Mercurial > repos > iuc > sra_tools
annotate fastq_dump.xml @ 14:1790dcf3c32d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 30ec06de1f3056967f5cc2d8ef57f9692d5533d7
author | iuc |
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date | Tue, 04 Dec 2018 15:00:55 -0500 |
parents | c38286ea7047 |
children | f5ea3ce9b9b0 |
rev | line source |
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9
6c60903f70ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 6252dc2340b2fb6c7fdab2bdadfa4779c6f1aefd
iuc
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1 <tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@.3"> |
7
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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2 <description>format from NCBI SRA</description> |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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3 <macros> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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changeset
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4 <import>sra_macros.xml</import> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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changeset
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5 </macros> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
changeset
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6 <expand macro="requirements"/> |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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changeset
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7 <version_command>fastq-dump --version</version_command> |
13
c38286ea7047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
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8 <command detect_errors="exit_code"><![CDATA[ |
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c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents:
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9 |
13
c38286ea7047
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
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10 @SET_ACCESSIONS@ |
2
f256cb398262
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
iuc
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11 |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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changeset
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12 ## Need to set the home directory to the current working directory, |
2
f256cb398262
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
iuc
parents:
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13 ## else the tool tries to write to home/.ncbi and fails when used |
f256cb398262
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
iuc
parents:
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14 ## with a cluster manager. |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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15 export HOME=\$PWD && |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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changeset
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16 vdb-config --restore-defaults && |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
changeset
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17 #if $input.input_select == "file": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
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18 fastq-dump --log-level fatal --accession '${input.file.name}' |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
changeset
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19 #else: |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
changeset
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20 vdb-config -s "/repository/user/main/public/root=\$PWD" && |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
changeset
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21 ## Do not use prefetch if region is specified, to avoid downloading |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
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22 ## the complete sra file. |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
changeset
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23 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ): |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
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24 ASCP_PATH=`command -v ascp` && |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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25 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true && |
3
4732693f4661
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit f30369bef4e2cef17395cdd62ce81768c93f5edd
iuc
parents:
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26 prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" && |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
changeset
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27 ## Duplicate vdb-config, in case settings changed between prefetch and |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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28 ## dump command. |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
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29 vdb-config -s "/repository/user/main/public/root=\$PWD" && |
1
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
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30 #end if |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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31 fastq-dump --accession "\$acc" |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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32 --split-files |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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33 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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34 --defline-seq '@\$sn[_\$rn]/\$ri' |
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1920e0508831
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 39ca11da7daeb3fa030fcb28e8987f8d7f24aec3
iuc
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35 --defline-qual '+' |
1
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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36 |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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37 $adv.split |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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38 #if str( $adv.alignments ) == "aligned": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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39 --aligned |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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40 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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41 #if str( $adv.alignments ) == "unaligned": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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42 --unaligned |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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43 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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44 #if str( $adv.minID ) != "": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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45 --minSpotId "$adv.minID" |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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46 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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47 #if str( $adv.maxID ) != "": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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48 --maxSpotId "$adv.maxID" |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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49 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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50 #if str( $adv.minlen ) != "": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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51 --minReadLen "$adv.minlen" |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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52 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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53 #if str( $adv.readfilter ) != "": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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54 --read-filter "$adv.readfilter" |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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55 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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56 #if str( $adv.region ) != "": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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57 --aligned-region "$adv.region" |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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58 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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59 #if str( $adv.spotgroups ) != "": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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60 --spot-groups "$adv.spotgroups" |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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61 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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62 #if str( $adv.matepairDist ) != "": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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63 --matepair-distance "$adv.matepairDist" |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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64 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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65 $adv.clip |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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66 $adv.skip_technical |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
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67 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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68 #if str( $outputformat ) == "fastqsanger.gz": |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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69 --gzip |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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70 #elif str( $outputformat ) == "fastqsanger.bz2": |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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71 --bzip2 |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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72 #end if |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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73 #if $input.input_select=="file": |
1
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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74 --stdout |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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75 "$input.file" > "$output_file" |
7
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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76 |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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77 #elif $input.input_select=="accession_number": |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
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78 --stdout |
1
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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79 "\$acc" > "$output_accession" ) |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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80 #end if |
1
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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81 |
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82 #if $input.input_select=="file_list": |
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83 ) ; done |
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84 |
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85 ; |
1
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86 |
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87 for i in `ls *.fast* | cut -f 1 -d '_' | uniq` ; do |
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88 count=`ls \$i* | wc -l` ; |
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89 data=(\$(ls -d \$i*)); |
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90 |
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91 if [ "\$count" -eq 2 ]; then |
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92 mv "\${data[0]}" "\${data[0]}"_forward.$outputformat; mv "\${data[1]}" "\${data[1]}"_reverse.$outputformat ; |
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93 elif [ "\$count" -eq 1 ]; then |
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94 mv "\${data[0]}" "\${data[0]}"__single.$outputformat ; |
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95 fi; |
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96 done |
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97 |
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98 |
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99 #end if |
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100 |
2
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101 |
0
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102 ]]> |
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103 </command> |
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104 <inputs> |
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105 <expand macro="input_conditional"/> |
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106 <param name="outputformat" type="select" display="radio" label="Select output format" help="Compression will greatly reduce the amount of space occupied by downloaded data. Downstream applications such as a short-read mappers will accept compressed data as input. Consider this example: an uncoimpressed 400 Mb fastq datasets compresses to 100 Mb or 80 Mb by gzip or bzip2, respectively. " argument="--gzip --bzip2"> |
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107 <option value="fastqsanger.gz">gzip compressed fastq</option> |
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108 <option value="fastqsanger">Uncompressed fastq</option> |
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109 <option value="fastqsanger.bz2">bzip2 compressed fastq</option> |
0
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110 </param> |
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111 <section name="adv" title="Advanced Options" expanded="False"> |
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112 <param name="minID" type="integer" label="Minimum spot ID" optional="true" help="Minimum spot id to be dumped." argument="--minSpotId"/> |
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113 <param name="maxID" type="integer" label="Maximum spot ID" optional="true" help="Maximum spot id to be dumped." argument="--maxSpotId"/> |
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114 <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--minReadLen"/> |
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115 <param name="split" type="boolean" checked="true" truevalue="--split-spot" falsevalue="" label="Split spot by read pairs" help="Split spots into individual reads." argument="--split-spot"/> |
0
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116 <expand macro="alignments"/> |
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117 <expand macro="region"/> |
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118 <expand macro="matepairDist"/> |
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119 <param name="readfilter" type="select" value="" label="filter by value" argument="--read-filter"> |
0
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120 <option value="">None</option> |
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121 <option value="pass">pass</option> |
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122 <option value="reject">reject</option> |
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123 <option value="criteria">criteria</option> |
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124 <option value="redacted">redacted</option> |
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125 </param> |
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126 <param name="spotgroups" type="text" label="Filter by spot-groups" optional="true" argument="--spot-groups"/> |
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127 <param name="clip" type="boolean" truevalue="--clip" falsevalue="" argument="--clip" label="Apply left and right clips" /> |
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128 <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads" argument="--skip-technical"/> |
0
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129 </section> |
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130 </inputs> |
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131 <outputs> |
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132 <collection name="list_paired" type="list:paired" label="Pair-end data (fastq-dump)"> |
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133 <filter>input['input_select'] == "file_list"</filter> |
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134 |
1
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135 <!-- Use named regex group to grab pattern |
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136 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list |
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137 identifier in the nested collection and identifier_1 is either |
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138 forward or reverse (for instance samp1_forward.fq). |
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139 --> |
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140 |
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141 <discover_datasets pattern="(?P<identifier_0>[^_]+)_\d+.fastq_(?P<identifier_1>[^_]+)\.fastqsanger" ext="fastqsanger" /> |
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142 <discover_datasets pattern="(?P<identifier_0>[^_]+)_\d+.fastq.gz_(?P<identifier_1>[^_]+)\.fastqsanger.gz" ext="fastqsanger.gz" /> |
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143 <discover_datasets pattern="(?P<identifier_0>[^_]+)_\d+.fastq.bz2_(?P<identifier_1>[^_]+)\.fastqsanger.bz2" ext="fastqsanger.bz2" /> |
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144 </collection> |
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145 <collection name="output_collection" type='list' label="Single-end data (fastq-dump)"> |
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146 <filter>input['input_select'] == "file_list"</filter> |
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147 <discover_datasets pattern="(?P<designation>.+)_\d+.fastq__single\.fastqsanger" directory="." ext='fastqsanger'/> |
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148 <discover_datasets pattern="(?P<designation>.+)_\d+.fastq.gz__single\.fastqsanger.gz" directory="." ext='fastqsanger.gz'/> |
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149 <discover_datasets pattern="(?P<designation>.+)_\d+.fastq.bz2__single\.fastqsanger.bz2" directory="." ext='fastqsanger.bz2'/> |
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150 </collection> |
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151 <data format="fastqsanger" name="output_accession" label="${input.accession} (fastq-dump)"> |
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152 <filter>input['input_select'] == "accession_number"</filter> |
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153 <change_format> |
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154 <when input="outputformat" value="fastqsanger.gz" format="fastqsanger.gz"/> |
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155 <when input="outputformat" value="fastqsanger.bz2" format="fastqsanger.bz2"/> |
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156 </change_format> |
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157 </data> |
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158 <data format="fastqsanger" name="output_file" label="${input.file.name} (fastq-dump)"> |
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159 <filter>input['input_select'] == "file"</filter> |
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160 <change_format> |
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161 <when input="outputformat" value="fastqsanger.gz" format="fastqsanger.gz"/> |
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162 <when input="outputformat" value="fastqsanger.bz2" format="fastqsanger.bz2"/> |
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163 </change_format> |
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164 </data> |
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165 </outputs> |
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166 <tests> |
7
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167 <test> |
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168 <param name="input_select" value="accession_number"/> |
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169 <param name="outputformat" value="fastqsanger"/> |
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170 <param name="accession" value="SRR044777"/> |
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171 <param name="skip_technical" value="True"/> |
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172 <output name="output_accession"> |
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173 <assert_contents> |
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174 <not_has_text text="rRNA_primer"/> |
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175 <has_text text="F47USSH02GNP1D" /> |
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176 </assert_contents> |
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177 </output> |
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178 </test> |
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179 <test> |
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180 <param name="input_select" value="accession_number"/> |
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181 <param name="outputformat" value="fastqsanger.gz"/> |
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182 <param name="accession" value="SRR925743"/> |
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183 <param name="maxID" value="5"/> |
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184 <output name="output_accession" file="fastq_dump_result.fastq.gz" decompress="True"/> |
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185 </test> |
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186 <test> |
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187 <param name="input_select" value="accession_number"/> |
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188 <param name="outputformat" value="fastqsanger"/> |
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189 <param name="accession" value="SRR925743"/> |
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190 <param name="maxID" value="5"/> |
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191 <output name="output_accession" file="fastq_dump_result.fastq" ftype="fastqsanger"/> |
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192 </test> |
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193 <test> |
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194 <param name="input_select" value="file_list"/> |
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195 <param name="outputformat" value="fastqsanger"/> |
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196 <param name="file_list" value="list_pe"/> |
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197 <param name="maxID" value="5"/> |
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198 <output_collection name="list_paired" type="list:paired"> |
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199 <element name="DRR015708"> |
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200 <element name="forward" file="DRR015708_forward.fastqsanger"> |
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201 </element> |
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202 <element name="reverse" file="DRR015708_reverse.fastqsanger"> |
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203 </element> |
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204 </element> |
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205 </output_collection> |
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206 </test> |
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207 <test> |
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208 <param name="input_select" value="file_list"/> |
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209 <param name="outputformat" value="fastqsanger"/> |
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210 <param name="file_list" value="list_pe2"/> |
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211 <param name="maxID" value="5"/> |
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212 <output_collection name="list_paired" type="list:paired"> |
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213 <element name="ERR027433"> |
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214 <element name="forward" file="ERR027433_forward.fastqsanger"> |
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215 </element> |
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216 <element name="reverse" file="ERR027433_reverse.fastqsanger"> |
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217 </element> |
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218 </element> |
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219 </output_collection> |
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220 </test> |
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221 <test> |
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222 <param name="input_select" value="file_list"/> |
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223 <param name="outputformat" value="fastqsanger"/> |
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224 <param name="file_list" value="list_se"/> |
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225 <param name="maxID" value="5"/> |
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226 <output_collection name="output_collection" type="list"> |
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227 <element name="SRR1993644" file="SRR1993644.fastqsanger"/> |
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228 </output_collection> |
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229 </test> |
0
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230 </tests> |
7
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231 <help><![CDATA[ |
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232 **What it does?** |
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233 |
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234 This tool extracts data (in fastq_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the fastq-dump_ utility of the SRA Toolkit. |
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235 |
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236 **How to use it?** |
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237 |
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238 There are three ways in which you can download data: |
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239 |
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240 1. Data for single accession |
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241 2. Multiple datasets using a list of accessions |
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242 3. Extract data from already uploaded SRA dataset |
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243 |
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244 Below we discuss each in detail. |
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245 |
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246 ------ |
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247 |
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248 **Uploading data for a single accession** |
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249 |
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250 When you type a single accession number (e.g., `SRR1582967`) into **Accession** box and click **Execute** the tool will fetch data for you. It is important to keep the following in mind: |
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251 |
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252 - if data is paired-ended (or mate-paired) the tool will generate a single *interleaved* dataset, in which forward and reverse mates are alternating (see an example dataset below) |
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253 - if data is single ended, a standard single fastq dataset will be produced |
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254 |
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255 ----- |
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256 |
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257 **Uploading multiple datasets using a list of accessions** |
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258 |
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259 A more realistic scenario is when you want to upload a number of datasets at once. To do this you need a list of accession, where there is only one accession per line (see below for information on how to generate such a file). Once you have this file: |
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260 |
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261 1. Upload it into your history using Galaxy's upload tool |
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262 2. Once the list of accessions is uploaded choose *List of SRA accessions, one per line* from **select input type** dropdown |
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263 3. Choose uploaded file within the **sra accession list** field |
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264 4. Click **Execute** |
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265 |
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266 .. class:: warningmark |
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267 |
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268 Fastq datasets produced by this option will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets. In fact, two collections will be produced: one containing paired-end data and another containing single-end data. Single-end or pair-end collections may be empty if the accessions provided in the list contain only SINGLE or PAIRED data, respectively. |
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269 |
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270 ----- |
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271 |
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272 **Extract data from already uploaded SRA dataset** |
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273 |
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274 If a SRA dataset is present in the history, it can be converted into fastq dataset by setting **select input type** drop-down to *SRA archive in current history*. Just like in the case of extracting data for single accession number the following applies: |
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275 |
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276 - if data is paired-ended (or mate-pair) the tool will generate a single *interleaved* dataset, in which forward and reverse mates are alternating (see example below). |
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277 - if data is single ended, a standard fastq dataset will be produced |
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278 |
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279 @ACCESSION_LIST_HOWTO@ |
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280 |
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281 ----- |
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282 |
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283 **Paired-end (and mate-pair) data in fastq format** |
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284 |
7
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285 Paired end datasets can be represented as two individual datasets: |
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286 |
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287 First dataset:: |
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288 |
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289 @1/1 |
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290 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
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291 + |
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292 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED |
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293 @2/1 |
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294 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
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295 + |
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296 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG |
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297 |
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298 Second dataset:: |
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299 |
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300 @1/2 |
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301 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
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302 + |
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303 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF |
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304 @2/2 |
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305 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
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306 + |
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307 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH |
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308 |
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309 Or a single *interleaved* dataset:: |
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310 |
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311 @1/1 |
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312 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
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313 + |
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314 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED |
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315 @1/2 |
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316 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
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317 + |
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318 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF |
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319 @2/1 |
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320 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA |
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321 + |
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322 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG |
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323 @2/2 |
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324 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC |
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325 + |
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326 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH |
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327 |
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328 ---- |
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329 |
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330 |
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331 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format |
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332 .. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html |
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333 .. _collection: https://galaxyproject.org/tutorials/collections/ |
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334 .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies |
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335 |
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336 @SRATOOLS_ATTRRIBUTION@ |
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337 |
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338 ]]> |
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339 </help> |
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340 <expand macro="citation"/> |
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341 </tool> |