Mercurial > repos > iuc > enasearch_retrieve_data
diff macros.xml @ 0:cbc24be56f7b draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87
author | iuc |
---|---|
date | Tue, 29 Aug 2017 04:13:09 -0400 |
parents | |
children | 0719cfc3ebcb |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Aug 29 04:13:09 2017 -0400 @@ -0,0 +1,96 @@ +<?xml version="1.0" ?> +<macros> + <token name="@WRAPPER_VERSION@">0.1.1</token> + <xml name="version"> + <version_command>@WRAPPER_VERSION@</version_command> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@WRAPPER_VERSION@">enasearch</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"/> + <token name="@IDS@"> +<![CDATA[ + #for $id in str($ids).split(',') + --ids '$id' + #end for +]]> + </token> + <xml name="display_opt"> + <conditional name="display_opt"> + <param argument="--display" type="select" label="Display option to specify the display format"> + <expand macro="display_options"/> + </param> + <expand macro="when_display_options"/> + </conditional> + </xml> + <token name="@DISPLAY@"> +<![CDATA[ + --display '$display_opt.display' + #if $display_opt.display == 'fasta' or $display_opt.display == 'fastq' + #if str($display_opt.range_start) != '' and str($display_opt.range_stop) != '' + --subseq_range '$display_opt.range_start'-'$display_opt.range_stop' + #end if + #else + #if str($display_opt.offset) != '' + --offset '$display_opt.offset' + #end if + #if str($display_opt.length) != '' + --length '$display_opt.length' + #end if + #end if +]]> + </token> + <xml name="expanded"> + <param argument="--expanded" type="boolean" truevalue="--expanded" falsevalue="" label="Expand a CON record?"/> + </xml> + <xml name="header"> + <param argument="--header" type="boolean" truevalue="--header" falsevalue="" label="Obtain only the header of a record?"/> + </xml> + <xml name="accession"> + <param argument="--accession" type="text" label="Accession id" help="Study accessions (ERP, SRP, DRP, PRJ prefixes), experiment accessions (ERX, SRX, DRX prefixes), sample accessions (ERS, SRS, DRS, SAM prefixes) and run accessions"/> + </xml> + <token name="@FIELDS@"> +<![CDATA[ + #if $fields + #for $f in str($fields).split(',') + --fields '$f' + #end for + #end if +]]> + </token> + <xml name="change_format"> + <change_format> + <when input="display_opt.display" value="fasta" format="fasta" /> + <when input="display_opt.display" value="fastq" format="fastq" /> + <when input="display_opt.display" value="html" format="html" /> + <when input="display_opt.display" value="text" format="text" /> + <when input="display_opt.display" value="xml" format="xml" /> + </change_format> + </xml> + <token name="@SEARCH_DATA_DISPLAY@"> +<![CDATA[ + --display '$query_type.res.display_opt.display' + #if $query_type.res.display_opt.display != 'fasta' and $query_type.res.display_opt.display != 'fastq' + #if str($query_type.res.display_opt.offset) != '' + --offset '$query_type.res.display_opt.offset' + #end if + #if str($query_type.res.display_opt.length) != '' + --length '$query_type.res.display_opt.length' + #end if + #if $query_type.res.display_opt.display == 'report' + #for $f in str($query_type.res.display_opt.fields).split(',') + --fields '$f' + #end for + #if $query_type.res.display_opt.sortfields + #for $f in str($query_type.res.display_opt.sortfields).split(',') + --sortfields '$f' + #end for + #end if + #end if + #end if +]]> + </token> +</macros>