Mercurial > repos > iuc > sra_tools
diff sra_macros.xml @ 13:c38286ea7047 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
author | iuc |
---|---|
date | Wed, 17 Oct 2018 11:44:12 -0400 |
parents | 5534eb46de20 |
children | 1790dcf3c32d |
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--- a/sra_macros.xml Wed Sep 26 05:33:56 2018 -0400 +++ b/sra_macros.xml Wed Oct 17 11:44:12 2018 -0400 @@ -1,10 +1,34 @@ <macros> <token name="@VERSION@">2.9.1</token> + <token name="@ACCESSIONS_FROM_FILE@"> + grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$' + </token> + <token name="@SET_ACCESSIONS@"><![CDATA[ + #if $input.input_select=="file_list": + for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ; + do ( + #elif $input.input_select=="accession_number": + acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && ( + #end if + ]]></token> + <macro name="requirements"> <requirements> <requirement type="package" version="2.9.1">sra-tools</requirement> </requirements> </macro> + <macro name="sanitize_query"> + <sanitizer> + <valid initial="string.printable"> + <remove value=" "/> + <remove value="'" /> + </valid> + <mapping initial="none"> + <add source=" " target=""/> + <add source="'" target="'"'"'" /> + </mapping> + </sanitizer> + </macro> <macro name="input_conditional"> <conditional name="input"> <param name="input_select" type="select" label="select input type"> @@ -14,14 +38,7 @@ </param> <when value="accession_number"> <param name="accession" type="text" label="Accession" help="Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809"> - <sanitizer> - <valid initial="string.printable"> - <remove value=" "/> - </valid> - <mapping initial="none"> - <add source=" " target=""/> - </mapping> - </sanitizer> + <expand macro="sanitize_query" /> <validator type="empty_field" message="An accession is required"/> </param> </when>