Mercurial > repos > iuc > sra_tools
annotate sam_dump.xml @ 8:1920e0508831 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 39ca11da7daeb3fa030fcb28e8987f8d7f24aec3
author | iuc |
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date | Mon, 03 Jul 2017 06:30:15 -0400 |
parents | c7620aa7e1f0 |
children | 6c60903f70ac |
rev | line source |
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7
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents:
4
diff
changeset
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1 <tool id="sam_dump" name="Extract reads in BAM" version="@VERSION@.2"> |
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents:
4
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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
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changeset
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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
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diff
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
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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
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changeset
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7 <version_command>sam-dump --version</version_command> |
4
62e4d56ebb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4091428e9e28ca06263bc00cdf938d20f620aa4d
iuc
parents:
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8 <command detect_errors="exit_code"> |
0
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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9 <![CDATA[ |
1
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
0
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10 #if $input.input_select=="file_list": |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
0
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11 for acc in `cat $input.file_list` ; |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
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12 do |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
0
diff
changeset
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13 #elif $input.input_select=="accession_number": |
7
c7620aa7e1f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents:
4
diff
changeset
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14 acc="${input.accession}" && |
1
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
0
diff
changeset
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15 #end if |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
0
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16 |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
0
diff
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17 #if $input.input_select=="file_list" or $input.input_select=="accession_number": |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
0
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18 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && ( |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
0
diff
changeset
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19 #end if |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
0
diff
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20 |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
0
diff
changeset
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21 |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
0
diff
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22 |
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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23 ## 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
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1
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24 ## 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:
1
diff
changeset
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25 ## 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:
diff
changeset
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26 export HOME=\$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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27 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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28 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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29 ## 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
changeset
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30 ## 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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31 #if ( str( $adv.region ) == "" ): |
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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32 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:
diff
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33 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
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2
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34 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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35 ## 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:
diff
changeset
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36 ## dump command. |
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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37 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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38 #end if |
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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39 sam-dump --log-level fatal --disable-multithreading |
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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40 #if str( $adv.region ) != "": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
changeset
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41 --aligned-region "$adv.region" |
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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42 #end if |
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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43 #if str( $adv.matepairDist ) != "": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
changeset
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44 --matepair-distance "$adv.matepairDist" |
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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45 #end if |
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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46 #if str( $adv.minMapq ) != "": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff
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47 --min-mapq "$adv.minMapq" |
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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48 #end if |
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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49 #if str( $adv.header ) == "yes": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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50 --header |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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51 #else: |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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52 --no-header |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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53 #end if |
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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54 #if str( $adv.alignments ) == "both": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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55 --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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56 #end if |
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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57 #if str( $adv.alignments ) == "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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58 --unaligned-spots-only |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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59 #end if |
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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60 #if (str( $adv.primary ) == "yes") and (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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61 --primary |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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62 #end if |
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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63 #if $input.input_select == "file": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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64 "$input.file" |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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65 #elif $input.input_select == "accession_number": |
1
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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66 "\$acc" |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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67 #elif $input.input_select=="file_list": |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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0
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68 "\$acc" |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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69 #end if |
2
f256cb398262
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
iuc
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70 |
0
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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71 #if str( $outputformat ) == "bam": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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72 | samtools view -Sb - 2> /dev/null |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
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73 #end if |
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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74 #if $input.input_select == "file": |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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75 > "$output_file" |
b723c120161a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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76 #elif $input.input_select == "accession_number": |
1
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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77 > "$output_accession" ) |
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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78 #end if |
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 |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
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80 #if $input.input_select=="file_list": |
462ee06c9358
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents:
0
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81 #if str( $outputformat ) == "bam": |
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82 > "\$acc.bam" |
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83 #elif str( $outputformat ) == "sam": |
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84 > "\$acc.sam" |
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85 #end if |
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86 ) ; done |
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87 #end if |
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88 |
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89 |
0
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90 ]]> |
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91 </command> |
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92 <inputs> |
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93 <expand macro="input_conditional"/> |
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94 <param name="outputformat" type="select" display="radio" label="select output format" help="In vast majority of cases you want to download data in bam format. It is more compact and is accepted by all downstream tools."> |
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95 <option value="bam">bam</option> |
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96 <option value="sam">sam</option> |
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97 </param> |
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98 <section name="adv" title="Advanced Options" expanded="False"> |
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99 <param name="header" type="select" value="yes"> |
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100 <label>output header</label> |
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101 <option value="yes">Yes</option> |
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102 <option value="no">No</option> |
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103 </param> |
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104 <expand macro="alignments"/> |
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105 <expand macro="region"/> |
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106 <expand macro="matepairDist"/> |
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107 <param name="primary" type="select" value="no"> |
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108 <label>only primary aligments</label> |
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109 <option value="no">No</option> |
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110 <option value="yes">Yes</option> |
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111 </param> |
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112 <expand macro="minMapq"></expand> |
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113 </section> |
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114 </inputs> |
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115 <outputs> |
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116 <collection name="output_collection" type="list" label="SAM/BAM data (fastq-dump)"> |
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117 <filter>input['input_select'] == "file_list"</filter> |
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118 <discover_datasets pattern="(?P<designation>.+)\.bam" directory="." ext='bam'/> |
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119 <discover_datasets pattern="(?P<designation>.+)\.sam" directory="." ext='sam'/> |
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120 </collection> |
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121 <data name="output_accession" format="bam" label="${input.accession} (sam-dump)"> |
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122 <filter>input['input_select'] == "accession_number"</filter> |
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123 <change_format> |
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124 <when input="outputformat" value="sam" format="sam"/> |
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125 </change_format> |
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126 </data> |
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127 <data name="output_file" format="bam" label="${input.file.name} (sam-dump)"> |
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128 <filter>input['input_select'] == "file"</filter> |
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129 <change_format> |
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130 <when input="outputformat" value="sam" format="sam"/> |
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131 </change_format> |
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132 </data> |
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133 </outputs> |
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134 <tests> |
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135 <test> |
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136 <param name="input_select" value="accession_number"/> |
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137 <param name="accession" value="SRR925743"/> |
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138 <param name="outputformat" value="sam"/> |
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139 <param name="region" value="17:41243452-41277500"/> |
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140 <output name="output_accession" file="sam_dump_result.sam" compare="contains" ftype="sam"/> |
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141 </test> |
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142 </tests> |
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143 <help><![CDATA[ |
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144 **What it does?** |
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145 |
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146 This tool extracts data (in BAM_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the sam-dump_ utility of the SRA Toolkit. |
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147 |
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148 **How to use it?** |
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149 |
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150 There are three ways in which you can download data: |
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151 |
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152 1. Data for single accession |
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153 2. Multiple datasets using a list of accessions |
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154 3. Extract data from already uploaded SRA dataset |
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155 |
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156 Below we discuss each in detail. |
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157 |
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158 ------ |
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159 |
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160 **Uploading data for a single accession** |
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161 |
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162 When you type a single accession number (e.g., `SRR1582967`) into **Accession** box and click **Execute** the tool will fetch data for you. As a result you will get a single BAM (or SAM) dataset in the history. |
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163 |
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164 ----- |
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165 |
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166 **Uploading multiple datasets using a list of accessions** |
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167 |
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168 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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169 |
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170 1. Upload it into your history using Galaxy's upload tool |
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171 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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172 3. Choose uploaded file within the **sra accession list** field |
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173 4. Click **Execute** |
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174 |
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175 .. class:: warningmark |
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176 |
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177 BAM datasets produced by this option will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets. |
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178 |
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179 ----- |
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180 |
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181 **Extract data from already uploaded SRA dataset** |
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182 |
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183 If a SRA dataset is present in the history, it can be converted into BAM 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 a single BAM dataset will be generated in the history. |
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184 |
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185 @ACCESSION_LIST_HOWTO@ |
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186 |
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187 ----- |
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188 |
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189 .. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf |
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190 .. _sam-dump: http://ncbi.github.io/sra-tools/sam-dump.html |
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191 .. _collection: https://galaxyproject.org/tutorials/collections/ |
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192 .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies |
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193 |
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194 |
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195 @SRATOOLS_ATTRRIBUTION@ |
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196 ]]></help> |
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197 <expand macro="citation"/> |
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198 </tool> |