Mercurial > repos > iuc > sra_tools

comparison macros.xml @ 30:4317d3cb6cba 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 173bdd37f6353cd869526d193e8d06038ae12787
author iuc
date Mon, 11 Sep 2023 08:37:23 +0000
parents 6ea73833cf67
children 734abc7ac21d
comparison
equal deleted inserted replaced
29:6ea73833cf67 30:4317d3cb6cba
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">3.0.5</token> 2 <token name="@TOOL_VERSION@">3.0.5</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 -->
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> 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 </valid>
148 </sanitizer>
149 <validator type="regex" message="Must start with @">^.*</validator>
150
151 </param>
152 </macro>
126 <macro name="citation"> 153 <macro name="citation">
127 <citations> 154 <citations>
128 <citation type="doi">10.1093/nar/gkq1019</citation> 155 <citation type="doi">10.1093/nar/gkq1019</citation>
129 <citation type="bibtex"> 156 <citation type="bibtex">
130 @misc{github_sratools, 157 @misc{github_sratools,