Mercurial > repos > peterjc > get_orfs_or_cdss
comparison tools/get_orfs_or_cdss/get_orfs_or_cdss.xml @ 10:01b0488d9cfb draft
v0.2.2 Internal changes to command line handling
| author | peterjc |
|---|---|
| date | Tue, 16 May 2017 09:11:27 -0400 |
| parents | a06ad07431ba |
| children | d51db443aaa4 |
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| 9:a06ad07431ba | 10:01b0488d9cfb |
|---|---|
| 1 <tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.1"> | 1 <tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.2"> |
| 2 <description>e.g. to get peptides from ESTs</description> | 2 <description>e.g. to get peptides from ESTs</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.67">biopython</requirement> | 4 <requirement type="package" version="1.67">biopython</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <stdio> | 6 <version_command> |
| 7 <!-- Anything other than zero is an error --> | 7 python $__tool_directory__/get_orfs_or_cdss.py --version |
| 8 <exit_code range="1:" /> | 8 </version_command> |
| 9 <exit_code range=":-1" /> | 9 <command detect_errors="aggressive"> |
| 10 </stdio> | 10 python $__tool_directory__/get_orfs_or_cdss.py |
| 11 <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command> | 11 -i '$input_file' |
| 12 <command interpreter="python"> | 12 -f '$input_file.ext' |
| 13 get_orfs_or_cdss.py -i $input_file -f $input_file.ext --table $table -t $ftype -e $ends -m $mode --min_len $min_len -s $strand --on $out_nuc_file --op $out_prot_file --ob $out_bed_file --og $out_gff3_file | 13 --table '$table' |
| 14 -t '$ftype' | |
| 15 -e '$ends' | |
| 16 -m '$mode' | |
| 17 --min_len '$min_len' | |
| 18 -s '$strand' | |
| 19 --on '$out_nuc_file' | |
| 20 --op '$out_prot_file' | |
| 21 --ob '$out_bed_file' | |
| 22 --og '$out_gff3_file' | |
| 14 </command> | 23 </command> |
| 15 <inputs> | 24 <inputs> |
| 16 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." /> | 25 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." /> |
| 17 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> | 26 <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> |
| 18 <option value="1">1. Standard</option> | 27 <option value="1">1. Standard</option> |