Mercurial > repos > peterjc > seq_primer_clip
comparison tools/seq_primer_clip/seq_primer_clip.xml @ 5:530c8d6fedd8 draft
v0.0.15 - internal changes
| author | peterjc |
|---|---|
| date | Wed, 10 May 2017 13:09:52 -0400 |
| parents | 9b074c1db68e |
| children | b9dc7c967ee6 |
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| 4:9b074c1db68e | 5:530c8d6fedd8 |
|---|---|
| 1 <tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.14"> | 1 <tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.15"> |
| 2 <description>Trim off 5' or 3' primers</description> | 2 <description>Trim off 5' or 3' primers</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> | 4 <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> |
| 5 <requirement type="package" version="1.67">biopython</requirement> | 5 <requirement type="package" version="1.67">biopython</requirement> |
| 6 <requirement type="python-module">Bio</requirement> | |
| 7 </requirements> | 6 </requirements> |
| 8 <stdio> | 7 <version_command> |
| 9 <!-- Anything other than zero is an error --> | 8 python $__tool_directory__/seq_primer_clip.py --version |
| 10 <exit_code range="1:" /> | 9 </version_command> |
| 11 <exit_code range=":-1" /> | 10 <command detect_errors="aggressive"> |
| 12 </stdio> | 11 python $__tool_directory__/seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file |
| 13 <version_command interpreter="python">seq_primer_clip.py --version</version_command> | |
| 14 <command interpreter="python"> | |
| 15 seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file | |
| 16 </command> | 12 </command> |
| 17 <inputs> | 13 <inputs> |
| 18 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" help="FASTA, FASTQ, or SFF format."/> | 14 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" help="FASTA, FASTQ, or SFF format."/> |
| 19 <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/> | 15 <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/> |
| 20 <param name="primer_type" type="select" label="Type of primers"> | 16 <param name="primer_type" type="select" label="Type of primers"> |