Mercurial > repos > devteam > data_manager_bowtie2_index_builder
diff data_manager/bowtie2_index_builder.xml @ 1:9bf4eb559ed5 draft
planemo upload commit 4381f4022eca6f3c58ae1d01096795cd28c15062
| author | devteam |
|---|---|
| date | Mon, 10 Aug 2015 16:44:10 -0400 |
| parents | 9458af1ab90b |
| children | e87aeff2cf88 |
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--- a/data_manager/bowtie2_index_builder.xml Tue Apr 14 12:06:01 2015 -0400 +++ b/data_manager/bowtie2_index_builder.xml Mon Aug 10 16:44:10 2015 -0400 @@ -1,9 +1,9 @@ -<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="0.0.1"> +<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="0.0.2"> <description>builder</description> <requirements> <requirement type="package" version="2.2.4">bowtie2</requirement> </requirements> - <command interpreter="python">bowtie2_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "bowtie2_indexes"</command> + <command interpreter="python">bowtie2_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "bowtie2_indexes" ${tophat2}</command> <stdio> <exit_code range=":-1" /> <exit_code range="1:" /> @@ -14,6 +14,7 @@ </param> <param type="text" name="sequence_name" value="" label="Name of sequence" /> <param type="text" name="sequence_id" value="" label="ID for sequence" /> + <param type="boolean" name="tophat2" label="Also make available for TopHat" checked="True" truevalue="--data_table_name tophat2_indexes" falsevalue="" help="Adds values to tophat2_indexes tool data table." /> </inputs> <outputs> <data name="out_file" format="data_manager_json"/>