Mercurial > repos > iuc > sra_tools
diff macros.xml @ 30:4317d3cb6cba draft
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 |
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--- a/macros.xml Fri Jun 23 21:32:08 2023 +0000 +++ b/macros.xml Mon Sep 11 08:37:23 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.0.5</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">22.01</token> <xml name="edam_ontology"> <edam_topics> @@ -123,6 +123,33 @@ <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true" 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"/> </macro> + <macro name="defline" tokens="defline_param,defline_default"> + <param argument="@DEFLINE_PARAM@" value="@DEFLINE_DEFAULT@" type="text" label="Defline format specification for sequence"> + <help>A string of characters and/or variables. The variables can be one of: + $ac: accession, $si: spot id, $sn: spot name, $sg: spot group (barcode), $sl: spot length in bases, $ri: read number, $rn: read name, $rl: read length in bases. + '[]' could be used for an optional output: if all vars in [] yield empty values whole group is not printed. Empty value is empty string or for numeric variables. + Ex: @$sn[_$rn]/$ri '_$rn' is omitted if name is empty"</help> + <!-- allow many chars, but quotes and backslash --> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="@" /> + <add value="$" /> + <add value="[" /> + <add value="]" /> + <add value="_" /> + <add value="-" /> + <add value="+" /> + <add value="." /> + <add value=";" /> + <add value=":" /> + <add value="/" /> + <add value="?" /> + </valid> + </sanitizer> + <validator type="regex" message="Must start with @">^.*</validator> + + </param> + </macro> <macro name="citation"> <citations> <citation type="doi">10.1093/nar/gkq1019</citation>