Mercurial > repos > drosofff > msp_sr_bowtie
annotate sRbowtie.xml @ 2:316124e85b8d draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | mvdbeek |
|---|---|
| date | Mon, 25 May 2015 12:44:36 -0400 |
| parents | b50d7228b678 |
| children | c9c931695e72 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.0"> |
| 1 | 2 <description>for FASTA small reads</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.12.7">bowtie</requirement> | |
| 0 | 5 <requirement type="package" version="0.1.18">samtools</requirement> |
| 1 | 6 </requirements> |
| 7 <command interpreter="python"> sRbowtie.py --input $input | |
| 8 --input-format $input.extension | |
| 0 | 9 --method $method |
| 10 --v-mismatches $v_mismatches | |
| 11 --output-format $output_format | |
| 12 --output $output | |
| 13 --index-from $refGenomeSource.genomeSource | |
| 14 ## the very source of the index (indexed or fasta file) | |
| 15 --index-source | |
| 16 #if $refGenomeSource.genomeSource == "history": | |
| 17 $refGenomeSource.ownFile | |
| 18 #else: | |
| 19 $refGenomeSource.index.fields.path | |
| 20 #end if | |
| 21 --aligned $aligned | |
| 22 --unaligned $unaligned | |
| 23 --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie | |
| 24 </command> | |
| 1 | 25 <inputs> |
| 26 <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" /> | |
| 27 <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"> | |
| 28 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option> | |
| 29 <option value="unique">Match unique mappers on DNA reference index</option> | |
| 30 <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option> | |
| 31 <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option> | |
| 32 <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option> | |
| 33 <option value="a_option">Match and report all valid alignments</option> | |
| 34 </param> | |
| 35 <param help="specify the -v bowtie option" label="Number of mismatches allowed" name="v_mismatches" type="select"> | |
| 36 <option value="0">0</option> | |
| 37 <option selected="true" value="1">1</option> | |
| 38 <option value="2">2</option> | |
| 39 <option value="3">3</option> | |
| 40 </param> | |
| 41 <conditional name="refGenomeSource"> | |
| 42 <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"> | |
| 43 <option value="indexed">Use a built-in index</option> | |
| 44 <option value="history">Use one from the history</option> | |
| 45 </param> | |
| 46 <when value="indexed"> | |
|
2
316124e85b8d
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
mvdbeek
parents:
1
diff
changeset
|
47 <param help="if your genome of interest is not listed - contact instance administrator" label="Select a DNA reference index" name="index" type="select"> |
| 1 | 48 <options from_data_table="bowtie_indexes"> |
| 49 | |
| 0 | 50 </options> |
| 1 | 51 </param> |
| 52 </when> | |
| 53 <when value="history"> | |
| 54 <param format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" /> | |
| 55 </when> | |
| 56 </conditional> | |
| 57 <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"> | |
| 58 <option select="true" value="tabular">tabular</option> | |
| 59 <option value="sam">sam</option> | |
| 60 <option value="bam">bam</option> | |
| 61 </param> | |
| 62 <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select"> | |
| 63 <option select="true" value="No">No</option> | |
| 64 <option value="al">aligned</option> | |
| 65 <option value="unal">unaligned</option> | |
| 66 <option value="al_and_unal">both aligned and unaligned</option> | |
| 0 | 67 </param> |
| 1 | 68 </inputs> |
| 69 <outputs> | |
| 70 <data format="tabular" label="Bowtie Output" name="output"> | |
| 71 <change_format> | |
| 72 <when format="sam" input="output_format" value="sam" /> | |
| 73 <when format="bam" input="output_format" value="bam" /> | |
| 74 </change_format> | |
| 75 <actions> | |
| 76 <conditional name="refGenomeSource.genomeSource"> | |
| 77 <when value="indexed"> | |
| 78 <action name="dbkey" type="metadata"> | |
| 79 <option column="1" name="bowtie_indexes" offset="0" type="from_data_table"> | |
| 80 <filter column="0" compare="startswith" keep="False" type="param_value" value="#" /> | |
| 81 <filter column="0" ref="refGenomeSource.index" type="param_value" /> | |
| 82 </option> | |
| 83 </action> | |
| 84 </when> | |
| 85 <when value="history"> | |
| 86 <action name="dbkey" type="metadata"> | |
| 87 <option name="refGenomeSource.ownFile" param_attribute="dbkey" type="from_param" /> | |
| 88 </action> | |
| 89 </when> | |
| 90 </conditional> | |
| 91 </actions> | |
| 92 </data> | |
| 93 <data format="fasta" label="Matched reads" name="aligned"> | |
| 94 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter> | |
| 95 </data> | |
| 96 <data format="fasta" label="Unmatched reads" name="unaligned"> | |
| 97 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter> | |
| 98 </data> | |
| 99 </outputs> | |
| 100 <tests> | |
| 101 <test> | |
| 102 <param name="genomeSource" value="history" /> | |
| 103 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> | |
| 104 <param name="method" value="unique" /> | |
| 105 <param ftype="fasta" name="input" value="input.fa" /> | |
| 106 <param name="v_mismatches" value="1" /> | |
| 107 <param name="output_format" value="bam" /> | |
| 108 <output file="output.bam" ftype="bam" lines_diff="4" name="output" /> | |
| 109 </test> | |
| 110 <test> | |
| 111 <param name="genomeSource" value="history" /> | |
| 112 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> | |
| 113 <param name="method" value="unique" /> | |
| 114 <param ftype="fastq" name="input" value="input.fastq" /> | |
| 115 <param name="v_mismatches" value="1" /> | |
| 116 <param name="output_format" value="bam" /> | |
| 117 <output file="output2.bam" ftype="bam" lines_diff="4" name="output" /> | |
| 118 </test> | |
| 119 </tests> | |
| 120 <help> | |
| 0 | 121 |
| 122 **What it does** | |
| 123 | |
| 124 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. | |
| 125 | |
| 126 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml | |
| 127 | |
| 128 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution. | |
| 129 | |
| 130 However, this Bowtie wrapper tool only takes FASTQ files as inputs. | |
| 131 | |
| 132 The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode) | |
| 133 | |
| 134 ------ | |
| 135 | |
| 136 **OPTIONS** | |
| 137 | |
| 138 .. class:: infomark | |
| 139 | |
| 140 This script uses Bowtie to match reads on a reference index. | |
| 141 | |
| 142 Depending on the type of matching, different bowtie options are used: | |
| 143 | |
| 144 **Match on sense strand RNA reference index, multiple mappers randomly matched at a single position** | |
| 145 | |
| 146 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: | |
| 147 | |
| 148 *-v [0,1,2,3] -M 1 --best --strata -p 12 --norc --suppress 2,6,7,8* | |
| 149 | |
| 150 **Match unique mappers on DNA reference index** | |
| 151 | |
| 152 Match ONLY unique mappers on DNA reference index | |
| 153 | |
| 154 *-v [0,1,2,3] -m 1 -p 12 --suppress 6,7,8* | |
| 155 | |
| 156 Note that using this option with -v values other than 0 is questionnable... | |
| 157 | |
| 158 **Match on DNA, multiple mappers randomly matched at a single position** | |
| 159 | |
| 160 Match multiple mappers, randomly attributing multiple mapper to target with least mismatches, number of mismatch allowed specified by -v option: | |
| 161 | |
| 162 *-v [0,1,2,3] -M 1 --best --strata -p 12 --suppress 6,7,8* | |
| 163 | |
| 164 **Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)** | |
| 165 | |
| 166 Match with highest speed, not guaranteeing best hit for speed gain: | |
| 167 | |
| 168 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8* | |
| 169 | |
| 170 | |
| 171 ----- | |
| 172 | |
| 173 **Input formats** | |
| 174 | |
| 175 .. class:: warningmark | |
| 176 | |
| 177 *The only accepted format for the script is a raw fasta list of reads, clipped from their adapter* | |
| 178 | |
| 179 ----- | |
| 180 | |
| 181 **OUTPUTS** | |
| 182 | |
| 183 If you choose tabular as the output format, you will obtain the matched reads in standard bowtie output format, having the following columns:: | |
| 184 | |
| 185 Column Description | |
| 186 -------- -------------------------------------------------------- | |
| 187 1 FastaID fasta identifier | |
| 188 2 polarity + or - depending whether the match was reported on the forward or reverse strand | |
| 189 3 target name of the matched target | |
| 190 4 Offset O-based coordinate of the miR on the miRBase pre-miR sequence | |
| 191 5 Seq sequence of the matched Read | |
| 192 | |
| 193 If you choose SAM, you will get the output in unordered SAM format. | |
| 194 | |
| 195 .. class:: warningmark | |
| 196 | |
| 197 if you choose BAM, the output will be in sorted BAM format. | |
| 198 To be viewable in Trackster, several condition must be fulfilled: | |
| 199 | |
| 200 .. class:: infomark | |
| 201 | |
| 202 Reads must have been matched to a genome whose chromosome names are compatible with Trackster genome indexes | |
| 203 | |
| 204 .. class:: infomark | |
| 205 | |
| 206 the database/Build (dbkey) which is indicated for the dataset (Pencil - Database/Build field) must match a Trackster genome index. | |
| 207 | |
| 208 Please contact the Galaxy instance administrator if your genome is not referenced | |
| 209 | |
| 210 **Matched and unmatched fasta reads can be retrieved, for further analyses** | |
| 211 | |
| 212 </help> | |
| 1 | 213 <citations> |
| 214 <citation type="doi">10.1186/gb-2009-10-3-r25</citation> | |
| 215 </citations> | |
| 0 | 216 </tool> |