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1 <tool id="fastq_dump_paired" name="FASTQ Dump paired downloader" version="1.1.4">
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2 <description>Downloads a set of paired reads by their accession number using fastq-dump tool from sra-toolkit.</description>
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3 <requirements>
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4 <!-- Should just use the samtools that's installed in the path -->
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5 <requirement type="binary">fastq-dump</requirement>
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6 </requirements>
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7 <command>
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8 ## The command is a Cheetah template which allows some Python based syntax.
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9 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
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10 ## ! We only have a simple single command here.
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11 fastq-dump --log-level fatal --split-3 --accession ${accession_number} --ncbi_error_report never;
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12 ls -lh | grep ${accession_number};
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13 mv -v ${accession_number}_1.fastq R1.fastq;
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14 mv -v ${accession_number}_2.fastq R2.fastq;
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15 echo "Deleting any stored files in ~/ncbi";
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16 rm -rf ~/ncbi/*
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17 </command>
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18 <inputs>
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19 <param name="accession_number" size="10" type="text" value="" label="Accession Number"/>
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20 </inputs>
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21 <outputs>
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22 <data format="fastqsanger" label="${accession_number}_1" name="forward_reads" from_work_dir="R1.fastq" >
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23 </data>
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24 <data format="fastqsanger" label="${accession_number}_2" name="reverse_reads" from_work_dir="R2.fastq" >
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25 </data>
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26 </outputs>
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27
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28 <tests>
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29 <!-- Empty -->
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30 </tests>
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31
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32 <help>
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33
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34 .. class:: infomark
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35
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36 **What it does**
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37
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38 Performs a fastq-dump with the split-3 option.
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39
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40 ::
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41
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42 fastq-dump --log-level fatal --split-3 --accession accession_number --ncbi_error_report never
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43
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44
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45 Data is stored in fastqsanger format.
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46
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47 The metadata is now named to make it easier for collection lists to
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48 fetch when you search for reads in your history.
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49
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50 ------
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51
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52 .. class:: infomark
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53
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54 **Tool Author**
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55
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56 Mando Rodriguez
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57
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58 </help>
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59 </tool> |
