Mercurial > repos > peterjc > seq_select_by_id
comparison tools/seq_select_by_id/seq_select_by_id.xml @ 7:a5602454b0ad draft
v0.0.12 Depends on Biopython 1.67 via legacy Tool Shed package or bioconda; Python 3 compatible print function
| author | peterjc |
|---|---|
| date | Thu, 11 May 2017 06:26:05 -0400 |
| parents | 91f55ee8fea5 |
| children | 8e1a90917fa7 |
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| 6:91f55ee8fea5 | 7:a5602454b0ad |
|---|---|
| 1 <tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.11"> | 1 <tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.12"> |
| 2 <description>from a tabular file</description> | 2 <description>from a tabular file</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.62">biopython</requirement> | 4 <requirement type="package" version="1.67">biopython</requirement> |
| 5 <requirement type="python-module">Bio</requirement> | |
| 6 </requirements> | 5 </requirements> |
| 7 <stdio> | 6 <version_command> |
| 8 <!-- Anything other than zero is an error --> | 7 python $__tool_directory__/seq_select_by_id.py --version |
| 9 <exit_code range="1:" /> | 8 </version_command> |
| 10 <exit_code range=":-1" /> | 9 <command detect_errors="aggressive"> |
| 11 </stdio> | 10 python $__tool_directory__/seq_select_by_id.py '$input_tabular' '$column' '$input_file' '$input_file.ext' '$output_file' |
| 12 <version_command interpreter="python">seq_select_by_id.py --version</version_command> | |
| 13 <command interpreter="python"> | |
| 14 seq_select_by_id.py "$input_tabular" "$column" "$input_file" "$input_file.ext" "$output_file" | |
| 15 </command> | 11 </command> |
| 16 <inputs> | 12 <inputs> |
| 17 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." /> | 13 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." /> |
| 18 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> | 14 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> |
| 19 <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> | 15 <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> |