Mercurial > repos > peterjc > get_orfs_or_cdss
changeset 23:583f155494c3 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss commit acaced2b77f2789558b3d4c210ec373f8bdbb7e9-dirty
| author | peterjc |
|---|---|
| date | Thu, 11 May 2017 18:35:11 -0400 |
| parents | 992b1ff45bb0 |
| children | 84232d9e269c |
| files | tools/get_orfs_or_cdss/README.rst tools/get_orfs_or_cdss/get_orfs_or_cdss.xml |
| diffstat | 2 files changed, 20 insertions(+), 9 deletions(-) [+] |
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--- a/tools/get_orfs_or_cdss/README.rst Wed May 10 12:43:13 2017 -0400 +++ b/tools/get_orfs_or_cdss/README.rst Thu May 11 18:35:11 2017 -0400 @@ -80,6 +80,8 @@ v0.2.1 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. - Added NCBI genetic code table 24, Candidate Division SR1 and Gracilibacteria. +v0.2.2 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ======================================================================
--- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Wed May 10 12:43:13 2017 -0400 +++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Thu May 11 18:35:11 2017 -0400 @@ -1,16 +1,25 @@ -<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.1"> +<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.2"> <description>e.g. to get peptides from ESTs</description> <requirements> <requirement type="package" version="1.67">biopython</requirement> </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command> - <command interpreter="python"> -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 + <version_command> +python $__tool_directory__/get_orfs_or_cdss.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/get_orfs_or_cdss.py +-i '$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' </command> <inputs> <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." />