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comparison tools/cgatools17/testvariants_v17.xml @ 13:ff641b41735f draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit b55aad42004c821b66aaa7d871ebf314a4adf7f4-dirty
author yhoogstrate
date Wed, 11 Nov 2015 04:59:04 -0500
parents 64017ce705b6
children 59a2f9ad76dd
comparison
equal deleted inserted replaced
12:3c1b706e7f5f 13:ff641b41735f
10 <command> 10 <command>
11 cgatools testvariants 11 cgatools testvariants
12 --beta 12 --beta
13 --reference 13 --reference
14 14
15 #if $reference_gene_sets_source.source_select == "indexed_filtered" 15 #if $reference_genome_source.source_select == "indexed_filtered"
16 ${reference_gene_sets_source.crr.fields.crr_path} 16 ${reference_genome_source.crr.fields.crr_path}
17 #else if $reference_gene_sets_source.source_select == "history" 17 #else if $reference_genome_source.source_select == "history"
18 ${reference_gene_sets_source.crr} 18 ${reference_genome_source.crr}
19 #end if 19 #end if
20 20
21 --output $output 21 --output $output
22 --input $listing 22 --input $listing
23 --variants 23 --variants
27 </command> 27 </command>
28 28
29 <inputs> 29 <inputs>
30 <!--form field to select crr file--> 30 <!--form field to select crr file-->
31 31
32 <conditional name="reference_gene_sets_source"> 32 <conditional name="reference_genome_source">
33 <param name="source_select" type="select" label="GFF/GTF Source"> 33 <param name="source_select" type="select" label="CRR Genome reference Source">
34 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option> 34 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
35 <option value="history">Use reference from the history</option> 35 <option value="history">Use reference from the history</option>
36 </param> 36 </param>
37 <when value="indexed_filtered"> 37 <when value="indexed_filtered">
38 <param name="crr" type="select" label="Reference Build"> 38 <param name="crr" type="select" label="Reference Build">