Mercurial > repos > jtilman > flexbar
comparison flexbar.xml @ 37:497da23fee84 draft
Uploaded
| author | jtilman |
|---|---|
| date | Sun, 01 Jul 2018 06:45:19 -0400 |
| parents | 4e47e1caf21a |
| children | ae7d2b47ad07 |
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| 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 |