annotate sRbowtie.xml @ 0:de9cd3998571 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
author artbio
date Sat, 02 Sep 2017 10:52:05 -0400
parents
children 5f4fbba31b6a
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de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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1 <tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.0">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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2 <description>for small RNA short reads</description>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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3 <requirements>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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4 <requirement type="package" version="1.1.2=py27_2">bowtie</requirement>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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5 <requirement type="package" version="1.2">samtools</requirement>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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6 </requirements>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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7 <command detect_errors="exit_code"><![CDATA[
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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8 #if $refGenomeSource.genomeSource == "history":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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9 bowtie-build -f $refGenomeSource.ownFile genome &&
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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10 ln -s -f '$refGenomeSource.ownFile' genome.fa &&
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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11 #set index_path = 'genome'
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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12 #else:
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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13 #set index_path = $refGenomeSource.index.fields.path
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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14 #end if
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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15 #if $input.extension == "fasta":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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16 #set format = "-f"
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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17 #elif $input.extension == "fastq":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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18 #set format = "-q"
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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19 #end if
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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20
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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21 ## set the method_prefix
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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22 #if $method == "RNA":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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23 #set method_prefix = "-v %s -M 1 --best --strata --norc" % str($v_mismatches)
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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24 #elif $method == "unique":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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25 #set method_prefix = "-v %s -m 1" % str($v_mismatches)
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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26 #elif $method == "multiple":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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27 #set method_prefix = "-v %s -M 1 --best --strata" % str($v_mismatches)
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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28 #elif $method == "k_option":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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29 #set method_prefix = "-v %s -k 1 --best" % str($v_mismatches)
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
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30 #elif $method == "n_option":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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31 #set method_prefix = "-n %s -M 1 --best" % str($v_mismatches)
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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32 #elif $method == "a_option":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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33 #set method_prefix = "-v %s -a --best" % str($v_mismatches)
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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34 #end if
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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35
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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36 ## set the extra_output
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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37 #if $additional_fasta == "No":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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38 #set extra_output = ""
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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39 #elif $additional_fasta == "al":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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40 #set extra_output = " --al %s " % str($aligned)
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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41 #elif $additional_fasta == "unal":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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42 #set extra_output = " --un %s " % str($unaligned)
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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43 #else:
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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44 #set extra_output = " --al %s --un %s " % (str($aligned), str($unaligned))
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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45 #end if
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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46
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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47 #set $method_postfix = " %s %s " % ($method_prefix, $extra_output)
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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48
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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49 ## run the bowtie alignement
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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50 #if $output_format == "tabular":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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51 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 $index_path $format '$input' > $output
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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52 #elif $output_format == "sam":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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53 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' > '$output'
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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54 #elif $output_format == "bam":
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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55 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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56 #end if
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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57 ##### | samtools view -uS
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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58 ]]></command>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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59 <inputs>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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60 <param format="fasta, fastq" help="Only with clipped, fasta or fastq read files" label="Input fasta or fastq file: reads clipped from their adapter" name="input" type="data" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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61 <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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62 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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63 <option value="unique">Match unique mappers on DNA reference index</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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64 <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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65 <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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66 <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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67 <option value="a_option">Match and report all valid alignments</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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68 </param>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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69 <param help="specify the -v bowtie option" label="Number of mismatches allowed" name="v_mismatches" type="select">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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70 <option value="0">0</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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71 <option selected="true" value="1">1</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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72 <option value="2">2</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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73 <option value="3">3</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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74 </param>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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75 <conditional name="refGenomeSource">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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76 <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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77 <option value="indexed">Use a built-in index</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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78 <option value="history">Use one from the history</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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79 </param>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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80 <when value="indexed">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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81 <param help="if your genome of interest is not listed - contact instance administrator" label="Select a DNA reference index" name="index" type="select">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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82 <options from_data_table="bowtie_indexes">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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83
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
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parents:
diff changeset
84 </options>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
85 </param>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
86 </when>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
87 <when value="history">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
88 <param format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
89 </when>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
90 </conditional>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
91 <param help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below" label="Select output format" name="output_format" type="select">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
92 <option selected="true" value="tabular">tabular</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
93 <option value="sam">sam</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
94 <option value="bam">bam</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
95 </param>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
96 <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
97 <option selected="true" value="No">No</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
98 <option value="al">aligned</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
99 <option value="unal">unaligned</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
100 <option value="al_and_unal">both aligned and unaligned</option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
101 </param>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
102 </inputs>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
103 <outputs>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
104 <data format="tabular" label="Bowtie Output" name="output">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
105 <change_format>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
106 <when format="sam" input="output_format" value="sam" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
107 <when format="bam" input="output_format" value="bam" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
108 </change_format>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
109 <actions>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
110 <conditional name="refGenomeSource.genomeSource">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
111 <when value="indexed">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
112 <action name="dbkey" type="metadata">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
113 <option column="1" name="bowtie_indexes" offset="0" type="from_data_table">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
114 <filter column="0" compare="startswith" keep="False" type="param_value" value="#" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
115 <filter column="0" ref="refGenomeSource.index" type="param_value" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
116 </option>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
117 </action>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
118 </when>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
119 <when value="history">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
120 <action name="dbkey" type="metadata">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
121 <option name="refGenomeSource.ownFile" param_attribute="dbkey" type="from_param" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
122 </action>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
123 </when>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
124 </conditional>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
125 </actions>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
126 </data>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
127 <data format="fasta" label="Matched reads" name="aligned">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
128 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
129 </data>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
130 <data format="fasta" label="Unmatched reads" name="unaligned">
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
131 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
132 </data>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
133 </outputs>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
134 <tests>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
135 <test>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
136 <param name="genomeSource" value="history" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
137 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
138 <param name="method" value="unique" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
139 <param ftype="fasta" name="input" value="input.fa" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
140 <param name="v_mismatches" value="1" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
141 <param name="output_format" value="bam" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
142 <output file="output.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
143 </test>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
144 <test>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
145 <param name="genomeSource" value="history" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
146 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
147 <param name="method" value="unique" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
148 <param ftype="fastq" name="input" value="input.fastq" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
149 <param name="v_mismatches" value="1" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
150 <param name="output_format" value="bam" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
151 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
152 </test>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
153 <test>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
154 <param name="genomeSource" value="history" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
155 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
156 <param name="method" value="multiple" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
157 <param ftype="fasta" name="input" value="input.fa" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
158 <param name="v_mismatches" value="1" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
159 <param name="output_format" value="tabular" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
160 <output file="output.tab" ftype="tabular" name="output" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
161 </test>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
162 <test>
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
163 <param name="genomeSource" value="history" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
164 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
165 <param name="method" value="multiple" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
166 <param ftype="fasta" name="input" value="input.fa" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
167 <param name="v_mismatches" value="1" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
168 <param name="additional_fasta" value="al" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
169 <param name="output_format" value="tabular" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
170 <output file="output.tab" ftype="tabular" name="output" />
de9cd3998571 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
artbio
parents:
diff changeset
171 <output file="al.fa" ftype="fasta" name="aligned" />
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172 </test>
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173 </tests>
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174 <help>
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175
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176 **What it does**
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177
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178 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
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179
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180 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
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181
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182 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
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183
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184 However, this Bowtie wrapper tool only takes FASTQ files as inputs.
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185
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186 The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis.
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187
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188 ------
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189
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190 **OPTIONS**
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191
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192 .. class:: infomark
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193
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194 This script uses Bowtie to match reads on a reference index.
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195
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196 Depending on the type of matching, different bowtie options are used:
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197
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198 **Match on sense strand RNA reference index, multiple mappers randomly matched at a single position**
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199
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200 Align on RNA reference, SENSE strand, randomly attributing multiple mapper to target with least mismatches:
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201
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202 *-v [0,1,2,3] -M 1 --best --strata -p 12 --norc*
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203
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204 **Match unique mappers on DNA reference index**
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205
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206 Align ONLY unique mappers on DNA reference index
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207
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208 *-v [0,1,2,3] -m 1 -p 12*
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209
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210 Note that using this option with -v values other than 0 is questionnable...
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211
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212 **Match on DNA, multiple mappers randomly matched at a single position**
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213
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214 Align multiple mappers, randomly attributing multiple mapper to target with least mismatches, number of mismatch allowed specified by -v option:
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215
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216 *-v [0,1,2,3] -M 1 --best --strata -p 12*
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217
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218 **Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)**
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219
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220 Align with highest speed, not guaranteeing best hit for speed gain:
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221
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222 *-v [0,1,2,3] -k 1 --best -p 12*
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223
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224 **Match on DNA - RNAseq mode (-n bowtie option)**
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225
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226 Align reads in as for RNAseq data alignment
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227
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228 *-n [0,1,2,3] -M 1 --best -p 12*
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229
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230 **Match and report all valid alignments**
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231
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232 Align reads and report all valid alignments
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233
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234 *-v [0,1,2,3] -a --best -p 12*
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235
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236
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237
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238 -----
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239
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240 **Input formats**
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241
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242 .. class:: warningmark
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243
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244 *Lists of reads, in fasta or fastq format, clipped from their adapter sequence*
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245
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246 -----
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247
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248 **OUTPUTS**
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249
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250 If you choose tabular as the output format, you will obtain the matched reads in tabular bowtie output format (--suppress 6,7,8), having the following columns::
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251
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252 Column Description
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253 -------- --------------------------------------------------------
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254 1 FastaID fasta identifier
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255 2 polarity + or - depending whether the match was reported on the forward or reverse strand
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256 3 target name of the matched target
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257 4 Offset O-based coordinate of the miR on the miRBase pre-miR sequence
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258 5 Seq sequence of the matched Read
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259
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260 If you choose SAM, you will get the output in unordered SAM format.
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261
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262 .. class:: warningmark
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264 if you choose BAM, the output will be in sorted BAM format.
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265 To be viewable in Trackster, several condition must be fulfilled:
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266
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267 .. class:: infomark
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269 Reads must have been matched to a genome whose chromosome names are compatible with Trackster genome indexes
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271 .. class:: infomark
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273 the database/Build (dbkey) which is indicated for the dataset (Pencil - Database/Build field) must match a Trackster genome index.
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275 Please contact the Galaxy instance administrator if your genome is not referenced
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277 **Matched and unmatched fasta reads can be retrieved, for further analyses**
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279 </help>
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280 <citations>
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281 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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282 </citations>
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283 </tool>