Mercurial > repos > iuc > mothur_trim_seqs

comparison trim.seqs.xml @ 5:4929eb3e0037 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 13:33:54 -0400
parents e695fda56931
children
comparison
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4:91118e125331 5:4929eb3e0037
112 </conditional> 112 </conditional>
113 <param name="flip" type="boolean" truevalue="true" falsevalue="false" checked="false" label="flip - reverse complement the trimmed sequences"/> 113 <param name="flip" type="boolean" truevalue="true" falsevalue="false" checked="false" label="flip - reverse complement the trimmed sequences"/>
114 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. If you run trim.seqs with an oligos file that contains group labels, trim.seqs will create a new *.trim.count_table with the group information included. "/> 114 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. If you run trim.seqs with an oligos file that contains group labels, trim.seqs will create a new *.trim.count_table with the group information included. "/>
115 <param name="logtransform" type="boolean" truevalue="true" falsevalue="false" checked="false" label="logtransform" help="allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform."/> 115 <param name="logtransform" type="boolean" truevalue="true" falsevalue="false" checked="false" label="logtransform" help="allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform."/>
116 <param name="checkorient" type="boolean" truevalue="true" falsevalue="false" checked="false" label="checkorient - search the reverse complement?" help="If you are running the trim.seqs command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can't find the barcodes and primers, it will search the reverse compliment. "/> 116 <param name="checkorient" type="boolean" truevalue="true" falsevalue="false" checked="false" label="checkorient - search the reverse complement?" help="If you are running the trim.seqs command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can't find the barcodes and primers, it will search the reverse compliment. "/>
117 <expand macro="param-savelog"/>
117 </inputs> 118 </inputs>
118 <outputs> 119 <outputs>
119 <expand macro="logfile-output"/> 120 <expand macro="logfile-output"/>
120 <data name="trim_fasta" format_source="fasta" from_work_dir="fasta.trim" label="${tool.name} on ${on_string}: trim.fasta"/> 121 <data name="trim_fasta" format_source="fasta" from_work_dir="fasta.trim" label="${tool.name} on ${on_string}: trim.fasta"/>
121 <data name="scrap_fasta" format_source="fasta" from_work_dir="fasta.scrap" label="${tool.name} on ${on_string}: scrap.fasta"/> 122 <data name="scrap_fasta" format_source="fasta" from_work_dir="fasta.scrap" label="${tool.name} on ${on_string}: scrap.fasta"/>
156 <param name="maxhomop" value="4"/> 157 <param name="maxhomop" value="4"/>
157 <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/> 158 <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
158 <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/> 159 <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
159 <output name="trim_names" md5="1b8c6c47052bb69524ef56ebb764fb8f" ftype="mothur.names"/> 160 <output name="trim_names" md5="1b8c6c47052bb69524ef56ebb764fb8f" ftype="mothur.names"/>
160 <output name="scrap_names" md5="80f9252837e4b189f06ec00469b88e85" ftype="mothur.names"/> 161 <output name="scrap_names" md5="80f9252837e4b189f06ec00469b88e85" ftype="mothur.names"/>
162 <param name="savelog" value="true"/>
161 <expand macro="logfile-test"/> 163 <expand macro="logfile-test"/>
162 </test> 164 </test>
163 <test><!-- test with count table --> 165 <test><!-- test with count table -->
164 <param name="fasta" value="amazon.fasta" ftype="fasta"/> 166 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
165 <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/> 167 <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
166 <param name="maxhomop" value="4"/> 168 <param name="maxhomop" value="4"/>
167 <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/> 169 <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
168 <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/> 170 <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
169 <output name="trim_count" md5="836b4d72a8cda3741ef435741783b384" ftype="mothur.count_table"/> 171 <output name="trim_count" md5="836b4d72a8cda3741ef435741783b384" ftype="mothur.count_table"/>
170 <output name="scrap_count" md5="04ae9f50c1b6f0d8d7e1ac28f845dd4c" ftype="mothur.count_table"/> 172 <output name="scrap_count" md5="04ae9f50c1b6f0d8d7e1ac28f845dd4c" ftype="mothur.count_table"/>
173 <param name="savelog" value="true"/>
171 <expand macro="logfile-test"/> 174 <expand macro="logfile-test"/>
172 </test> 175 </test>
173 <test><!-- test with oligos --> 176 <test><!-- test with oligos -->
174 <param name="fasta" value="amazon.fasta" ftype="fasta"/> 177 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
175 <param name="add" value="yes"/> 178 <param name="add" value="yes"/>
177 <param name="bdiffs" value="100"/> 180 <param name="bdiffs" value="100"/>
178 <param name="pdiffs" value="100"/> 181 <param name="pdiffs" value="100"/>
179 <output name="trim_fasta" md5="75a8a3ae2d1fe1ff2b860480b84e9bd6" ftype="fasta"/> 182 <output name="trim_fasta" md5="75a8a3ae2d1fe1ff2b860480b84e9bd6" ftype="fasta"/>
180 <output name="scrap_fasta" md5="c4fd14e70ab7d1c21d238e87624829d7" ftype="fasta"/> 183 <output name="scrap_fasta" md5="c4fd14e70ab7d1c21d238e87624829d7" ftype="fasta"/>
181 <output name="groups_file" md5="198957282c234e825414e175d926046a" ftype="mothur.groups"/> 184 <output name="groups_file" md5="198957282c234e825414e175d926046a" ftype="mothur.groups"/>
185 <param name="savelog" value="true"/>
182 <expand macro="logfile-test"/> 186 <expand macro="logfile-test"/>
183 </test> 187 </test>
184 <test><!-- test with oligos and allfiles parameter --> 188 <test><!-- test with oligos and allfiles parameter -->
185 <param name="fasta" value="amazon.fasta" ftype="fasta"/> 189 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
186 <param name="add" value="yes"/> 190 <param name="add" value="yes"/>
194 <element name="F003D144" md5="445124b06d0c9146ae353631794c8093" ftype="mothur.groups"/> 198 <element name="F003D144" md5="445124b06d0c9146ae353631794c8093" ftype="mothur.groups"/>
195 </output_collection> 199 </output_collection>
196 <output_collection name="fasta_allfiles" count="9"> 200 <output_collection name="fasta_allfiles" count="9">
197 <element name="F003D144" md5="025ff271ac24ecb898863d7fcbfabf10" ftype="fasta"/> 201 <element name="F003D144" md5="025ff271ac24ecb898863d7fcbfabf10" ftype="fasta"/>
198 </output_collection> 202 </output_collection>
203 <param name="savelog" value="true"/>
199 <expand macro="logfile-test"/> 204 <expand macro="logfile-test"/>
200 </test> 205 </test>
201 <test><!-- test with qfile--> 206 <test><!-- test with qfile-->
202 <param name="fasta" value="Fasting_Example1.fasta" ftype="fasta"/> 207 <param name="fasta" value="Fasting_Example1.fasta" ftype="fasta"/>
203 <param name="add2" value="yes"/> 208 <param name="add2" value="yes"/>
205 <param name="maxhomop" value="4"/> 210 <param name="maxhomop" value="4"/>
206 <output name="trim_fasta" md5="d02f74acd6d9fb52b04a93869bb79302" ftype="fasta"/> 211 <output name="trim_fasta" md5="d02f74acd6d9fb52b04a93869bb79302" ftype="fasta"/>
207 <output name="scrap_fasta" md5="a4d3ef3d91b4c0146ec84bb7aad3987c" ftype="fasta"/> 212 <output name="scrap_fasta" md5="a4d3ef3d91b4c0146ec84bb7aad3987c" ftype="fasta"/>
208 <output name="trim_qual" md5="3d4e2d3c7dd43b90660ab9c923d9eab1" ftype="qual454"/> 213 <output name="trim_qual" md5="3d4e2d3c7dd43b90660ab9c923d9eab1" ftype="qual454"/>
209 <output name="scrap_qual" md5="22931236d082c2b77811bbf912c1f4b1" ftype="qual454"/> 214 <output name="scrap_qual" md5="22931236d082c2b77811bbf912c1f4b1" ftype="qual454"/>
215 <param name="savelog" value="true"/>
210 <expand macro="logfile-test"/> 216 <expand macro="logfile-test"/>
211 </test> 217 </test>
212 </tests> 218 </tests>
213 <help><![CDATA[ 219 <help><![CDATA[
214 220