msp_sr_bowtie: sRbowtie.xml annotate

annotate sRbowtie.xml @ 32:ed6edd0c3b48 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 8cf5537e298d9a0e0c119ca484b95e2761780aae-dirty

author	drosofff
date	Sun, 02 Jul 2017 13:27:58 -0400
parents	e0a3a72719f3
children	5cb36185f910

rev	line source
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	1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.2">
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	2 <description>for FASTA small reads</description>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	3 <requirements>
32 ed6edd0c3b48 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 8cf5537e298d9a0e0c119ca484b95e2761780aae-dirty drosofff parents: 31 diff changeset	4 <requirement type="package" version="2.7.13">python</requirement>
ed6edd0c3b48 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 8cf5537e298d9a0e0c119ca484b95e2761780aae-dirty drosofff parents: 31 diff changeset	5 <requirement type="package" version="1.2">bowtie</requirement>
24 2f4e22f2177d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit cc96644a48fed1476e854fb7116b5f51c42f9f17 drosofff parents: 23 diff changeset	6 <requirement type="package" version="1.4.1">samtools</requirement>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	7 </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	8 <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	9 #if $refGenomeSource.genomeSource == "history":
28 c1ae0c9ad7d1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty drosofff parents: 27 diff changeset	10 bowtie-build -f $refGenomeSource.ownFile local_index &&
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	11 #else:
28 c1ae0c9ad7d1 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty drosofff parents: 27 diff changeset	12 ln -f -s $refGenomeSource.index.fields.path local_index &&
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	13 #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	14 #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	15 #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	16 #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	17 #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	18 #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	19
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 ## 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	21 #if $method == "RNA":
22 764181d43c36 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 1793456e6d76453825d92c76ca1051f6eccde0ab drosofff parents: 21 diff changeset	22 #set method_prefix = "-v %s -M 1 --best --strata --norc" % str($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	23 #elif $method == "unique":
22 764181d43c36 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 1793456e6d76453825d92c76ca1051f6eccde0ab drosofff parents: 21 diff changeset	24 #set method_prefix = "-v %s -m 1" % str($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	25 #elif $method == "multiple":
22 764181d43c36 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 1793456e6d76453825d92c76ca1051f6eccde0ab drosofff parents: 21 diff changeset	26 #set method_prefix = "-v %s -M 1 --best --strata" % str($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	27 #elif $method == "k_option":
22 764181d43c36 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 1793456e6d76453825d92c76ca1051f6eccde0ab drosofff parents: 21 diff changeset	28 #set method_prefix = "-v %s -k 1 --best" % str($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	29 #elif $method == "n_option":
22 764181d43c36 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 1793456e6d76453825d92c76ca1051f6eccde0ab drosofff parents: 21 diff changeset	30 #set method_prefix = "-n %s -M 1 --best" % str($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	31 #elif $method == "a_option":
22 764181d43c36 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 1793456e6d76453825d92c76ca1051f6eccde0ab drosofff parents: 21 diff changeset	32 #set method_prefix = "-v %s -a --best" % str($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	33 #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	34
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 ## 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	36 #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	37 #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	38 #elif $additional_fasta == "al":
15 44d61fa7fb75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 52409b39598052ed0eae765a8a9e277c82611e8d drosofff parents: 14 diff changeset	39 #set extra_output = " --al %s " % str($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	40 #elif $additional_fasta == "unal":
44d61fa7fb75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 52409b39598052ed0eae765a8a9e277c82611e8d drosofff parents: 14 diff changeset	41 #set extra_output = " --un %s " % str($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	42 #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	43 #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	44 #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	45
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	46 #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	47
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 ## 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	49 #if $output_format == "tabular":
30 5bd8c555390d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty drosofff parents: 29 diff changeset	50 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$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	51 #elif $output_format == "sam":
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	52 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$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	53 #elif $output_format == "bam":
30 5bd8c555390d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty drosofff parents: 29 diff changeset	54 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' \| samtools sort -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	55 #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	56 ##### \| 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	57 ]]></command>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	58 <inputs>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	59 <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	60 <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	61 <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	62 <option value="unique">Match unique mappers on DNA reference index</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	63 <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	64 <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	65 <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	66 <option value="a_option">Match and report all valid alignments</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	67 </param>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	68 <param help="specify the -v bowtie option" label="Number of mismatches allowed" name="v_mismatches" type="select">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	69 <option value="0">0</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	70 <option selected="true" value="1">1</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	71 <option value="2">2</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	72 <option value="3">3</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	73 </param>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	74 <conditional name="refGenomeSource">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	75 <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	76 <option value="indexed">Use a built-in index</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	77 <option value="history">Use one from the history</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	78 </param>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	79 <when value="indexed">
2 316124e85b8d planemo upload for repository https://bitbucket.org/drosofff/gedtools/ mvdbeek parents: 1 diff changeset	80 <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	81 <options from_data_table="bowtie_indexes">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	82
0 64064dccdb11 Imported from capsule None drosofff parents: diff changeset	83 </options>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	84 </param>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	85 </when>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	86 <when value="history">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	87 <param format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	88 </when>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	89 </conditional>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	90 <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	91 <option selected="true" value="tabular">tabular</option>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	92 <option value="sam">sam</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	93 <option value="bam">bam</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	94 </param>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	95 <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	96 <option selected="true" value="No">No</option>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	97 <option value="al">aligned</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	98 <option value="unal">unaligned</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	99 <option value="al_and_unal">both aligned and unaligned</option>
0 64064dccdb11 Imported from capsule None drosofff parents: diff changeset	100 </param>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	101 </inputs>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	102 <outputs>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	103 <data format="tabular" label="Bowtie Output" name="output">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	104 <change_format>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	105 <when format="sam" input="output_format" value="sam" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	106 <when format="bam" input="output_format" value="bam" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	107 </change_format>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	108 <actions>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	109 <conditional name="refGenomeSource.genomeSource">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	110 <when value="indexed">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	111 <action name="dbkey" type="metadata">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	112 <option column="1" name="bowtie_indexes" offset="0" type="from_data_table">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	113 <filter column="0" compare="startswith" keep="False" type="param_value" value="#" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	114 <filter column="0" ref="refGenomeSource.index" type="param_value" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	115 </option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	116 </action>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	117 </when>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	118 <when value="history">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	119 <action name="dbkey" type="metadata">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	120 <option name="refGenomeSource.ownFile" param_attribute="dbkey" type="from_param" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	121 </action>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	122 </when>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	123 </conditional>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	124 </actions>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	125 </data>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	126 <data format="fasta" label="Matched reads" name="aligned">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	127 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	128 </data>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	129 <data format="fasta" label="Unmatched reads" name="unaligned">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	130 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	131 </data>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	132 </outputs>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	133 <tests>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	134 <test>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	135 <param name="genomeSource" value="history" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	136 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	137 <param name="method" value="unique" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	138 <param ftype="fasta" name="input" value="input.fa" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	139 <param name="v_mismatches" value="1" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	140 <param name="output_format" value="bam" />
6 738a39851eae planemo upload for repository https://bitbucket.org/drosofff/gedtools/ mvdbeek parents: 4 diff changeset	141 <output file="output.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	142 </test>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	143 <test>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	144 <param name="genomeSource" value="history" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	145 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	146 <param name="method" value="unique" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	147 <param ftype="fastq" name="input" value="input.fastq" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	148 <param name="v_mismatches" value="1" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	149 <param name="output_format" value="bam" />
6 738a39851eae planemo upload for repository https://bitbucket.org/drosofff/gedtools/ mvdbeek parents: 4 diff changeset	150 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	151 </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	152 <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	153 <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	154 <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	155 <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	156 <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	157 <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	158 <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	159 <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	160 </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	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 <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	163 <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	164 <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	165 <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	166 <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	167 <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	168 <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	169 <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	170 <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	171 </test>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	172 </tests>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	173 <help>
0 64064dccdb11 Imported from capsule None drosofff parents: diff changeset	174
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	175 What it does
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	176
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	177 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	178
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	179 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	180
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	181 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	182
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	183 However, this Bowtie wrapper tool only takes FASTQ files as inputs.
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	184
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	185 The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode)
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	186
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 OPTIONS
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	190
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	191 .. class:: infomark
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	192
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	193 This script uses Bowtie to match reads on a reference index.
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	194
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	195 Depending on the type of matching, different bowtie options are used:
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	196
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	197 Match on sense strand RNA reference index, multiple mappers randomly matched at a single position
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	198
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	199 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	200
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	201 -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	202
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	203 Match unique mappers on DNA reference index
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	204
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	205 Match ONLY unique mappers on DNA reference index
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	206
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	207 -v [0,1,2,3] -m 1 -p 12 --suppress 6,7,8
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	208
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	209 Note that using this option with -v values other than 0 is questionnable...
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	210
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	211 Match on DNA, multiple mappers randomly matched at a single position
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	212
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	213 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	214
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	215 -v [0,1,2,3] -M 1 --best --strata -p 12 --suppress 6,7,8
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	216
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	217 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	218
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	219 Match with highest speed, not guaranteeing best hit for speed gain:
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	220
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	221 -v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	222
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 Input formats
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	227
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	228 .. class:: warningmark
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	229
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	230 The only accepted format for the script is a raw fasta list of reads, clipped from their adapter
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	231
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 OUTPUTS
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	235
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	236 If you choose tabular as the output format, you will obtain the matched reads in standard bowtie output format, having the following columns::
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	237
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	238 Column Description
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	239 -------- --------------------------------------------------------
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	240 1 FastaID fasta identifier
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	241 2 polarity + or - depending whether the match was reported on the forward or reverse strand
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	242 3 target name of the matched target
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	243 4 Offset O-based coordinate of the miR on the miRBase pre-miR sequence
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	244 5 Seq sequence of the matched Read
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	245
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	246 If you choose SAM, you will get the output in unordered SAM format.
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	247
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	248 .. class:: warningmark
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	249
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	250 if you choose BAM, the output will be in sorted BAM format.
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	251 To be viewable in Trackster, several condition must be fulfilled:
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	252
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	253 .. class:: infomark
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	254
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	255 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	256
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	257 .. class:: infomark
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	258
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	259 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	260
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	261 Please contact the Galaxy instance administrator if your genome is not referenced
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	262
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	263 Matched and unmatched fasta reads can be retrieved, for further analyses
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	264
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	265 </help>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	266 <citations>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	267 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	268 </citations>
0 64064dccdb11 Imported from capsule None drosofff parents: diff changeset	269 </tool>

Mercurial > repos > drosofff > msp_sr_bowtie

annotate sRbowtie.xml @ 32:ed6edd0c3b48 draft