Mercurial > repos > jtilman > flexbar

comparison flexbar.xml @ 37:497da23fee84 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jtilman
date Sun, 01 Jul 2018 06:45:19 -0400
parents 4e47e1caf21a
children ae7d2b47ad07
comparison
equal deleted inserted replaced
36:4e47e1caf21a 37:497da23fee84
1 1
2 <!-- Flexbar tool definition for Galaxy, version 3.4.1 --> 2 <!-- Flexbar tool definition for Galaxy, version 3.4.2 -->
3 <!-- Author: Johannes Roehr --> 3 <!-- Author: Johannes Roehr -->
4 4
5 5
6 <tool id="flexbar" name="Flexbar" version="3.4.1"> 6 <tool id="flexbar" name="Flexbar" version="3.4.2">
7 7
8 <description>- flexible barcode and adapter removal</description> 8 <description>- flexible barcode and adapter removal</description>
9 9
10 <requirements> 10 <requirements>
11 <requirement type="package" version="3.4.0">flexbar</requirement> 11 <requirement type="package" version="3.4.0">flexbar</requirement>
15 15
16 <command detect_errors="aggressive"> 16 <command detect_errors="aggressive">
17 17
18 <![CDATA[ 18 <![CDATA[
19 19
20 flexbar 20 #if $reads.mode == "se":
21 ln -s '$reads.rs' '$rsout'_input.'$reads.rs.extension' &&
22 #elif $reads.mode == "pe":
23 ln -s '$reads.r1' '$r1out'_input.'$reads.r1.extension' &&
24 ln -s '$reads.r2' '$r2out'_input.'$reads.r2.extension' &&
25 #else:
26 ln -s '$reads.rc.forward' '$rcout.forward'_input.'$reads.rc.forward.extension' &&
27 ln -s '$reads.rc.reverse' '$rcout.reverse'_input.'$reads.rc.reverse.extension' &&
28 #end if
29
30 '$__tool_directory__/flexbar.pl' flexbar
21 31
22 --threads \${GALAXY_SLOTS:-1} 32 --threads \${GALAXY_SLOTS:-1}
23 33
24 #if $reads.mode == "se": 34 #if $reads.mode == "se":
25 --reads '$reads.rs' 35 --reads '$rsout'_input.'$reads.rs.extension'
26 #elif $reads.mode == "pe": 36 #elif $reads.mode == "pe":
27 --reads '$reads.r1' 37 --reads '$r1out'_input.'$reads.r1.extension'
28 --reads2 '$reads.r2' 38 --reads2 '$r2out'_input.'$reads.r2.extension'
29 #else: 39 #else:
30 --reads '$reads.rc.forward' 40 --reads '$rcout.forward'_input.'$reads.rc.forward.extension'
31 --reads2 '$reads.rc.reverse' 41 --reads2 '$rcout.reverse'_input.'$reads.rc.reverse.extension'
32 #end if 42 #end if
33 43
34 --max-uncalled $maxUncalled 44 --max-uncalled $maxUncalled
35 --min-read-length $minReadLen 45 --min-read-length $minReadLen
36 46
186 #end if 196 #end if
187 #end if 197 #end if
188 198
189 199
190 #if $reads.mode == "se": 200 #if $reads.mode == "se":
191 --output-reads '$rsout' 201 --output-reads '$rsout'.'$reads.rs.extension'
192 #elif $reads.mode == "pe": 202 #elif $reads.mode == "pe":
193 --output-reads '$r1out' 203 --output-reads '$r1out'.'$reads.r1.extension'
194 --output-reads2 '$r2out' 204 --output-reads2 '$r2out'.'$reads.r2.extension'
195 #else: 205 #else:
196 --output-reads '$rcout.forward' 206 --output-reads '$rcout.forward'.'$reads.rc.forward.extension'
197 --output-reads2 '$rcout.reverse' 207 --output-reads2 '$rcout.reverse'.'$reads.rc.reverse.extension'
198 #end if 208 #end if
199 209
200 --output-log '$outlog' 210 --output-log '$outlog'
201 211
202 ]]> 212 ]]>
210 <option value="se">Single read file</option> 220 <option value="se">Single read file</option>
211 <option value="pe" selected="true">Paired read files</option> 221 <option value="pe" selected="true">Paired read files</option>
212 <option value="pc">Paired read collection</option> 222 <option value="pc">Paired read collection</option>
213 </param> 223 </param>
214 <when value="se"> 224 <when value="se">
215 <param name="rs" type="data" format="fastqsanger,fastqsolexa,fastqillumina" label="Fastq read file"/> 225 <param name="rs" type="data" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" label="Fastq read file"/>
216 </when> 226 </when>
217 <when value="pe"> 227 <when value="pe">
218 <param name="r1" type="data" format="fastqsanger,fastqsolexa,fastqillumina" label="Fastq read file 1"/> 228 <param name="r1" type="data" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" label="Fastq read file 1"/>
219 <param name="r2" type="data" format="fastqsanger,fastqsolexa,fastqillumina" label="Fastq read file 2"/> 229 <param name="r2" type="data" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" label="Fastq read file 2"/>
220 </when> 230 </when>
221 <when value="pc"> 231 <when value="pc">
222 <param name="rc" format="fastqsanger,fastqsolexa,fastqillumina" type="data_collection" collection_type="paired" label="Fastq pair collection"/> 232 <param name="rc" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" type="data_collection" collection_type="paired" label="Fastq pair collection"/>
223 </when> 233 </when>
224 </conditional> 234 </conditional>
225 235
226 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Maximum uncalled bases"/> 236 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Maximum uncalled bases"/>
227 237