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comparison macros.xml @ 26:f7732611d0fc draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 7632986831e24fcd189a57d824b9e6b1d5dc5c4c
author iuc
date Mon, 26 Aug 2024 14:59:07 +0000
parents 0c5a5e670ac0
children
comparison
equal deleted inserted replaced
25:0c5a5e670ac0 26:f7732611d0fc
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">3.0.5</token> 2 <token name="@TOOL_VERSION@">3.1.1</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">1</token>
4 <token name="@PROFILE@">22.01</token> 4 <token name="@PROFILE@">22.01</token>
5 <xml name="edam_ontology"> 5 <xml name="edam_ontology">
6 <edam_topics> 6 <edam_topics>
7 <edam_topic>topic_0622</edam_topic> <!-- Genomics --> 7 <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
8 <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics --> 8 <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->
13 </edam_operations> 13 </edam_operations>
14 </xml> 14 </xml>
15 <macro name="requirements"> 15 <macro name="requirements">
16 <requirements> 16 <requirements>
17 <requirement type="package" version="@TOOL_VERSION@">sra-tools</requirement> 17 <requirement type="package" version="@TOOL_VERSION@">sra-tools</requirement>
18 <requirement type="package" version="2.6">pigz</requirement> 18 <requirement type="package" version="2.8">pigz</requirement>
19 <requirement type="package" version="1.17">samtools</requirement> 19 <requirement type="package" version="1.20">samtools</requirement>
20 <yield/> 20 <yield/>
21 </requirements> 21 </requirements>
22 </macro> 22 </macro>
23 <token name="@ACCESSIONS_FROM_FILE@"> 23 <token name="@ACCESSIONS_FROM_FILE@">
24 grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$' 24 grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
34 </xrefs> 34 </xrefs>
35 </xml> 35 </xml>
36 <token name="@COPY_CONFIGFILE@"><![CDATA[ 36 <token name="@COPY_CONFIGFILE@"><![CDATA[
37 mkdir -p ~/.ncbi && 37 mkdir -p ~/.ncbi &&
38 cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg && 38 cp '$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> 39 ]]></token>
45 <token name="@SET_ACCESSIONS@"><![CDATA[ 40 <token name="@SET_ACCESSIONS@"><![CDATA[
46 #if $input.input_select == "sra_file": 41 #if $input.input_select == "sra_file":
47 acc='${input.sra_file.name}' && 42 acc='${input.sra_file.name}' &&
48 ln -s '${input.sra_file}' "\$acc" && 43 ln -s '${input.sra_file}' "\$acc" &&
67 <configfile name="user_settings_mkfg"><![CDATA[ 62 <configfile name="user_settings_mkfg"><![CDATA[
68 /LIBS/GUID = "3cdc38d0-711a-49ce-9536-f544eaf69eec" 63 /LIBS/GUID = "3cdc38d0-711a-49ce-9536-f544eaf69eec"
69 /config/default = "false" 64 /config/default = "false"
70 /libs/temp_cache = "." 65 /libs/temp_cache = "."
71 /tools/prefetch/download_to_cache = "false" 66 /tools/prefetch/download_to_cache = "false"
67 /http/timeout/read = "1000"
68 /repository/user/main/public/root = "."
69 /repository/user/ad/public/root = "."
70 /repository/user/default-path = "."
71 /repository/user/main/public/root = "."
72 ]]></configfile> 72 ]]></configfile>
73 </configfiles> 73 </configfiles>
74 </macro> 74 </macro>
75 <macro name="sanitize_query"> 75 <macro name="sanitize_query">
76 <sanitizer> 76 <sanitizer>
114 </macro> 114 </macro>
115 <macro name="minMapq"> 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"/> 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> 117 </macro>
118 <macro name="region"> 118 <macro name="region">
119 <param format="text" name="region" type="text" label="aligned region" optional="true" 119 <param 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"/> 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> 121 </macro>
122 <macro name="matepairDist"> 122 <macro name="matepairDist">
123 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true" 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"/> 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="defline" tokens="defline_param,defline_default">
127 <param argument="@DEFLINE_PARAM@" value="@DEFLINE_DEFAULT@" type="text" label="Defline format specification for sequence">
128 <help>A string of characters and/or variables. The variables can be one of:
129 $ac: accession, $si: spot id, $sn: spot name, $sg: spot group (barcode), $sl: spot length in bases, $ri: read number, $rn: read name, $rl: read length in bases.
130 '[]' could be used for an optional output: if all vars in [] yield empty values whole group is not printed. Empty value is empty string or for numeric variables.
131 Ex: @$sn[_$rn]/$ri '_$rn' is omitted if name is empty"</help>
132 <!-- allow many chars, but quotes and backslash -->
133 <sanitizer>
134 <valid initial="string.ascii_letters,string.digits">
135 <add value="@" />
136 <add value="$" />
137 <add value="[" />
138 <add value="]" />
139 <add value="_" />
140 <add value="-" />
141 <add value="+" />
142 <add value="." />
143 <add value=";" />
144 <add value=":" />
145 <add value="/" />
146 <add value="?" />
147 <add value=" " />
148 <add value="=" />
149 </valid>
150 </sanitizer>
151 <validator type="regex" message="Must start with @">^.*</validator>
152
153 </param>
125 </macro> 154 </macro>
126 <macro name="citation"> 155 <macro name="citation">
127 <citations> 156 <citations>
128 <citation type="doi">10.1093/nar/gkq1019</citation> 157 <citation type="doi">10.1093/nar/gkq1019</citation>
129 <citation type="bibtex"> 158 <citation type="bibtex">