Mercurial > repos > drosofff > msp_sr_bowtie

annotate sRbowtie.xml @ 40:cdf2ffe2f8be draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 13:20:12 -0400
parents 0d961f45e43e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
40
cdf2ffe2f8be planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
drosofff
parents: 38
diff changeset
1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.3">
1
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
2 <description>for FASTA small reads</description>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
3 <requirements>
38
0d961f45e43e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b5e020763495240ddb730f757f0f30cafd208a6b-dirty
drosofff
parents: 37
diff changeset
4 <requirement type="package" version="1.1.2=py27_2">bowtie</requirement>
0d961f45e43e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b5e020763495240ddb730f757f0f30cafd208a6b-dirty
drosofff
parents: 37
diff changeset
5 <requirement type="package" version="1.2">samtools</requirement>
1
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
6 </requirements>
14
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
29
04685a1b3de1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty
drosofff
parents: 28
diff changeset
8 #if $refGenomeSource.genomeSource == "history":
40
cdf2ffe2f8be planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
drosofff
parents: 38
diff changeset
9 bowtie-build -f $refGenomeSource.ownFile genome &&
cdf2ffe2f8be planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
drosofff
parents: 38
diff changeset
10 ln -s -f '$refGenomeSource.ownFile' genome.fa &&
cdf2ffe2f8be planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
drosofff
parents: 38
diff changeset
11 #set index_path = 'genome'
12
a0bde9b84ca6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07
drosofff
parents: 11
diff changeset
12 #else:
40
cdf2ffe2f8be planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
drosofff
parents: 38
diff changeset
13 #set index_path = $refGenomeSource.index.fields.path
14
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
14 #end if
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
15 #if $input.extension == "fasta":
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
16 #set format = "-f"
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
17 #elif $input.extension == "fastq":
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
18 #set format = "-q"
12
a0bde9b84ca6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07
drosofff
parents: 11
diff changeset
19 #end if
14
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
20
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
21 ## set the method_prefix
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
22 #if $method == "RNA":
22
764181d43c36 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 1793456e6d76453825d92c76ca1051f6eccde0ab
drosofff
parents: 21
diff changeset
23 #set method_prefix = "-v %s -M 1 --best --strata --norc" % str($v_mismatches)
14
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
24 #elif $method == "unique":
22
764181d43c36 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 1793456e6d76453825d92c76ca1051f6eccde0ab
drosofff
parents: 21
diff changeset
25 #set method_prefix = "-v %s -m 1" % str($v_mismatches)
14
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
26 #elif $method == "multiple":
22
764181d43c36 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 1793456e6d76453825d92c76ca1051f6eccde0ab
drosofff
parents: 21
diff changeset
27 #set method_prefix = "-v %s -M 1 --best --strata" % str($v_mismatches)
14
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
28 #elif $method == "k_option":
22
764181d43c36 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 1793456e6d76453825d92c76ca1051f6eccde0ab
drosofff
parents: 21
diff changeset
29 #set method_prefix = "-v %s -k 1 --best" % str($v_mismatches)
14
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
30 #elif $method == "n_option":
22
764181d43c36 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 1793456e6d76453825d92c76ca1051f6eccde0ab
drosofff
parents: 21
diff changeset
31 #set method_prefix = "-n %s -M 1 --best" % str($v_mismatches)
14
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
32 #elif $method == "a_option":
22
764181d43c36 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 1793456e6d76453825d92c76ca1051f6eccde0ab
drosofff
parents: 21
diff changeset
33 #set method_prefix = "-v %s -a --best" % str($v_mismatches)
14
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
34 #end if
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
35
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
36 ## set the extra_output
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
37 #if $additional_fasta == "No":
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
38 #set extra_output = ""
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
39 #elif $additional_fasta == "al":
15
44d61fa7fb75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 52409b39598052ed0eae765a8a9e277c82611e8d
drosofff
parents: 14
diff changeset
40 #set extra_output = " --al %s " % str($aligned)
44d61fa7fb75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 52409b39598052ed0eae765a8a9e277c82611e8d
drosofff
parents: 14
diff changeset
41 #elif $additional_fasta == "unal":
44d61fa7fb75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 52409b39598052ed0eae765a8a9e277c82611e8d
drosofff
parents: 14
diff changeset
42 #set extra_output = " --un %s " % str($unaligned)
14
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
43 #else:
15
44d61fa7fb75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 52409b39598052ed0eae765a8a9e277c82611e8d
drosofff
parents: 14
diff changeset
44 #set extra_output = " --al %s --un %s " % (str($aligned), str($unaligned))
14
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
45 #end if
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
46
19
dd5985c5798d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit c23d8a44b40e7b6fc7f15dae5b23ceb5929c8ace
drosofff
parents: 18
diff changeset
47 #set $method_postfix = " %s %s " % ($method_prefix, $extra_output)
14
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
48
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
49 ## run the bowtie alignement
29
04685a1b3de1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty
drosofff
parents: 28
diff changeset
50 #if $output_format == "tabular":
40
cdf2ffe2f8be planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
drosofff
parents: 38
diff changeset
51 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 $index_path $format '$input' > $output
29
04685a1b3de1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty
drosofff
parents: 28
diff changeset
52 #elif $output_format == "sam":
40
cdf2ffe2f8be planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
drosofff
parents: 38
diff changeset
53 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' > '$output'
29
04685a1b3de1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty
drosofff
parents: 28
diff changeset
54 #elif $output_format == "bam":
40
cdf2ffe2f8be planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
drosofff
parents: 38
diff changeset
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
14
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
drosofff
parents: 13
diff changeset
56 #end if
27
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
57 ##### | samtools view -uS
12
a0bde9b84ca6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07
drosofff
parents: 11
diff changeset
58 ]]></command>
1
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
59 <inputs>
40
cdf2ffe2f8be planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
drosofff
parents: 38
diff changeset
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" />
1
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
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">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
62 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
63 <option value="unique">Match unique mappers on DNA reference index</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
64 <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
65 <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
66 <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
67 <option value="a_option">Match and report all valid alignments</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
68 </param>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
69 <param help="specify the -v bowtie option" label="Number of mismatches allowed" name="v_mismatches" type="select">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
70 <option value="0">0</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
71 <option selected="true" value="1">1</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
72 <option value="2">2</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
73 <option value="3">3</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
74 </param>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
75 <conditional name="refGenomeSource">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
76 <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
77 <option value="indexed">Use a built-in index</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
78 <option value="history">Use one from the history</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
79 </param>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
80 <when value="indexed">
2
316124e85b8d planemo upload for repository https://bitbucket.org/drosofff/gedtools/
mvdbeek
parents: 1
diff changeset
81 <param help="if your genome of interest is not listed - contact instance administrator" label="Select a DNA reference index" name="index" type="select">
1
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
82 <options from_data_table="bowtie_indexes">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
83
0
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
84 </options>
1
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
85 </param>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
86 </when>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
87 <when value="history">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
88 <param format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
89 </when>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
90 </conditional>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
91 <param help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below" label="Select output format" name="output_format" type="select">
7
5d82f9b15957 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 6
diff changeset
92 <option selected="true" value="tabular">tabular</option>
1
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
93 <option value="sam">sam</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
94 <option value="bam">bam</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
95 </param>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
96 <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select">
7
5d82f9b15957 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 6
diff changeset
97 <option selected="true" value="No">No</option>
1
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
98 <option value="al">aligned</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
99 <option value="unal">unaligned</option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
100 <option value="al_and_unal">both aligned and unaligned</option>
0
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
101 </param>
1
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
102 </inputs>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
103 <outputs>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
104 <data format="tabular" label="Bowtie Output" name="output">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
105 <change_format>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
106 <when format="sam" input="output_format" value="sam" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
107 <when format="bam" input="output_format" value="bam" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
108 </change_format>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
109 <actions>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
110 <conditional name="refGenomeSource.genomeSource">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
111 <when value="indexed">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
112 <action name="dbkey" type="metadata">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
113 <option column="1" name="bowtie_indexes" offset="0" type="from_data_table">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
114 <filter column="0" compare="startswith" keep="False" type="param_value" value="#" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
115 <filter column="0" ref="refGenomeSource.index" type="param_value" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
116 </option>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
117 </action>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
118 </when>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
119 <when value="history">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
120 <action name="dbkey" type="metadata">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
121 <option name="refGenomeSource.ownFile" param_attribute="dbkey" type="from_param" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
122 </action>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
123 </when>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
124 </conditional>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
125 </actions>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
126 </data>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
127 <data format="fasta" label="Matched reads" name="aligned">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
128 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
129 </data>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
130 <data format="fasta" label="Unmatched reads" name="unaligned">
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
131 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
132 </data>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
133 </outputs>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
134 <tests>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
135 <test>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
136 <param name="genomeSource" value="history" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
137 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
138 <param name="method" value="unique" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
139 <param ftype="fasta" name="input" value="input.fa" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
140 <param name="v_mismatches" value="1" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
141 <param name="output_format" value="bam" />
6
738a39851eae planemo upload for repository https://bitbucket.org/drosofff/gedtools/
mvdbeek
parents: 4
diff changeset
142 <output file="output.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
1
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
143 </test>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
144 <test>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
145 <param name="genomeSource" value="history" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
146 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
147 <param name="method" value="unique" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
148 <param ftype="fastq" name="input" value="input.fastq" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
149 <param name="v_mismatches" value="1" />
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
150 <param name="output_format" value="bam" />
6
738a39851eae planemo upload for repository https://bitbucket.org/drosofff/gedtools/
mvdbeek
parents: 4
diff changeset
151 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
1
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
152 </test>
27
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
153 <test>
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
154 <param name="genomeSource" value="history" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
155 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
156 <param name="method" value="multiple" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
157 <param ftype="fasta" name="input" value="input.fa" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
158 <param name="v_mismatches" value="1" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
159 <param name="output_format" value="tabular" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
160 <output file="output.tab" ftype="tabular" name="output" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
161 </test>
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
162 <test>
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
163 <param name="genomeSource" value="history" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
164 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
165 <param name="method" value="multiple" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
166 <param ftype="fasta" name="input" value="input.fa" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
167 <param name="v_mismatches" value="1" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
168 <param name="additional_fasta" value="al" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
169 <param name="output_format" value="tabular" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
170 <output file="output.tab" ftype="tabular" name="output" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
171 <output file="al.fa" ftype="fasta" name="aligned" />
2578aea69626 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
drosofff
parents: 26
diff changeset
172 </test>
1
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
173 </tests>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
174 <help>
0
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
175
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
176 **What it does**
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
177
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
178 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
179
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
180 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
181
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
182 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
183
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
184 However, this Bowtie wrapper tool only takes FASTQ files as inputs.
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
185
40
cdf2ffe2f8be planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
drosofff
parents: 38
diff changeset
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.
0
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
187
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
188 ------
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
189
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
190 **OPTIONS**
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
191
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
192 .. class:: infomark
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
193
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
194 This script uses Bowtie to match reads on a reference index.
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
195
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
196 Depending on the type of matching, different bowtie options are used:
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
197
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
198 **Match on sense strand RNA reference index, multiple mappers randomly matched at a single position**
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
199
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
200 Match on RNA reference, SENSE strand, randomly attributing multiple mapper to target with least mismatches, the polarity column is suppressed in the bowtie tabular report:
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
201
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
202 *-v [0,1,2,3] -M 1 --best --strata -p 12 --norc --suppress 2,6,7,8*
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
203
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
204 **Match unique mappers on DNA reference index**
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
205
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
206 Match ONLY unique mappers on DNA reference index
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
207
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
208 *-v [0,1,2,3] -m 1 -p 12 --suppress 6,7,8*
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
209
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
210 Note that using this option with -v values other than 0 is questionnable...
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
211
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
212 **Match on DNA, multiple mappers randomly matched at a single position**
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
213
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
214 Match multiple mappers, randomly attributing multiple mapper to target with least mismatches, number of mismatch allowed specified by -v option:
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
215
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
216 *-v [0,1,2,3] -M 1 --best --strata -p 12 --suppress 6,7,8*
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
217
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
218 **Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)**
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
219
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
220 Match with highest speed, not guaranteeing best hit for speed gain:
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
221
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
222 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
223
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
224
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
225 -----
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
226
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
227 **Input formats**
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
228
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
229 .. class:: warningmark
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
230
40
cdf2ffe2f8be planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
drosofff
parents: 38
diff changeset
231 *Lists of reads, in fasta or fastq format, clipped from their adapter sequence*
0
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
232
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
233 -----
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
234
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
235 **OUTPUTS**
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
236
40
cdf2ffe2f8be planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
drosofff
parents: 38
diff changeset
237 If you choose tabular as the output format, you will obtain the matched reads in tabular bowtie output format, having the following columns::
0
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
238
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
239 Column Description
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
240 -------- --------------------------------------------------------
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
241 1 FastaID fasta identifier
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
242 2 polarity + or - depending whether the match was reported on the forward or reverse strand
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
243 3 target name of the matched target
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
244 4 Offset O-based coordinate of the miR on the miRBase pre-miR sequence
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
245 5 Seq sequence of the matched Read
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
246
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
247 If you choose SAM, you will get the output in unordered SAM format.
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
248
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
249 .. class:: warningmark
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
250
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
251 if you choose BAM, the output will be in sorted BAM format.
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
252 To be viewable in Trackster, several condition must be fulfilled:
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
253
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
254 .. class:: infomark
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
255
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
256 Reads must have been matched to a genome whose chromosome names are compatible with Trackster genome indexes
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
257
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
258 .. class:: infomark
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
259
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
260 the database/Build (dbkey) which is indicated for the dataset (Pencil - Database/Build field) must match a Trackster genome index.
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
261
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
262 Please contact the Galaxy instance administrator if your genome is not referenced
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
263
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
264 **Matched and unmatched fasta reads can be retrieved, for further analyses**
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
265
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
266 </help>
1
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
267 <citations>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
268 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
b50d7228b678 Uploaded
mvdbeek
parents: 0
diff changeset
269 </citations>
0
64064dccdb11 Imported from capsule None
drosofff
parents:
diff changeset
270 </tool>