msp_sr_bowtie: sRbowtie.xml annotate

annotate sRbowtie.xml @ 14:a05b107fd0c4 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b

author	drosofff
date	Mon, 26 Jun 2017 12:06:12 -0400
parents	99009e0a7a4a
children	44d61fa7fb75

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>
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	4 <requirement type="package" version="1.1.2">bowtie</requirement>
11 88cdd6118bfe planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 763ba9879fe37a13d18d75a4a03150d3560a82f8 drosofff parents: 10 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[
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	8 #if $refGenomeSource.genomeSource == "history":
14 a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b drosofff parents: 13 diff changeset	9 bowtie-build -f '$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	10 #else:
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	11 ln -s local_index '$refGenomeSource.index.fields.path' &&
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b drosofff parents: 13 diff changeset	12 #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	13 #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	14 #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	15 #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	16 #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	17 #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	18
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 ## 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	20 #if $method == "RNA":
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b drosofff parents: 13 diff changeset	21 #set method_prefix = "-v %s -M 1 --best --strata --norc" % (str($v_mismatches))
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 #elif $method == "unique":
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b drosofff parents: 13 diff changeset	23 #set method_prefix = "-v %s -m 1" % (str($v_mismatches))
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 $method == "multiple":
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b drosofff parents: 13 diff changeset	25 #set method_prefix = "-v %s -M 1 --best --strata" % (str($v_mismatches))
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 $method == "k_option":
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b drosofff parents: 13 diff changeset	27 #set method_prefix = "-v %s -k 1 --best" % (str($v_mismatches))
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 $method == "n_option":
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b drosofff parents: 13 diff changeset	29 #set method_prefix = "-n %s -M 1 --best" % (str($v_mismatches))
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 $method == "a_option":
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b drosofff parents: 13 diff changeset	31 #set method_prefix = "-v %s -a --best" % (str($v_mismatches))
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 #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	33
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 ## 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	35 #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	36 #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	37 #elif $additional_fasta == "al":
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b drosofff parents: 13 diff changeset	38 #set extra_output = " --un %s" % str(unaligned)
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b drosofff parents: 13 diff changeset	39 #else:
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b drosofff parents: 13 diff changeset	40 #set extra_output = " --al %s --un %s" % (str($aligned), str(unaligned))
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b drosofff parents: 13 diff changeset	41 #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	42
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 #set $method_postfix = "$method_prefix" + "$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	44
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 ## run the bowtie alignement
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 #if $output_format == "tabular":
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 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix --suppress 6,7,8 "local_index" $format $input > $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	48 #elif $output_format == "sam":
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 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix -S "local_index" $format $input > $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	50 #elif $output_format == "bam":
a05b107fd0c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b drosofff parents: 13 diff changeset	51 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix -S "local_index" $format $input \|samtools view -bS - > $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	52 #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	53
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	54 ]]></command>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	55 <inputs>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	56 <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	57 <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	58 <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	59 <option value="unique">Match unique mappers on DNA reference index</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	60 <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	61 <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	62 <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	63 <option value="a_option">Match and report all valid alignments</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	64 </param>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	65 <param help="specify the -v bowtie option" label="Number of mismatches allowed" name="v_mismatches" type="select">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	66 <option value="0">0</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	67 <option selected="true" value="1">1</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	68 <option value="2">2</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	69 <option value="3">3</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	70 </param>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	71 <conditional name="refGenomeSource">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	72 <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	73 <option value="indexed">Use a built-in index</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	74 <option value="history">Use one from the history</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	75 </param>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	76 <when value="indexed">
2 316124e85b8d planemo upload for repository https://bitbucket.org/drosofff/gedtools/ mvdbeek parents: 1 diff changeset	77 <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	78 <options from_data_table="bowtie_indexes">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	79
0 64064dccdb11 Imported from capsule None drosofff parents: diff changeset	80 </options>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	81 </param>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	82 </when>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	83 <when value="history">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	84 <param format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	85 </when>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	86 </conditional>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	87 <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	88 <option selected="true" value="tabular">tabular</option>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	89 <option value="sam">sam</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	90 <option value="bam">bam</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	91 </param>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	92 <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	93 <option selected="true" value="No">No</option>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	94 <option value="al">aligned</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	95 <option value="unal">unaligned</option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	96 <option value="al_and_unal">both aligned and unaligned</option>
0 64064dccdb11 Imported from capsule None drosofff parents: diff changeset	97 </param>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	98 </inputs>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	99 <outputs>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	100 <data format="tabular" label="Bowtie Output" name="output">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	101 <change_format>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	102 <when format="sam" input="output_format" value="sam" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	103 <when format="bam" input="output_format" value="bam" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	104 </change_format>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	105 <actions>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	106 <conditional name="refGenomeSource.genomeSource">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	107 <when value="indexed">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	108 <action name="dbkey" type="metadata">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	109 <option column="1" name="bowtie_indexes" offset="0" type="from_data_table">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	110 <filter column="0" compare="startswith" keep="False" type="param_value" value="#" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	111 <filter column="0" ref="refGenomeSource.index" type="param_value" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	112 </option>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	113 </action>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	114 </when>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	115 <when value="history">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	116 <action name="dbkey" type="metadata">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	117 <option name="refGenomeSource.ownFile" param_attribute="dbkey" type="from_param" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	118 </action>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	119 </when>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	120 </conditional>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	121 </actions>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	122 </data>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	123 <data format="fasta" label="Matched reads" name="aligned">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	124 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	125 </data>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	126 <data format="fasta" label="Unmatched reads" name="unaligned">
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	127 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	128 </data>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	129 </outputs>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	130 <tests>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	131 <test>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	132 <param name="genomeSource" value="history" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	133 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	134 <param name="method" value="unique" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	135 <param ftype="fasta" name="input" value="input.fa" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	136 <param name="v_mismatches" value="1" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	137 <param name="output_format" value="bam" />
6 738a39851eae planemo upload for repository https://bitbucket.org/drosofff/gedtools/ mvdbeek parents: 4 diff changeset	138 <output file="output.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	139 </test>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	140 <test>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	141 <param name="genomeSource" value="history" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	142 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	143 <param name="method" value="unique" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	144 <param ftype="fastq" name="input" value="input.fastq" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	145 <param name="v_mismatches" value="1" />
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	146 <param name="output_format" value="bam" />
6 738a39851eae planemo upload for repository https://bitbucket.org/drosofff/gedtools/ mvdbeek parents: 4 diff changeset	147 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	148 </test>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	149 </tests>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	150 <help>
0 64064dccdb11 Imported from capsule None drosofff parents: diff changeset	151
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	152 What it does
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	153
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	154 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	155
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	156 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	157
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	158 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	159
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	160 However, this Bowtie wrapper tool only takes FASTQ files as inputs.
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	161
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	162 The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode)
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	163
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	164 ------
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	165
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	166 OPTIONS
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	167
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	168 .. class:: infomark
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	169
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	170 This script uses Bowtie to match reads on a reference index.
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	171
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	172 Depending on the type of matching, different bowtie options are used:
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	173
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	174 Match on sense strand RNA reference index, multiple mappers randomly matched at a single position
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	175
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	176 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	177
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	178 -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	179
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	180 Match unique mappers on DNA reference index
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	181
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	182 Match ONLY unique mappers on DNA reference index
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	183
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	184 -v [0,1,2,3] -m 1 -p 12 --suppress 6,7,8
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	185
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	186 Note that using this option with -v values other than 0 is questionnable...
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	187
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	188 Match on DNA, multiple mappers randomly matched at a single position
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	189
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	190 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	191
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	192 -v [0,1,2,3] -M 1 --best --strata -p 12 --suppress 6,7,8
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	193
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	194 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	195
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	196 Match with highest speed, not guaranteeing best hit for speed gain:
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	197
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	198 -v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	199
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	200
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	201 -----
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	202
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	203 Input formats
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	204
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	205 .. class:: warningmark
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	206
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	207 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	208
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	209 -----
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	210
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	211 OUTPUTS
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	212
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	213 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	214
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	215 Column Description
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	216 -------- --------------------------------------------------------
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	217 1 FastaID fasta identifier
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	218 2 polarity + or - depending whether the match was reported on the forward or reverse strand
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	219 3 target name of the matched target
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	220 4 Offset O-based coordinate of the miR on the miRBase pre-miR sequence
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	221 5 Seq sequence of the matched Read
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	222
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	223 If you choose SAM, you will get the output in unordered SAM format.
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	224
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	225 .. class:: warningmark
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	226
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	227 if you choose BAM, the output will be in sorted BAM format.
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	228 To be viewable in Trackster, several condition must be fulfilled:
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	229
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	230 .. class:: infomark
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	231
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	232 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	233
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	234 .. class:: infomark
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	235
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	236 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	237
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	238 Please contact the Galaxy instance administrator if your genome is not referenced
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	239
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	240 Matched and unmatched fasta reads can be retrieved, for further analyses
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	241
64064dccdb11 Imported from capsule None drosofff parents: diff changeset	242 </help>
1 b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	243 <citations>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	244 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
b50d7228b678 Uploaded mvdbeek parents: 0 diff changeset	245 </citations>
0 64064dccdb11 Imported from capsule None drosofff parents: diff changeset	246 </tool>

Mercurial > repos > drosofff > msp_sr_bowtie

annotate sRbowtie.xml @ 14:a05b107fd0c4 draft