Mercurial > repos > iuc > mothur_make_contigs

comparison make.contigs.xml @ 4:b1b4240133f5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
author iuc
date Tue, 20 Mar 2018 13:36:31 -0400
parents 0f563b96b60d
children 80fcd4bf633a
comparison
equal deleted inserted replaced
3:0f563b96b60d 4:b1b4240133f5
105 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/> 105 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
106 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/> 106 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
107 <param name="rename" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Renames sequences" 107 <param name="rename" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Renames sequences"
108 help="reduce file sizes and greatly reduce the size of the column formatted distance matrix downstream. 108 help="reduce file sizes and greatly reduce the size of the column formatted distance matrix downstream.
109 Uses the rename.seqs command to rename which creates a map file so you can revert to original names at any time"/> 109 Uses the rename.seqs command to rename which creates a map file so you can revert to original names at any time"/>
110 <expand macro="param-savelog"/>
110 </inputs> 111 </inputs>
111 <outputs> 112 <outputs>
112 <expand macro="logfile-output"/> 113 <expand macro="logfile-output"/>
113 <data name="fasta" format="fasta" from_work_dir="*fastq.trim.*.fasta" label="${tool.name} on ${on_string}: trim.contigs.fasta"/> 114 <data name="fasta" format="fasta" from_work_dir="*fastq.trim.*.fasta" label="${tool.name} on ${on_string}: trim.contigs.fasta"/>
114 <data name="qual" format="qual" from_work_dir="*fastq*.trim.*.qual" label="${tool.name} on ${on_string}: trim.contigs.qual"/> 115 <data name="qual" format="qual" from_work_dir="*fastq*.trim.*.qual" label="${tool.name} on ${on_string}: trim.contigs.qual"/>
128 <param name="reverse_fastq" value="Mock_S280_L001_R2_001_small.fastq" ftype="fastq"/> 129 <param name="reverse_fastq" value="Mock_S280_L001_R2_001_small.fastq" ftype="fastq"/>
129 </conditional> 130 </conditional>
130 <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"/>
131 <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"/>
132 <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"/>
133 <expand macro="logfile-test"/> 135 <expand macro="logfile-test"/>
134 </test> 136 </test>
135 <!-- Test with a simple paired collection as input --> 137 <!-- Test with a simple paired collection as input -->
136 <test> 138 <test>
137 <conditional name="input_type"> 139 <conditional name="input_type">
144 </param> 146 </param>
145 </conditional> 147 </conditional>
146 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/> 148 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
147 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/> 149 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/>
148 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/> 150 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
151 <param name="savelog" value="true"/>
149 <expand macro="logfile-test"/> 152 <expand macro="logfile-test"/>
150 </test> 153 </test>
151 <!-- Test with a simple paired collection as input + extra parameters specified --> 154 <!-- Test with a simple paired collection as input + extra parameters specified -->
152 <test> 155 <test>
153 <conditional name="input_type"> 156 <conditional name="input_type">
165 <param name="gapopen" value="-3"/> 168 <param name="gapopen" value="-3"/>
166 <param name="gapextend" value="-2"/> 169 <param name="gapextend" value="-2"/>
167 <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta"/> 170 <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta"/>
168 <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual"/> 171 <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual"/>
169 <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt"/> 172 <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt"/>
173 <param name="savelog" value="true"/>
170 <expand macro="logfile-test"/> 174 <expand macro="logfile-test"/>
171 </test> 175 </test>
172 <!-- Test with a list:paired collection as input --> 176 <!-- Test with a list:paired collection as input -->
173 <test> 177 <test>
174 <conditional name="input_type"> 178 <conditional name="input_type">
192 </conditional> 196 </conditional>
193 <output name="fasta" md5="91bd3b91adc6559182ad118b767f0a07" ftype="fasta"/> 197 <output name="fasta" md5="91bd3b91adc6559182ad118b767f0a07" ftype="fasta"/>
194 <output name="qual" md5="7094d1ac82a40e9f89cc6cdf5e214da7" ftype="qual"/> 198 <output name="qual" md5="7094d1ac82a40e9f89cc6cdf5e214da7" ftype="qual"/>
195 <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/> 199 <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/>
196 <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/> 200 <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/>
201 <param name="savelog" value="true"/>
197 <expand macro="logfile-test"/> 202 <expand macro="logfile-test"/>
198 </test> 203 </test>
199 </tests> 204 </tests>
200 <help><![CDATA[ 205 <help><![CDATA[
201 206