msp_sr_bowtie: sRbowtie.xml annotate

annotate sRbowtie.xml @ 5:b2c1ffe6579a draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c

author	drosofff
date	Tue, 04 Jul 2017 18:29:02 -0400
parents	615d2550977f
children	b7173c0011f3

rev	line source
5 b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.2">
0 e8bdae1a2bdc Uploaded drosofff parents: diff changeset	2 <description>for FASTA small reads</description>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	3 <requirements>
5 b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	4 <requirement type="package" version="1.1.2=py27_2">bowtie</requirement>
1 71b072cf5dde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 0 diff changeset	5 <requirement type="package" version="1.2">samtools</requirement>
0 e8bdae1a2bdc Uploaded drosofff parents: diff changeset	6 </requirements>
5 b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	7 <command detect_errors="exit_code"><![CDATA[
4 615d2550977f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 3 diff changeset	8 #if $refGenomeSource.genomeSource == "history":
5 b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	9 bowtie-build -f $refGenomeSource.ownFile local_index &&
4 615d2550977f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 3 diff changeset	10 #else:
5 b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	11 ln -f -s $refGenomeSource.index.fields.path local_index &&
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	12 #end if
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	13 #if $input.extension == "fasta":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	14 #set format = "-f"
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	15 #elif $input.extension == "fastq":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	16 #set format = "-q"
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	17 #end if
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	18
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	19 ## set the method_prefix
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	20 #if $method == "RNA":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	21 #set method_prefix = "-v %s -M 1 --best --strata --norc" % str($v_mismatches)
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	22 #elif $method == "unique":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	23 #set method_prefix = "-v %s -m 1" % str($v_mismatches)
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	24 #elif $method == "multiple":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	25 #set method_prefix = "-v %s -M 1 --best --strata" % str($v_mismatches)
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	26 #elif $method == "k_option":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	27 #set method_prefix = "-v %s -k 1 --best" % str($v_mismatches)
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	28 #elif $method == "n_option":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	29 #set method_prefix = "-n %s -M 1 --best" % str($v_mismatches)
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	30 #elif $method == "a_option":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	31 #set method_prefix = "-v %s -a --best" % str($v_mismatches)
4 615d2550977f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 3 diff changeset	32 #end if
5 b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	33
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	34 ## set the extra_output
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	35 #if $additional_fasta == "No":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	36 #set extra_output = ""
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	37 #elif $additional_fasta == "al":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	38 #set extra_output = " --al %s " % str($aligned)
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	39 #elif $additional_fasta == "unal":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	40 #set extra_output = " --un %s " % str($unaligned)
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	41 #else:
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	42 #set extra_output = " --al %s --un %s " % (str($aligned), str($unaligned))
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	43 #end if
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	44
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	45 #set $method_postfix = " %s %s " % ($method_prefix, $extra_output)
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	46
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	47 ## run the bowtie alignement
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	48 #if $output_format == "tabular":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	49 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$input' > $output
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	50 #elif $output_format == "sam":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	51 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output'
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	52 #elif $output_format == "bam":
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	53 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' \| samtools view -u - \| samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	54 #end if
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	55 ##### \| samtools view -uS
4 615d2550977f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 3 diff changeset	56 ]]></command>
0 e8bdae1a2bdc Uploaded drosofff parents: diff changeset	57 <inputs>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	58 <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	59 <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	60 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	61 <option value="unique">Match unique mappers on DNA reference index</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	62 <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	63 <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	64 <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	65 <option value="a_option">Match and report all valid alignments</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	66 </param>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	67 <param help="specify the -v bowtie option" label="Number of mismatches allowed" name="v_mismatches" type="select">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	68 <option value="0">0</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	69 <option selected="true" value="1">1</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	70 <option value="2">2</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	71 <option value="3">3</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	72 </param>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	73 <conditional name="refGenomeSource">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	74 <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">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	75 <option value="indexed">Use a built-in index</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	76 <option value="history">Use one from the history</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	77 </param>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	78 <when value="indexed">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	79 <param help="if your genome of interest is not listed - contact instance administrator" label="Select a DNA reference index" name="index" type="select">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	80 <options from_data_table="bowtie_indexes">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	81
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	82 </options>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	83 </param>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	84 </when>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	85 <when value="history">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	86 <param format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	87 </when>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	88 </conditional>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	89 <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">
1 71b072cf5dde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 0 diff changeset	90 <option selected="true" value="tabular">tabular</option>
0 e8bdae1a2bdc Uploaded drosofff parents: diff changeset	91 <option value="sam">sam</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	92 <option value="bam">bam</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	93 </param>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	94 <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select">
1 71b072cf5dde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 0 diff changeset	95 <option selected="true" value="No">No</option>
0 e8bdae1a2bdc Uploaded drosofff parents: diff changeset	96 <option value="al">aligned</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	97 <option value="unal">unaligned</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	98 <option value="al_and_unal">both aligned and unaligned</option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	99 </param>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	100 </inputs>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	101 <outputs>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	102 <data format="tabular" label="Bowtie Output" name="output">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	103 <change_format>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	104 <when format="sam" input="output_format" value="sam" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	105 <when format="bam" input="output_format" value="bam" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	106 </change_format>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	107 <actions>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	108 <conditional name="refGenomeSource.genomeSource">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	109 <when value="indexed">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	110 <action name="dbkey" type="metadata">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	111 <option column="1" name="bowtie_indexes" offset="0" type="from_data_table">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	112 <filter column="0" compare="startswith" keep="False" type="param_value" value="#" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	113 <filter column="0" ref="refGenomeSource.index" type="param_value" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	114 </option>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	115 </action>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	116 </when>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	117 <when value="history">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	118 <action name="dbkey" type="metadata">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	119 <option name="refGenomeSource.ownFile" param_attribute="dbkey" type="from_param" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	120 </action>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	121 </when>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	122 </conditional>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	123 </actions>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	124 </data>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	125 <data format="fasta" label="Matched reads" name="aligned">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	126 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	127 </data>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	128 <data format="fasta" label="Unmatched reads" name="unaligned">
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	129 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	130 </data>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	131 </outputs>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	132 <tests>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	133 <test>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	134 <param name="genomeSource" value="history" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	135 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	136 <param name="method" value="unique" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	137 <param ftype="fasta" name="input" value="input.fa" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	138 <param name="v_mismatches" value="1" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	139 <param name="output_format" value="bam" />
1 71b072cf5dde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 0 diff changeset	140 <output file="output.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
0 e8bdae1a2bdc Uploaded drosofff parents: diff changeset	141 </test>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	142 <test>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	143 <param name="genomeSource" value="history" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	144 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	145 <param name="method" value="unique" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	146 <param ftype="fastq" name="input" value="input.fastq" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	147 <param name="v_mismatches" value="1" />
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	148 <param name="output_format" value="bam" />
1 71b072cf5dde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 0 diff changeset	149 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
0 e8bdae1a2bdc Uploaded drosofff parents: diff changeset	150 </test>
5 b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	151 <test>
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	152 <param name="genomeSource" value="history" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	153 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	154 <param name="method" value="multiple" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	155 <param ftype="fasta" name="input" value="input.fa" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	156 <param name="v_mismatches" value="1" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	157 <param name="output_format" value="tabular" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	158 <output file="output.tab" ftype="tabular" name="output" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	159 </test>
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	160 <test>
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	161 <param name="genomeSource" value="history" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	162 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	163 <param name="method" value="multiple" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	164 <param ftype="fasta" name="input" value="input.fa" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	165 <param name="v_mismatches" value="1" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	166 <param name="additional_fasta" value="al" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	167 <param name="output_format" value="tabular" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	168 <output file="output.tab" ftype="tabular" name="output" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	169 <output file="al.fa" ftype="fasta" name="aligned" />
b2c1ffe6579a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 783b6d807f921a7214d53ddace3954d6eb5f2e5c drosofff parents: 4 diff changeset	170 </test>
0 e8bdae1a2bdc Uploaded drosofff parents: diff changeset	171 </tests>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	172 <help>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	173
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	174 What it does
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	175
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	176 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.
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	177
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	178 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	179
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	180 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	181
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	182 However, this Bowtie wrapper tool only takes FASTQ files as inputs.
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	183
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	184 The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode)
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	185
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	186 ------
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	187
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	188 OPTIONS
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	189
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	190 .. class:: infomark
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	191
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	192 This script uses Bowtie to match reads on a reference index.
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	193
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	194 Depending on the type of matching, different bowtie options are used:
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	195
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	196 Match on sense strand RNA reference index, multiple mappers randomly matched at a single position
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	197
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	198 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:
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	199
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	200 -v [0,1,2,3] -M 1 --best --strata -p 12 --norc --suppress 2,6,7,8
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	201
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	202 Match unique mappers on DNA reference index
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	203
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	204 Match ONLY unique mappers on DNA reference index
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	205
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	206 -v [0,1,2,3] -m 1 -p 12 --suppress 6,7,8
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	207
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	208 Note that using this option with -v values other than 0 is questionnable...
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	209
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	210 Match on DNA, multiple mappers randomly matched at a single position
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	211
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	212 Match multiple mappers, randomly attributing multiple mapper to target with least mismatches, number of mismatch allowed specified by -v option:
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	213
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	214 -v [0,1,2,3] -M 1 --best --strata -p 12 --suppress 6,7,8
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	215
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	216 Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	217
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	218 Match with highest speed, not guaranteeing best hit for speed gain:
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	219
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	220 -v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	221
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	222
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	223 -----
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	224
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	225 Input formats
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	226
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	227 .. class:: warningmark
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	228
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	229 The only accepted format for the script is a raw fasta list of reads, clipped from their adapter
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	230
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	231 -----
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	232
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	233 OUTPUTS
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	234
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	235 If you choose tabular as the output format, you will obtain the matched reads in standard bowtie output format, having the following columns::
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	236
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	237 Column Description
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	238 -------- --------------------------------------------------------
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	239 1 FastaID fasta identifier
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	240 2 polarity + or - depending whether the match was reported on the forward or reverse strand
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	241 3 target name of the matched target
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	242 4 Offset O-based coordinate of the miR on the miRBase pre-miR sequence
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	243 5 Seq sequence of the matched Read
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	244
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	245 If you choose SAM, you will get the output in unordered SAM format.
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	246
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	247 .. class:: warningmark
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	248
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	249 if you choose BAM, the output will be in sorted BAM format.
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	250 To be viewable in Trackster, several condition must be fulfilled:
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	251
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	252 .. class:: infomark
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	253
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	254 Reads must have been matched to a genome whose chromosome names are compatible with Trackster genome indexes
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	255
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	256 .. class:: infomark
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	257
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	258 the database/Build (dbkey) which is indicated for the dataset (Pencil - Database/Build field) must match a Trackster genome index.
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	259
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	260 Please contact the Galaxy instance administrator if your genome is not referenced
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	261
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	262 Matched and unmatched fasta reads can be retrieved, for further analyses
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	263
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	264 </help>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	265 <citations>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	266 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	267 </citations>
e8bdae1a2bdc Uploaded drosofff parents: diff changeset	268 </tool>

Mercurial > repos > drosofff > msp_sr_bowtie

annotate sRbowtie.xml @ 5:b2c1ffe6579a draft