| Previous changeset 9:a06ad07431ba (2017-05-10) Next changeset 11:d51db443aaa4 (2018-05-30) |
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Commit message:
v0.2.2 Internal changes to command line handling |
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modified:
tools/get_orfs_or_cdss/README.rst tools/get_orfs_or_cdss/get_orfs_or_cdss.xml |
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| diff -r a06ad07431ba -r 01b0488d9cfb tools/get_orfs_or_cdss/README.rst --- a/tools/get_orfs_or_cdss/README.rst Wed May 10 13:24:46 2017 -0400 +++ b/tools/get_orfs_or_cdss/README.rst Tue May 16 09:11:27 2017 -0400 |
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| @@ -45,7 +45,7 @@ You will also need to install Biopython 1.65 or later (slightly older versions should be fine, but will not have the latest NCBI genetic code tables). -If you wish to run the unit tests, also move/copy the ``test-data/`` files +If you wish to run the unit tests, also move/copy the ``test-data/`` files under Galaxy's ``test-data/`` folder. Then:: ./run_tests.sh -id get_orfs_or_cdss @@ -79,7 +79,9 @@ v0.2.0 - Tool now also outputs GFF3 formatted calls (Eric Rasche). 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. + Gracilibacteria. +v0.2.2 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ====================================================================== |
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| diff -r a06ad07431ba -r 01b0488d9cfb tools/get_orfs_or_cdss/get_orfs_or_cdss.xml --- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Wed May 10 13:24:46 2017 -0400 +++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Tue May 16 09:11:27 2017 -0400 |
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| @@ -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." /> |