Mercurial > repos > iuc > sra_tools

annotate macros.xml @ 32:fb723c531be5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ac10fe34f1b2d5e8109dcaaf42b7870bee57827b
author iuc
date Wed, 25 Oct 2023 07:10:06 +0000
parents 734abc7ac21d
children 6591f049cf7e
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9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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1 <macros>
32
fb723c531be5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ac10fe34f1b2d5e8109dcaaf42b7870bee57827b
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2 <token name="@TOOL_VERSION@">3.0.8</token>
fb723c531be5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ac10fe34f1b2d5e8109dcaaf42b7870bee57827b
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3 <token name="@VERSION_SUFFIX@">0</token>
27
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4 <token name="@PROFILE@">22.01</token>
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5 <xml name="edam_ontology">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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6 <edam_topics>
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7 <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
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8 <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->
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9 </edam_topics>
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10 <edam_operations>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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11 <edam_operation>operation_2422</edam_operation> <!-- Data retrieval -->
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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12 <edam_operation>operation_0335</edam_operation> <!-- Formatting -->
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13 </edam_operations>
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14 </xml>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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15 <macro name="requirements">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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16 <requirements>
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17 <requirement type="package" version="@TOOL_VERSION@">sra-tools</requirement>
32
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18 <requirement type="package" version="2.8">pigz</requirement>
fb723c531be5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ac10fe34f1b2d5e8109dcaaf42b7870bee57827b
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19 <requirement type="package" version="1.18">samtools</requirement>
27
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20 <yield/>
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21 </requirements>
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22 </macro>
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23 <token name="@ACCESSIONS_FROM_FILE@">
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24 grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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25 </token>
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26 <token name="@COMPRESS@"><![CDATA[pigz -cqp \${GALAXY_SLOTS:-1}]]></token>
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27 <token name="@CONFIGURE_RETRY@"><![CDATA[
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28 export SRA_PREFETCH_RETRIES=3 &&
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29 export SRA_PREFETCH_ATTEMPT=1 &&
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30 ]]></token>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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31 <xml name="bio_tools">
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32 <xrefs>
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33 <xref type="bio.tools">sra-tools</xref>
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34 </xrefs>
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35 </xml>
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36 <token name="@COPY_CONFIGFILE@"><![CDATA[
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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37 mkdir -p ~/.ncbi &&
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38 cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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39 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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40 vdb-config -s "/repository/user/ad/public/root=\$PWD" &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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41 vdb-config -s "/repository/user/default-path=\$PWD" &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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42 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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43 vdb-config -s /http/timeout/read=10000 &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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44 ]]></token>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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45 <token name="@SET_ACCESSIONS@"><![CDATA[
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46 #if $input.input_select == "sra_file":
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
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47 acc='${input.sra_file.name}' &&
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48 ln -s '${input.sra_file}' "\$acc" &&
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49 #else
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50 #if $input.input_select == "file_list":
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51 #if $input.file_list.is_of_type('sra_manifest.tabular'):
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52 #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1
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53 cut -f $column '$input.file_list'| tail -n +2 > accessions &&
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54 #else
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55 @ACCESSIONS_FROM_FILE@ '$input.file_list' > accessions &&
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56 #end if
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57 #elif $input.input_select == "accession_number":
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58 echo '${input.accession}' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions &&
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59 #end if
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60 for acc in \$(cat ./accessions);
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61 do (
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62 echo "Downloading accession: \$acc..." &&
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63 #end if
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64 ]]></token>
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65 <macro name="configfile_hack">
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66 <configfiles>
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67 <configfile name="user_settings_mkfg"><![CDATA[
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68 /LIBS/GUID = "3cdc38d0-711a-49ce-9536-f544eaf69eec"
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69 /config/default = "false"
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70 /libs/temp_cache = "."
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71 /tools/prefetch/download_to_cache = "false"
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72 ]]></configfile>
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73 </configfiles>
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74 </macro>
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75 <macro name="sanitize_query">
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76 <sanitizer>
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77 <valid initial="string.printable">
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78 <remove value=" "/>
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79 <remove value="&apos;" />
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80 </valid>
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81 <mapping initial="none">
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82 <add source=" " target=""/>
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83 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
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84 </mapping>
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85 </sanitizer>
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86 </macro>
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87 <macro name="input_conditional">
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88 <conditional name="input">
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89 <param name="input_select" type="select" label="select input type">
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90 <option value="accession_number">SRR accession</option>
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91 <option value="file_list">List of SRA accession, one per line</option>
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92 <option value="sra_file">SRA archive in current history</option>
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93 </param>
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94 <when value="accession_number">
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95 <param name="accession" type="text" label="Accession" multiple="true" help="Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809">
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96 <expand macro="sanitize_query"/>
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97 <validator type="empty_field" message="An accession is required"/>
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98 </param>
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99 </when>
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100 <when value="sra_file">
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101 <param format="sra" name="sra_file" type="data" label="sra archive"/>
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102 </when>
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103 <when value="file_list">
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104 <param format="txt" name="file_list" type="data" label="sra accession list"/>
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105 </when>
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106 </conditional>
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107 </macro>
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108 <macro name="alignments">
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109 <param name="alignments" type="select" value="both" label="Output aligned or unaligned reads" help="Output reads according to their alignment status." argument="--aligned and --unaligned">
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110 <option value="both">both</option>
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111 <option value="aligned">aligned only</option>
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112 <option value="unaligned">unaligned only</option>
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113 </param>
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114 </macro>
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115 <macro name="minMapq">
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116 <param name="minMapq" type="integer" min="0" max="42" label="Minimum mapping quality" optional="true" help="Minimum mapping quality an alignment has to have, to be dumped." argument="--min-mapq"/>
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117 </macro>
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118 <macro name="region">
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119 <param format="text" name="region" type="text" label="aligned region" optional="true"
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120 help="Filter by position on genome. Can be either accession.version (ex: NC_000001.10), chromosome name (ex:chr1 or 1) or 1-based coordinates (ex: chr1:1-101)." argument="--aligned-region"/>
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121 </macro>
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122 <macro name="matepairDist">
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123 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
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124 help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference" argument="--matepair-distance"/>
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125 </macro>
30
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126 <macro name="defline" tokens="defline_param,defline_default">
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127 <param argument="@DEFLINE_PARAM@" value="@DEFLINE_DEFAULT@" type="text" label="Defline format specification for sequence">
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128 <help>A string of characters and/or variables. The variables can be one of:
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129 $ac: accession, $si: spot id, $sn: spot name, $sg: spot group (barcode), $sl: spot length in bases, $ri: read number, $rn: read name, $rl: read length in bases.
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130 '[]' could be used for an optional output: if all vars in [] yield empty values whole group is not printed. Empty value is empty string or for numeric variables.
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131 Ex: @$sn[_$rn]/$ri '_$rn' is omitted if name is empty"</help>
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132 <!-- allow many chars, but quotes and backslash -->
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133 <sanitizer>
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134 <valid initial="string.ascii_letters,string.digits">
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135 <add value="@" />
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136 <add value="$" />
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137 <add value="[" />
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138 <add value="]" />
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139 <add value="_" />
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140 <add value="-" />
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141 <add value="+" />
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142 <add value="." />
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143 <add value=";" />
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144 <add value=":" />
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145 <add value="/" />
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146 <add value="?" />
31
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147 <add value=" " />
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148 <add value="=" />
30
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149 </valid>
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150 </sanitizer>
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151 <validator type="regex" message="Must start with @">^.*</validator>
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152
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153 </param>
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154 </macro>
27
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155 <macro name="citation">
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156 <citations>
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157 <citation type="doi">10.1093/nar/gkq1019</citation>
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158 <citation type="bibtex">
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159 @misc{github_sratools,
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160 author = {NCBI},
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161 title = {sra-tools},
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162 publisher = {GitHub},
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163 journal = {GitHub repository},
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164 url = {https://github.com/ncbi/sra-tools},
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165 }</citation>
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166 </citations>
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167 </macro>
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168 <token name="@HOW_TO_USE_IT@">
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169 **How to use it?**
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170
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171 There are three ways in which you can download data:
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172
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173 1. Plain text input of accession number(s)
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174 2. Providing a list of accessions from file
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175 3. Extracting data from an already uploaded SRA dataset
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176
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177 Below we discuss each in detail.
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178
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179 ------
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180
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181 **Plain text input of accession number(s)**
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182
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183 When you type an accession number (e.g., `SRR1582967`) into **Accession** box and click **Execute** the tool will fetch the data for you. You can also provide a list of multiple accession numbers (e.g. `SRR3141592, SRR271828, SRR112358`).
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184
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185 -----
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186
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187 **Providing a list of accessions from file**
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188
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189 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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190
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191 1. Upload it into your history using Galaxy's upload tool
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192 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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193 3. Choose uploaded file within the **sra accession list** field
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194 4. Click **Execute**
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195
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196 -----
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197
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198 **Extract data from an already uploaded SRA dataset**
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199
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200 If an SRA dataset is already present in the history, the sequencing data can be extracted in a human-readable data format (fastq, sam, bam) by setting **select input type** drop-down to *SRA archive in current history*.
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201 </token>
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202 <token name="@ACCESSION_LIST_HOWTO@">
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203 -----
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204
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205 **How to generate accession lists**
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206
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207 1. Go to **SRA Run Selector** by clicking this link_
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208 2. Find the study you are interested in by typing a search term within the **Search** box. This can be a word (e.g., *mitochondria*) or an accession you have gotten from a paper (e.g., *SRR1582967*).
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209 3. Once you click on the study of interest you will see the number of datasets in this study within the **Related SRA data** box
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210 4. Click on the Runs number
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211 5. On the page that would open you will see **Accession List** button
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212 6. Clicking of this button will produce a file that you will need to upload into Galaxy and use as the input to this tool.
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213 </token>
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214 <token name="@SRATOOLS_ATTRRIBUTION@">
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215 For credits, information, support and bug reports, please refer ato https://github.com/galaxyproject/tools-iuc.
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216 </token>
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217 </macros>