Mercurial > repos > devteam > data_manager_bowtie2_index_builder
comparison data_manager/bowtie2_index_builder.xml @ 2:8de13c28d92e draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 10:17:27 -0400 |
| parents | eec64de5f7fb |
| children | 49331eedb1c5 |
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| 1:e0839cffd009 | 2:8de13c28d92e |
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| 1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="0.0.1"> | 1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="0.0.2"> |
| 2 <description>builder</description> | 2 <description>builder</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="2.2.4">bowtie2</requirement> | 4 <requirement type="package" version="2.2.4">bowtie2</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <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> | 6 <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> |
| 7 <stdio> | 7 <stdio> |
| 8 <exit_code range=":-1" /> | 8 <exit_code range=":-1" /> |
| 9 <exit_code range="1:" /> | 9 <exit_code range="1:" /> |
| 10 </stdio> | 10 </stdio> |
| 11 <inputs> | 11 <inputs> |
| 12 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | 12 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> |
| 13 <options from_data_table="all_fasta"/> | 13 <options from_data_table="all_fasta"/> |
| 14 </param> | 14 </param> |
| 15 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | 15 <param type="text" name="sequence_name" value="" label="Name of sequence" /> |
| 16 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | 16 <param type="text" name="sequence_id" value="" label="ID for sequence" /> |
| 17 <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." /> | |
| 17 </inputs> | 18 </inputs> |
| 18 <outputs> | 19 <outputs> |
| 19 <data name="out_file" format="data_manager_json"/> | 20 <data name="out_file" format="data_manager_json"/> |
| 20 </outputs> | 21 </outputs> |
| 21 | 22 |