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1 <tool id="sailfish" name="Sailfish" version="0.6.3.0">
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2 <description>transcript quantification from RNA-seq data</description>
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3 <version_command>sailfish -version</version_command>
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4 <expand macro="requirements" />
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5 <command>
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6 <![CDATA[
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7 sailfish quant -i $index_dir
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8 #if $single_or_paired-single_or_paired_opts == 'single':
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9 -l "TYPE=SE"
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10 -r $single_or_paired_opts.input_singles
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11 #else:
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12 -1 $single_or_paired_opts.input_mate1
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13 -2 $single_or_paired_opts.input_mate2
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14 #if $single_or_paired_opts.orientation == "same":
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15 -l "TYPE=PE:O=>>"
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16 #elif $single_or_paired_opts.orientation == "away":
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17 -l "TYPE=PE:O=<>"
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18 #else:
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19 -l "TYPE=PE:O=><"
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20 #end if
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21 #end if
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22 -o <quant_dir>
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23
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24 ]]>
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25 </command>
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26 <expand macro="stdio" />
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27 <inputs>
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28 <conditional name="single_or_paired">
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29 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
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30 <option value="single">Single-end</option>
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31 <option value="paired">Paired-end</option>
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32 </param>
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33 <when value="single">
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34 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." />
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35 </when>
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36 <when value="paired">
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37 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ file." />
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38 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ file." />
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39 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
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40 <option value="same">Mates are oriented in the same direction</option>
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41 <option value="away">Mates are oriented away from each other</option>
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42 <option value="toward" selected="True">Mates are oriented toward each other</option>
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43 </param>
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44 </when>
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45 </conditional>
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46
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47 <expand macro="input_conditional_index" />
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48
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49 </inputs>
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50 <outputs>
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51 <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@">
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52 <expand macro="output_change_format" />
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53 </data>
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54 </outputs>
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55 <tests>
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56 </tests>
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57 <help>
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58 <![CDATA[
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59 **What it does**
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60
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61
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62 The first option >> denotes that the mates are oriented in the same direction --- e.g. if the 5' end of mate 1 is
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63 upstream from the 3' end, then the 5' end of mate 2 is upstream from its 3' end and vice-versa.
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64
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65 The second option <> denotes that the mates are oriented away from each other. This implies that start
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66 of mate1 is closer to start of mate 2 than the end of mate 2, etc.
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67
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68 The third option >< is, perhaps, the most common relative orientation. It denotes that the mates are
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69 oriented toward each other, so that the start of mate 1 is farther from the start of mate 2 than it is from the end of mate 2 and vice-versa.
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70
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71 -------
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72
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73 **References**
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74
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75 If you use this Galaxy tool in work leading to a scientific publication please
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76 cite the following:
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77
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78
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79 ]]>
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80 </help>
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81 </tool>
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