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comparison tools/cgatools17/listvariants_v17.xml @ 14:59a2f9ad76dd draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 4df562cd801221f33652de8b8b4dbbf41deea8ea-dirty
author yhoogstrate
date Tue, 17 Nov 2015 04:43:00 -0500
parents ff641b41735f
children b5c879e950f5
comparison
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13:ff641b41735f 14:59a2f9ad76dd
11 <command> <!--run executable--> 11 <command> <!--run executable-->
12 cgatools 12 cgatools
13 listvariants 13 listvariants
14 --beta 14 --beta
15 15
16 #if $reference_genome_source.source_select == "indexed_filtered" 16 #if $reference_gene_sets_source.source_select == "indexed_filtered"
17 ${reference_genome_source.crr.fields.crr_path} 17 ${reference_gene_sets_source.crr.fields.crr_path}
18 #else if $reference_genome_source.source_select == "history" 18 #else if $reference_gene_sets_source.source_select == "history"
19 ${reference_genome_source.crr} 19 ${reference_gene_sets_source.crr}
20 #end if 20 #end if
21 21
22 --output $output 22 --output $output
23 #if $include_list.listing == "yes" <!--only added when yes--> 23 #if $include_list.listing == "yes" <!--only added when yes-->
24 --variant-listing $include_list.list 24 --variant-listing $include_list.list
31 31
32 </command> 32 </command>
33 33
34 <inputs> 34 <inputs>
35 <!--form field to select crr file--> 35 <!--form field to select crr file-->
36 <conditional name="reference_genome_source"> 36 <conditional name="reference_gene_sets_source">
37 <param name="source_select" type="select" label="CRR Genome reference Source"> 37 <param name="source_select" type="select" label="GFF/GTF Source">
38 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option> 38 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
39 <option value="history">Use reference from the history</option> 39 <option value="history">Use reference from the history</option>
40 </param> 40 </param>
41 <when value="indexed_filtered"> 41 <when value="indexed_filtered">
42 <param name="crr" type="select" label="Reference Build"> 42 <param name="crr" type="select" label="Reference Build">