 <param name="savelog" value="true"/>
140 <expand macro="logfile-test"/> 142 <expand macro="logfile-test"/>
141 <output name="fasta_out"> 143 <output name="fasta_out">
142 <assert_contents> 144 <assert_contents>
143 <expand macro="test-fasta-format"/> 145 <expand macro="test-fasta-format"/>
144 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> 146 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
146 </output> 148 </output>
147 </test> 149 </test>
148 <test> 150 <test>
149 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> 151 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
150 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> 152 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
153 <param name="savelog" value="true"/>
151 <expand macro="logfile-test"/> 154 <expand macro="logfile-test"/>
152 <output name="fastq_out"> 155 <output name="fastq_out">
153 <assert_contents> 156 <assert_contents>
154 <expand macro="test-fastq-format"/> 157 <expand macro="test-fastq-format"/>
155 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> 158 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
159 <test><!-- test two input files --> 162 <test><!-- test two input files -->
160 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> 163 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
161 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> 164 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
162 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> 165 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
163 <param name="dups" value=",dups=false"/> 166 <param name="dups" value=",dups=false"/>
167 <param name="savelog" value="true"/>
164 <expand macro="logfile-test"/> 168 <expand macro="logfile-test"/>
165 <output name="fasta_out"> 169 <output name="fasta_out">
166 <assert_contents> 170 <assert_contents>
167 <expand macro="test-fasta-format"/> 171 <expand macro="test-fasta-format"/>
168 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/> 172 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
176 </output> 180 </output>
177 </test> 181 </test>
178 <test> 182 <test>
179 <param name="accnos" value="amazon.bad.accnos"/> 183 <param name="accnos" value="amazon.bad.accnos"/>
180 <param name="count_in" value="amazon.count_table"/> 184 <param name="count_in" value="amazon.count_table"/>
185 <param name="savelog" value="true"/>
181 <expand macro="logfile-test"/> 186 <expand macro="logfile-test"/>
182 <output name="count_out"> 187 <output name="count_out">
183 <assert_contents> 188 <assert_contents>
184 <expand macro="test-count-format"/> 189 <expand macro="test-count-format"/>
185 <has_text text="U68595"/> 190 <has_text text="U68595"/>