Mercurial > repos > iuc > sra_tools

annotate sam_dump.xml @ 11:5e6237d58b0c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2d182cef61f6cf3f732b14d2fe8dea2255271421
author iuc
date Wed, 16 May 2018 16:56:35 -0400
parents 8c00bc7fd8de
children c38286ea7047
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10
8c00bc7fd8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 48c9d7f30655d48c9b46b9ca7a17c454eb54694d
iuc
parents: 9
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1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.3">
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2 <description>format from NCBI SRA</description>
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3 <macros>
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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
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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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8 <command detect_errors="exit_code">
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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
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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
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12 do
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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13 #elif $input.input_select=="accession_number":
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c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
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14 acc="${input.accession}" &&
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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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15 #end if
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17 #if $input.input_select=="file_list" or $input.input_select=="accession_number":
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
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18 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
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
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20
0
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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21 ## Need to set the home directory to the current working directory,
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22 ## 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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23 ## 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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24 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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25 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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26 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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27 ## 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
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28 ## the complete sra file.
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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29 #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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30 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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31 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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32 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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33 ## 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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34 ## dump command.
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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35 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
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36 #end if
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37 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
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38 #if str( $adv.region ) != "":
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39 --aligned-region '$adv.region'
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b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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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
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41 #if str( $adv.matepairDist ) != "":
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42 --matepair-distance '$adv.matepairDist'
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43 #end if
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44 #if str( $adv.minMapq ) != "":
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8c00bc7fd8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 48c9d7f30655d48c9b46b9ca7a17c454eb54694d
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45 --min-mapq '$adv.minMapq'
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46 #end if
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47 --header
0
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48 #if str( $adv.alignments ) == "both":
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49 --unaligned
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50 #end if
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51 #if str( $adv.alignments ) == "unaligned":
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52 --unaligned-spots-only
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53 #end if
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54 #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ):
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55 --primary
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56 #end if
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57 #if $input.input_select == "file":
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58 '$input.file'
0
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59 #elif $input.input_select == "accession_number":
1
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60 "\$acc"
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61 #elif $input.input_select=="file_list":
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62 "\$acc"
0
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63 #end if
2
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64
0
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65 #if str( $outputformat ) == "bam":
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66 | samtools view -Sb - 2> /dev/null
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67 #end if
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68 #if $input.input_select == "file":
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69 > '$output_file'
0
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70 #elif $input.input_select == "accession_number":
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71 > '$output_accession' )
0
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72 #end if
1
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73
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74 #if $input.input_select=="file_list":
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75 #if str( $outputformat ) == "bam":
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76 > "\$acc.bam"
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77 #elif str( $outputformat ) == "sam":
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78 > "\$acc.sam"
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79 #end if
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80 ) ; done
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81 #end if
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82
0
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83 ]]>
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84 </command>
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85 <inputs>
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86 <expand macro="input_conditional"/>
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87 <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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88 <option value="bam">bam</option>
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89 <option value="sam">sam</option>
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90 </param>
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91 <section name="adv" title="Advanced Options" expanded="False">
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92 <expand macro="alignments"/>
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93 <expand macro="region"/>
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94 <expand macro="matepairDist"/>
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95 <param name="primary" type="select" value="no">
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96 <label>only primary aligments</label>
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97 <option value="no">No</option>
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98 <option value="yes">Yes</option>
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99 </param>
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100 <expand macro="minMapq"></expand>
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101 </section>
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102 </inputs>
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103 <outputs>
7
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104 <collection name="output_collection" type="list" label="SAM/BAM data (fastq-dump)">
1
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105 <filter>input['input_select'] == "file_list"</filter>
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106 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="." ext='bam'/>
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107 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sam" directory="." ext='sam'/>
2
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108 </collection>
7
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109 <data name="output_accession" format="bam" label="${input.accession} (sam-dump)">
0
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110 <filter>input['input_select'] == "accession_number"</filter>
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111 <change_format>
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112 <when input="outputformat" value="sam" format="sam"/>
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113 </change_format>
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114 </data>
7
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115 <data name="output_file" format="bam" label="${input.file.name} (sam-dump)">
0
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116 <filter>input['input_select'] == "file"</filter>
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117 <change_format>
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118 <when input="outputformat" value="sam" format="sam"/>
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119 </change_format>
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120 </data>
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121 </outputs>
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122 <tests>
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123 <test>
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124 <param name="input_select" value="accession_number"/>
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125 <param name="accession" value="SRR925743"/>
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126 <param name="outputformat" value="sam"/>
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127 <param name="region" value="17:41243452-41277500"/>
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128 <output name="output_accession" file="sam_dump_result.sam" compare="contains" ftype="sam"/>
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129 </test>
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130 </tests>
7
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131 <help><![CDATA[
10
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132
7
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133 **What it does?**
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134
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135 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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136
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137 **How to use it?**
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138
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139 There are three ways in which you can download data:
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140
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141 1. Data for single accession
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142 2. Multiple datasets using a list of accessions
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143 3. Extract data from already uploaded SRA dataset
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144
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145 Below we discuss each in detail.
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146
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147 ------
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148
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149 **Uploading data for a single accession**
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150
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151 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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152
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153 -----
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154
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155 **Uploading multiple datasets using a list of accessions**
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156
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157 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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158
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159 1. Upload it into your history using Galaxy's upload tool
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160 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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161 3. Choose uploaded file within the **sra accession list** field
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162 4. Click **Execute**
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163
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164 .. class:: warningmark
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165
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166 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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167
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168 -----
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169
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170 **Extract data from already uploaded SRA dataset**
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171
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172 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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173
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174 @ACCESSION_LIST_HOWTO@
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175
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176 -----
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177
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178 .. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf
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179 .. _sam-dump: http://ncbi.github.io/sra-tools/sam-dump.html
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180 .. _collection: https://galaxyproject.org/tutorials/collections/
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181 .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
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182
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183 @SRATOOLS_ATTRRIBUTION@
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184 ]]></help>
0
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185 <expand macro="citation"/>
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186 </tool>