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comparison sRbowtie.xml @ 6:b7173c0011f3 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
author drosofff
date Mon, 10 Jul 2017 13:20:28 -0400
parents b2c1ffe6579a
children
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5:b2c1ffe6579a 6:b7173c0011f3
1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.2"> 1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.3">
2 <description>for FASTA small reads</description> 2 <description>for FASTA small reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.2=py27_2">bowtie</requirement> 4 <requirement type="package" version="1.1.2=py27_2">bowtie</requirement>
5 <requirement type="package" version="1.2">samtools</requirement> 5 <requirement type="package" version="1.2">samtools</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #if $refGenomeSource.genomeSource == "history": 8 #if $refGenomeSource.genomeSource == "history":
9 bowtie-build -f $refGenomeSource.ownFile local_index && 9 bowtie-build -f $refGenomeSource.ownFile genome &&
10 ln -s -f '$refGenomeSource.ownFile' genome.fa &&
11 #set index_path = 'genome'
10 #else: 12 #else:
11 ln -f -s $refGenomeSource.index.fields.path local_index && 13 #set index_path = $refGenomeSource.index.fields.path
12 #end if 14 #end if
13 #if $input.extension == "fasta": 15 #if $input.extension == "fasta":
14 #set format = "-f" 16 #set format = "-f"
15 #elif $input.extension == "fastq": 17 #elif $input.extension == "fastq":
16 #set format = "-q" 18 #set format = "-q"
44 46
45 #set $method_postfix = " %s %s " % ($method_prefix, $extra_output) 47 #set $method_postfix = " %s %s " % ($method_prefix, $extra_output)
46 48
47 ## run the bowtie alignement 49 ## run the bowtie alignement
48 #if $output_format == "tabular": 50 #if $output_format == "tabular":
49 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$input' > $output 51 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 $index_path $format '$input' > $output
50 #elif $output_format == "sam": 52 #elif $output_format == "sam":
51 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output' 53 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' > '$output'
52 #elif $output_format == "bam": 54 #elif $output_format == "bam":
53 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output 55 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output
54 #end if 56 #end if
55 ##### | samtools view -uS 57 ##### | samtools view -uS
56 ]]></command> 58 ]]></command>
57 <inputs> 59 <inputs>
58 <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" /> 60 <param format="fasta, fastq" help="Only with clipped, fasta or fastq read files" label="Input fasta or fastq file: reads clipped from their adapter" name="input" type="data" />
59 <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select"> 61 <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select">
60 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option> 62 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
61 <option value="unique">Match unique mappers on DNA reference index</option> 63 <option value="unique">Match unique mappers on DNA reference index</option>
62 <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option> 64 <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option>
63 <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option> 65 <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option>
179 181
180 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution. 182 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
181 183
182 However, this Bowtie wrapper tool only takes FASTQ files as inputs. 184 However, this Bowtie wrapper tool only takes FASTQ files as inputs.
183 185
184 The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode) 186 The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis.
185 187
186 ------ 188 ------
187 189
188 **OPTIONS** 190 **OPTIONS**
189 191
224 226
225 **Input formats** 227 **Input formats**
226 228
227 .. class:: warningmark 229 .. class:: warningmark
228 230
229 *The only accepted format for the script is a raw fasta list of reads, clipped from their adapter* 231 *Lists of reads, in fasta or fastq format, clipped from their adapter sequence*
230 232
231 ----- 233 -----
232 234
233 **OUTPUTS** 235 **OUTPUTS**
234 236
235 If you choose tabular as the output format, you will obtain the matched reads in standard bowtie output format, having the following columns:: 237 If you choose tabular as the output format, you will obtain the matched reads in tabular bowtie output format, having the following columns::
236 238
237 Column Description 239 Column Description
238 -------- -------------------------------------------------------- 240 -------- --------------------------------------------------------
239 1 FastaID fasta identifier 241 1 FastaID fasta identifier
240 2 polarity + or - depending whether the match was reported on the forward or reverse strand 242 2 polarity + or - depending whether the match was reported on the forward or reverse strand