Mercurial > repos > iuc > data_manager_star_index_builder

comparison data_manager/rna_star_index_builder.xml @ 5:f5eb9afa8f8a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
author iuc
date Thu, 15 Aug 2019 11:30:16 -0400
parents 6ef6520f14fc
children 64deddb6a8ec
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4:6ef6520f14fc 5:f5eb9afa8f8a
1 <tool id="rna_star_index_builder_data_manager" name="rnastar index2" tool_type="manage_data" version="0.0.5" profile="17.01"> 1 <tool id="rna_star_index_builder_data_manager" name="rnastar index2" tool_type="manage_data" version="2.7.1a" profile="17.01">
2 <description>builder</description> 2 <description>builder</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
39 39
40 python '${__tool_directory__}/rna_star_index_builder.py' 40 python '${__tool_directory__}/rna_star_index_builder.py'
41 --config-file '${out_file}' 41 --config-file '${out_file}'
42 --value '${all_fasta_source.fields.value}' 42 --value '${all_fasta_source.fields.value}'
43 --dbkey '${all_fasta_source.fields.dbkey}' 43 --dbkey '${all_fasta_source.fields.dbkey}'
44 --index-version '@IDX_VERSION@'
44 #if $name: 45 #if $name:
45 --name '$name' 46 --name '$name'
46 #else 47 #else
47 --name '${all_fasta_source.fields.name}' 48 --name '${all_fasta_source.fields.name}'
48 #end if 49 #end if
49 #if str($GTFconditional.GTFselect) == "withGTF": 50 #if str($GTFconditional.GTFselect) == "withGTF":
50 --withGTF 1 51 --with-gene-model
51 #end if 52 #end if
52 --data-table rnastar_index2 53 --data-table rnastar_index2_versioned
53 --subdir '${subdir}' 54 --subdir '${subdir}'
54 ]]></command> 55 ]]></command>
55 <inputs> 56 <inputs>
56 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> 57 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
57 <options from_data_table="all_fasta"/> 58 <options from_data_table="all_fasta"/>