Mercurial > repos > iuc > bedtools
diff getfastaBed.xml @ 10:c78cf6fe3018 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
author | iuc |
---|---|
date | Mon, 03 Oct 2016 07:36:08 -0400 |
parents | 607c0576c6ab |
children | 7308cc546a36 |
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--- a/getfastaBed.xml Wed Sep 14 17:30:10 2016 -0400 +++ b/getfastaBed.xml Mon Oct 03 07:36:08 2016 -0400 @@ -7,19 +7,38 @@ <expand macro="stdio" /> <command> <![CDATA[ + #if str( $fasta_source.fasta_source_selector ) == 'history': + #set $fasta_file = $fasta_source.fasta + #else + #set $fasta_file = $fasta_source.fasta_id.fields.path + #end if bedtools getfasta $name $tab $strand $split - -fi $fasta - -bed $input - -fo $output + -fi '$fasta_file' + -bed '$input' + -fo '$output' ]]> </command> <inputs> <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" /> - <param format="fasta" name="fasta" type="data" label="Fasta file" /> + + <conditional name="fasta_source"> + <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file"> + <option value="history" selected="True">History</option> + <option value="preloaded">Server indexed files</option> + </param> + <when value="history"> + <param name="fasta" format="fasta" type="data" label="Fasta file" /> + </when> + <when value="preloaded"> + <param name="fasta_id" type="select"> + <options from_data_table="all_fasta" /> + </param> + </when> + </conditional> <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue="" label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" help="(-name)" />