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comparison flexbar.xml @ 30:18acb52de258 draft

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author jtilman
date Tue, 05 Jun 2018 11:47:53 -0400
parents db26fb0c6389
children d43903772a88
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29:9709dbd13ee3 30:18acb52de258
1 1
2 <!-- Flexbar tool definition for Galaxy, version 2.7 --> 2 <!-- Flexbar tool definition for Galaxy, version 2.5 -->
3 <!-- Author: Johannes Roehr --> 3 <!-- Author: Johannes Roehr -->
4 4
5 5
6 <tool id="flexbar" name="Flexbar" version="2.7" force_history_refresh="True"> 6 <tool id="flexbar" name="Flexbar" version="2.5" 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="2.7">flexbar</requirement> 11 <requirement type="binary" version="2.5">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 --qtrim-format sanger 31 --format sanger
32 #end if 32 #end if
33 #if $reads.ext == "fastqsolexa": 33 #if $reads.ext == "fastqsolexa":
34 --qtrim-format solexa 34 --format solexa
35 #end if 35 #end if
36 #if $reads.ext == "fastqillumina": 36 #if $reads.ext == "fastqillumina":
37 --qtrim-format i1.3 37 --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
38 #end if 44 #end if
39 45
40 46
41 --max-uncalled $maxUncalled 47 --max-uncalled $maxUncalled
42 --min-read-length $minReadLen 48 --min-read-length $minReadLen
45 --pre-trim-left $trimEnds.trimLeft 51 --pre-trim-left $trimEnds.trimLeft
46 --pre-trim-right $trimEnds.trimRight 52 --pre-trim-right $trimEnds.trimRight
47 #end if 53 #end if
48 54
49 #if $cTrimPhred.select == "on": 55 #if $cTrimPhred.select == "on":
50 --qtrim TAIL --qtrim-threshold $cTrimPhred.trimPhred 56 --pre-trim-phred $cTrimPhred.trimPhred
51 #end if 57 #end if
52 58
53 #if $cTrimLen.select == "on": 59 #if $cTrimLen.select == "on":
54 --post-trim-length $cTrimLen.trimLen 60 --post-trim-length $cTrimLen.trimLen
55 #end if 61 #end if
136 </command> 142 </command>
137 143
138 144
139 <inputs> 145 <inputs>
140 146
141 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="reads" type="data" label="Sequencing reads" optional="false"/> 147 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
142 148
143 149
144 <conditional name="cReads2"> 150 <conditional name="cReads2">
145 <param name="select" type="select" label="2nd read set (paired)"> 151 <param name="select" type="select" label="2nd read set (paired)">
146 <option value="off" selected="true">Off</option> 152 <option value="off" selected="true">Off</option>
147 <option value="on">On</option> 153 <option value="on">On</option>
148 </param> 154 </param>
149 <when value="off"> 155 <when value="off">
150 </when> 156 </when>
151 <when value="on"> 157 <when value="on">
152 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/> 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"/>
153 </when> 159 </when>
154 </conditional> 160 </conditional>
155 161
156 162
157 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/> 163 <param name="maxUncalled" size="4" type="integer" value="0" label="1) Max uncalled" optional="false" help="allowed uncalled bases per read"/>
196 <param name="select" type="select" label="Separate barcode reads"> 202 <param name="select" type="select" label="Separate barcode reads">
197 <option value="no" selected="true">No</option> 203 <option value="no" selected="true">No</option>
198 <option value="yes">Yes</option> 204 <option value="yes">Yes</option>
199 </param> 205 </param>
200 <when value="yes"> 206 <when value="yes">
201 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" name="bReads" type="data" label="Separate barcode reads" optional="false"/> 207 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
202 </when> 208 </when>
203 <when value="no"> 209 <when value="no">
204 <param name="bKeep" type="select" label="Remove barcodes within reads"> 210 <param name="bKeep" type="select" label="Remove barcodes within reads">
205 <option value="" selected="true">Yes</option> 211 <option value="" selected="true">Yes</option>
206 <option value="--barcode-keep">No</option> 212 <option value="--barcode-keep">No</option>
420 426
421 <help> 427 <help>
422 428
423 **Description** 429 **Description**
424 430
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. 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.
426 432
427 .. _project: https://github.com/seqan/flexbar 433 .. _project: https://github.com/seqan/flexbar
428 434
429 ------ 435 ------
430 436