Mercurial > repos > iuc > sra_tools

annotate sam_dump.xml @ 9:6c60903f70ac draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 6252dc2340b2fb6c7fdab2bdadfa4779c6f1aefd
author iuc
date Wed, 12 Jul 2017 00:48:56 -0400
parents c7620aa7e1f0
children 8c00bc7fd8de
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9
6c60903f70ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 6252dc2340b2fb6c7fdab2bdadfa4779c6f1aefd
iuc
parents: 7
diff changeset
1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.2">
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
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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
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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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5 </macros>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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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
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7 <version_command>sam-dump --version</version_command>
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iuc
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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
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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
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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
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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
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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
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13 #elif $input.input_select=="accession_number":
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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14 acc="${input.accession}" &&
1
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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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
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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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17 #if $input.input_select=="file_list" or $input.input_select=="accession_number":
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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18 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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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
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462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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22
0
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23 ## Need to set the home directory to the current working directory,
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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
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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
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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
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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
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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
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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
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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
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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
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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
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33 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
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4732693f4661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit f30369bef4e2cef17395cdd62ce81768c93f5edd
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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
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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
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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
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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
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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
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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
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40 #if str( $adv.region ) != "":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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41 --aligned-region "$adv.region"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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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
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43 #if str( $adv.matepairDist ) != "":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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44 --matepair-distance "$adv.matepairDist"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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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
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46 #if str( $adv.minMapq ) != "":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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47 --min-mapq "$adv.minMapq"
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48 #end if
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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
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50 --header
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51 #else:
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52 --no-header
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53 #end if
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54 #if str( $adv.alignments ) == "both":
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55 --unaligned
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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
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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
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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
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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
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60 #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ):
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61 --primary
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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
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63 #if $input.input_select == "file":
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64 "$input.file"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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65 #elif $input.input_select == "accession_number":
1
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66 "\$acc"
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67 #elif $input.input_select=="file_list":
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68 "\$acc"
0
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69 #end if
2
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70
0
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71 #if str( $outputformat ) == "bam":
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72 | samtools view -Sb - 2> /dev/null
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73 #end if
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74 #if $input.input_select == "file":
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75 > "$output_file"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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76 #elif $input.input_select == "accession_number":
1
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77 > "$output_accession" )
0
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78 #end if
1
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79
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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
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81 #if str( $outputformat ) == "bam":
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82 > "\$acc.bam"
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
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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.">
0
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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&lt;designation&gt;.+)\.bam" directory="." ext='bam'/>
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119 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.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)">
0
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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)">
0
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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>
0
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197 <expand macro="citation"/>
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198 </tool>