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comparison flexbar.xml @ 27:db26fb0c6389 draft

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author jtilman
date Mon, 02 May 2016 04:58:38 -0400
parents dbe3c211ec57
children 18acb52de258
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26:2c6ab15e5964 27:db26fb0c6389
1 1
2 <!-- Flexbar tool definition for Galaxy, version 2.5 --> 2 <!-- Flexbar tool definition for Galaxy, version 2.7 -->
3 <!-- Author: Johannes Roehr --> 3 <!-- Author: Johannes Roehr -->
4 4
5 5
6 <tool id="flexbar" name="Flexbar" version="2.5" force_history_refresh="True"> 6 <tool id="flexbar" name="Flexbar" version="2.7" force_history_refresh="True">
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="binary" version="2.5">flexbar</requirement> 11 <requirement type="binary" version="2.7">flexbar</requirement>
12 </requirements> 12 </requirements>
13 13
14 <version_command>flexbar --version</version_command> 14 <version_command>flexbar --version</version_command>
15 15
16 <command interpreter="perl"> 16 <command interpreter="perl">
26 --reads2 $cReads2.reads2 26 --reads2 $cReads2.reads2
27 #end if 27 #end if
28 #end if 28 #end if
29 29
30 #if $reads.ext == "fastqsanger": 30 #if $reads.ext == "fastqsanger":
31 --format sanger 31 --qtrim-format sanger
32 #end if 32 #end if
33 #if $reads.ext == "fastqsolexa": 33 #if $reads.ext == "fastqsolexa":
34 --format solexa 34 --qtrim-format solexa
35 #end if 35 #end if
36 #if $reads.ext == "fastqillumina": 36 #if $reads.ext == "fastqillumina":
37 --format i1.3 37 --qtrim-format i1.3
38 #end if
39 #if $reads.ext == "csfasta":
40 --color-space
41 #end if
42 #if $reads.ext == "fastqcssanger":
43 --color-space
44 #end if 38 #end if
45 39
46 40
47 --max-uncalled $maxUncalled 41 --max-uncalled $maxUncalled
48 --min-read-length $minReadLen 42 --min-read-length $minReadLen
51 --pre-trim-left $trimEnds.trimLeft 45 --pre-trim-left $trimEnds.trimLeft
52 --pre-trim-right $trimEnds.trimRight 46 --pre-trim-right $trimEnds.trimRight
53 #end if 47 #end if
54 48
55 #if $cTrimPhred.select == "on": 49 #if $cTrimPhred.select == "on":
56 --pre-trim-phred $cTrimPhred.trimPhred 50 --qtrim TAIL --qtrim-threshold $cTrimPhred.trimPhred
57 #end if 51 #end if
58 52
59 #if $cTrimLen.select == "on": 53 #if $cTrimLen.select == "on":
60 --post-trim-length $cTrimLen.trimLen 54 --post-trim-length $cTrimLen.trimLen
61 #end if 55 #end if
142 </command> 136 </command>
143 137
144 138
145 <inputs> 139 <inputs>
146 140
147 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/> 141 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="reads" type="data" label="Sequencing reads" optional="false"/>
148 142
149 143
150 <conditional name="cReads2"> 144 <conditional name="cReads2">
151 <param name="select" type="select" label="2nd read set (paired)"> 145 <param name="select" type="select" label="2nd read set (paired)">
152 <option value="off" selected="true">Off</option> 146 <option value="off" selected="true">Off</option>
153 <option value="on">On</option> 147 <option value="on">On</option>
154 </param> 148 </param>
155 <when value="off"> 149 <when value="off">
156 </when> 150 </when>
157 <when value="on"> 151 <when value="on">
158 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/> 152 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/>
159 </when> 153 </when>
160 </conditional> 154 </conditional>
161 155
162 156
163 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/> 157 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/>
202 <param name="select" type="select" label="Separate barcode reads"> 196 <param name="select" type="select" label="Separate barcode reads">
203 <option value="no" selected="true">No</option> 197 <option value="no" selected="true">No</option>
204 <option value="yes">Yes</option> 198 <option value="yes">Yes</option>
205 </param> 199 </param>
206 <when value="yes"> 200 <when value="yes">
207 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/> 201 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
208 </when> 202 </when>
209 <when value="no"> 203 <when value="no">
210 <param name="bKeep" type="select" label="Remove barcodes within reads"> 204 <param name="bKeep" type="select" label="Remove barcodes within reads">
211 <option value="" selected="true">Yes</option> 205 <option value="" selected="true">Yes</option>
212 <option value="--barcode-keep">No</option> 206 <option value="--barcode-keep">No</option>
426 420
427 <help> 421 <help>
428 422
429 **Description** 423 **Description**
430 424
431 Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform. Flexbar is available on the project_ page. 425 Flexbar processes high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. It supports next-generation sequencing data in fasta and fastq format, e.g. from Roche 454 and the Illumina platform. Flexbar is available on the project_ page.
432 426
433 .. _project: https://github.com/seqan/flexbar 427 .. _project: https://github.com/seqan/flexbar
434 428
435 ------ 429 ------
436 430