Mercurial > repos > iuc > sra_tools

comparison macros.xml @ 27:9a776b080193 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 cbb1499906c801443d72bdf313d86f0182aca010
author iuc
date Sun, 22 Jan 2023 17:51:50 +0000
parents
children 4df8de2d0e48
comparison
equal deleted inserted replaced
26:83c7d564b128 27:9a776b080193
1 <macros>
2 <token name="@TOOL_VERSION@">3.0.0</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">22.01</token>
5 <xml name="edam_ontology">
6 <edam_topics>
7 <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
8 <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->
9 </edam_topics>
10 <edam_operations>
11 <edam_operation>operation_2422</edam_operation> <!-- Data retrieval -->
12 <edam_operation>operation_0335</edam_operation> <!-- Formatting -->
13 </edam_operations>
14 </xml>
15 <macro name="requirements">
16 <requirements>
17 <requirement type="package" version="@TOOL_VERSION@">sra-tools</requirement>
18 <requirement type="package" version="2.6">pigz</requirement>
19 <requirement type="package" version="1.16.1">samtools</requirement>
20 <yield/>
21 </requirements>
22 </macro>
23 <token name="@ACCESSIONS_FROM_FILE@">
24 grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
25 </token>
26 <token name="@COMPRESS@"><![CDATA[pigz -cqp \${GALAXY_SLOTS:-1}]]></token>
27 <token name="@CONFIGURE_RETRY@"><![CDATA[
28 export SRA_PREFETCH_RETRIES=3 &&
29 export SRA_PREFETCH_ATTEMPT=1 &&
30 ]]></token>
31 <xml name="bio_tools">
32 <xrefs>
33 <xref type="bio.tools">sra-tools</xref>
34 </xrefs>
35 </xml>
36 <token name="@COPY_CONFIGFILE@"><![CDATA[
37 mkdir -p ~/.ncbi &&
38 cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg &&
39 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
40 vdb-config -s "/repository/user/ad/public/root=\$PWD" &&
41 vdb-config -s "/repository/user/default-path=\$PWD" &&
42 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
43 vdb-config -s /http/timeout/read=10000 &&
44 ]]></token>
45 <token name="@SET_ACCESSIONS@"><![CDATA[
46 #if $input.input_select == "sra_file":
47 acc='${input.sra_file.name}' &&
48 ln -s '${input.sra_file}' "\$acc" &&
49 #else
50 #if $input.input_select == "file_list":
51 #if $input.file_list.is_of_type('sra_manifest.tabular'):
52 #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1
53 cut -f $column '$input.file_list'| tail -n +2 > accessions &&
54 #else
55 @ACCESSIONS_FROM_FILE@ '$input.file_list' > accessions &&
56 #end if
57 #elif $input.input_select == "accession_number":
58 echo '${input.accession}' | sed -r 's/(\,|\;|__cn__)/\n/g' > accessions &&
59 #end if
60 for acc in \$(cat ./accessions);
61 do (
62 echo "Downloading accession: \$acc..." &&
63 #end if
64 ]]></token>
65 <macro name="configfile_hack">
66 <configfiles>
67 <configfile name="user_settings_mkfg"><![CDATA[
68 /LIBS/GUID = "3cdc38d0-711a-49ce-9536-f544eaf69eec"
69 /config/default = "false"
70 /libs/temp_cache = "."
71 /tools/prefetch/download_to_cache = "false"
72 ]]></configfile>
73 </configfiles>
74 </macro>
75 <macro name="sanitize_query">
76 <sanitizer>
77 <valid initial="string.printable">
78 <remove value=" "/>
79 <remove value="&apos;" />
80 </valid>
81 <mapping initial="none">
82 <add source=" " target=""/>
83 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
84 </mapping>
85 </sanitizer>
86 </macro>
87 <macro name="input_conditional">
88 <conditional name="input">
89 <param name="input_select" type="select" label="select input type">
90 <option value="accession_number">SRR accession</option>
91 <option value="file_list">List of SRA accession, one per line</option>
92 <option value="sra_file">SRA archive in current history</option>
93 </param>
94 <when value="accession_number">
95 <param name="accession" type="text" label="Accession" multiple="true" help="Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809">
96 <expand macro="sanitize_query"/>
97 <validator type="empty_field" message="An accession is required"/>
98 </param>
99 </when>
100 <when value="sra_file">
101 <param format="sra" name="sra_file" type="data" label="sra archive"/>
102 </when>
103 <when value="file_list">
104 <param format="txt" name="file_list" type="data" label="sra accession list"/>
105 </when>
106 </conditional>
107 </macro>
108 <macro name="alignments">
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">
110 <option value="both">both</option>
111 <option value="aligned">aligned only</option>
112 <option value="unaligned">unaligned only</option>
113 </param>
114 </macro>
115 <macro name="minMapq">
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"/>
117 </macro>
118 <macro name="region">
119 <param format="text" name="region" type="text" label="aligned region" optional="true"
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"/>
121 </macro>
122 <macro name="matepairDist">
123 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
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"/>
125 </macro>
126 <macro name="citation">
127 <citations>
128 <citation type="doi">10.1093/nar/gkq1019</citation>
129 <citation type="bibtex">
130 @misc{github_sratools,
131 author = {NCBI},
132 title = {sra-tools},
133 publisher = {GitHub},
134 journal = {GitHub repository},
135 url = {https://github.com/ncbi/sra-tools},
136 }</citation>
137 </citations>
138 </macro>
139 <token name="@HOW_TO_USE_IT@">
140 **How to use it?**
141
142 There are three ways in which you can download data:
143
144 1. Plain text input of accession number(s)
145 2. Providing a list of accessions from file
146 3. Extracting data from an already uploaded SRA dataset
147
148 Below we discuss each in detail.
149
150 ------
151
152 **Plain text input of accession number(s)**
153
154 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`).
155
156 -----
157
158 **Providing a list of accessions from file**
159
160 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:
161
162 1. Upload it into your history using Galaxy's upload tool
163 2. Once the list of accessions is uploaded choose *List of SRA accessions, one per line* from **select input type** dropdown
164 3. Choose uploaded file within the **sra accession list** field
165 4. Click **Execute**
166
167 -----
168
169 **Extract data from an already uploaded SRA dataset**
170
171 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*.
172 </token>
173 <token name="@ACCESSION_LIST_HOWTO@">
174 -----
175
176 **How to generate accession lists**
177
178 1. Go to **SRA Run Selector** by clicking this link_
179 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*).
180 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
181 4. Click on the Runs number
182 5. On the page that would open you will see **Accession List** button
183 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.
184 </token>
185 <token name="@SRATOOLS_ATTRRIBUTION@">
186 For credits, information, support and bug reports, please refer ato https://github.com/galaxyproject/tools-iuc.
187 </token>
188 </macros>