Mercurial > repos > iuc > sra_tools

annotate macros.xml @ 31:734abc7ac21d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 3a7f854e8ebfb2bed11198fb83181f305af633f7
author iuc
date Thu, 14 Sep 2023 07:38:02 +0000
parents 4317d3cb6cba
children fb723c531be5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
27
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
1 <macros>
29
6ea73833cf67 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 32f3efb70a4000f7aaaf5230331c8988cc708f21
iuc
parents: 28
diff changeset
2 <token name="@TOOL_VERSION@">3.0.5</token>
31
734abc7ac21d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 3a7f854e8ebfb2bed11198fb83181f305af633f7
iuc
parents: 30
diff changeset
3 <token name="@VERSION_SUFFIX@">3</token>
27
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
4 <token name="@PROFILE@">22.01</token>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
5 <xml name="edam_ontology">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
6 <edam_topics>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
7 <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
8 <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
9 </edam_topics>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
10 <edam_operations>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
12 <edam_operation>operation_0335</edam_operation> <!-- Formatting -->
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
13 </edam_operations>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
14 </xml>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
15 <macro name="requirements">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
16 <requirements>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
17 <requirement type="package" version="@TOOL_VERSION@">sra-tools</requirement>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
18 <requirement type="package" version="2.6">pigz</requirement>
29
6ea73833cf67 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 32f3efb70a4000f7aaaf5230331c8988cc708f21
iuc
parents: 28
diff changeset
19 <requirement type="package" version="1.17">samtools</requirement>
27
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
20 <yield/>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
21 </requirements>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
22 </macro>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
23 <token name="@ACCESSIONS_FROM_FILE@">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
25 </token>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
26 <token name="@COMPRESS@"><![CDATA[pigz -cqp \${GALAXY_SLOTS:-1}]]></token>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
27 <token name="@CONFIGURE_RETRY@"><![CDATA[
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
28 export SRA_PREFETCH_RETRIES=3 &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
29 export SRA_PREFETCH_ATTEMPT=1 &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
30 ]]></token>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
31 <xml name="bio_tools">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
32 <xrefs>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
33 <xref type="bio.tools">sra-tools</xref>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
34 </xrefs>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
35 </xml>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
36 <token name="@COPY_CONFIGFILE@"><![CDATA[
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
37 mkdir -p ~/.ncbi &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
44 ]]></token>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
45 <token name="@SET_ACCESSIONS@"><![CDATA[
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
46 #if $input.input_select == "sra_file":
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
47 acc='${input.sra_file.name}' &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
48 ln -s '${input.sra_file}' "\$acc" &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
49 #else
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
50 #if $input.input_select == "file_list":
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
51 #if $input.file_list.is_of_type('sra_manifest.tabular'):
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
52 #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
53 cut -f $column '$input.file_list'| tail -n +2 > accessions &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
54 #else
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
55 @ACCESSIONS_FROM_FILE@ '$input.file_list' > accessions &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
56 #end if
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
57 #elif $input.input_select == "accession_number":
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
58 echo '${input.accession}' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
59 #end if
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
60 for acc in \$(cat ./accessions);
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
61 do (
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
62 echo "Downloading accession: \$acc..." &&
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
63 #end if
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
64 ]]></token>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
65 <macro name="configfile_hack">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
66 <configfiles>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
67 <configfile name="user_settings_mkfg"><![CDATA[
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
68 /LIBS/GUID = "3cdc38d0-711a-49ce-9536-f544eaf69eec"
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
69 /config/default = "false"
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
70 /libs/temp_cache = "."
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
71 /tools/prefetch/download_to_cache = "false"
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
72 ]]></configfile>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
73 </configfiles>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
74 </macro>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
75 <macro name="sanitize_query">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
76 <sanitizer>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
77 <valid initial="string.printable">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
78 <remove value=" "/>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
79 <remove value="&apos;" />
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
80 </valid>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
81 <mapping initial="none">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
82 <add source=" " target=""/>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
83 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
84 </mapping>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
85 </sanitizer>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
86 </macro>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
87 <macro name="input_conditional">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
88 <conditional name="input">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
89 <param name="input_select" type="select" label="select input type">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
90 <option value="accession_number">SRR accession</option>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
91 <option value="file_list">List of SRA accession, one per line</option>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
92 <option value="sra_file">SRA archive in current history</option>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
93 </param>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
94 <when value="accession_number">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
95 <param name="accession" type="text" label="Accession" multiple="true" help="Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
96 <expand macro="sanitize_query"/>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
97 <validator type="empty_field" message="An accession is required"/>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
98 </param>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
99 </when>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
100 <when value="sra_file">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
101 <param format="sra" name="sra_file" type="data" label="sra archive"/>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
102 </when>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
103 <when value="file_list">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
104 <param format="txt" name="file_list" type="data" label="sra accession list"/>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
105 </when>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
106 </conditional>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
107 </macro>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
108 <macro name="alignments">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
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">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
110 <option value="both">both</option>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
111 <option value="aligned">aligned only</option>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
112 <option value="unaligned">unaligned only</option>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
113 </param>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
114 </macro>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
115 <macro name="minMapq">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
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"/>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
117 </macro>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
118 <macro name="region">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
119 <param format="text" name="region" type="text" label="aligned region" optional="true"
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
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"/>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
121 </macro>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
122 <macro name="matepairDist">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
123 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
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"/>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
125 </macro>
30
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
126 <macro name="defline" tokens="defline_param,defline_default">
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
127 <param argument="@DEFLINE_PARAM@" value="@DEFLINE_DEFAULT@" type="text" label="Defline format specification for sequence">
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
128 <help>A string of characters and/or variables. The variables can be one of:
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
129 $ac: accession, $si: spot id, $sn: spot name, $sg: spot group (barcode), $sl: spot length in bases, $ri: read number, $rn: read name, $rl: read length in bases.
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
130 '[]' could be used for an optional output: if all vars in [] yield empty values whole group is not printed. Empty value is empty string or for numeric variables.
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
131 Ex: @$sn[_$rn]/$ri '_$rn' is omitted if name is empty"</help>
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
132 <!-- allow many chars, but quotes and backslash -->
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
133 <sanitizer>
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
134 <valid initial="string.ascii_letters,string.digits">
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
135 <add value="@" />
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
136 <add value="$" />
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
137 <add value="[" />
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
138 <add value="]" />
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
139 <add value="_" />
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
140 <add value="-" />
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
141 <add value="+" />
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
142 <add value="." />
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
143 <add value=";" />
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
144 <add value=":" />
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
145 <add value="/" />
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
146 <add value="?" />
31
734abc7ac21d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 3a7f854e8ebfb2bed11198fb83181f305af633f7
iuc
parents: 30
diff changeset
147 <add value=" " />
734abc7ac21d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 3a7f854e8ebfb2bed11198fb83181f305af633f7
iuc
parents: 30
diff changeset
148 <add value="=" />
30
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
149 </valid>
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
150 </sanitizer>
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
151 <validator type="regex" message="Must start with @">^.*</validator>
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
152
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
153 </param>
4317d3cb6cba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787
iuc
parents: 29
diff changeset
154 </macro>
27
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
155 <macro name="citation">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
156 <citations>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
157 <citation type="doi">10.1093/nar/gkq1019</citation>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
158 <citation type="bibtex">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
159 @misc{github_sratools,
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
160 author = {NCBI},
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
161 title = {sra-tools},
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
162 publisher = {GitHub},
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
163 journal = {GitHub repository},
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
164 url = {https://github.com/ncbi/sra-tools},
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
165 }</citation>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
166 </citations>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
167 </macro>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
168 <token name="@HOW_TO_USE_IT@">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
169 **How to use it?**
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
170
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
171 There are three ways in which you can download data:
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
172
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
173 1. Plain text input of accession number(s)
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
174 2. Providing a list of accessions from file
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
175 3. Extracting data from an already uploaded SRA dataset
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
176
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
177 Below we discuss each in detail.
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
178
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
179 ------
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
180
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
181 **Plain text input of accession number(s)**
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
182
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
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`).
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
184
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
185 -----
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
186
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
187 **Providing a list of accessions from file**
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
188
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
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:
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
190
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
191 1. Upload it into your history using Galaxy's upload tool
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
192 2. Once the list of accessions is uploaded choose *List of SRA accessions, one per line* from **select input type** dropdown
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
193 3. Choose uploaded file within the **sra accession list** field
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
194 4. Click **Execute**
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
195
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
196 -----
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
197
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
198 **Extract data from an already uploaded SRA dataset**
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
199
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
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*.
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
201 </token>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
202 <token name="@ACCESSION_LIST_HOWTO@">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
203 -----
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
204
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
205 **How to generate accession lists**
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
206
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
207 1. Go to **SRA Run Selector** by clicking this link_
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
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*).
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
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
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
210 4. Click on the Runs number
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
211 5. On the page that would open you will see **Accession List** button
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
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.
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
213 </token>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
214 <token name="@SRATOOLS_ATTRRIBUTION@">
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
215 For credits, information, support and bug reports, please refer ato https://github.com/galaxyproject/tools-iuc.
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
216 </token>
9a776b080193 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit cbb1499906c801443d72bdf313d86f0182aca010
iuc
parents:
diff changeset
217 </macros>