Mercurial > repos > da-intersect > test_ap11
changeset 28:e9aa05006fa7
Change to virtual_protein_merger
| author | da-intersect |
|---|---|
| date | Fri, 19 Apr 2013 01:51:12 -0400 |
| parents | 1847c7a8492e |
| children | 3c7f675ba9f9 |
| files | datatypes_conf.xml jars/virtual_protein_merger.jar protein_generator.xml protein_merger.xml result_analyser.xml tar.py |
| diffstat | 2 files changed, 5 insertions(+), 2 deletions(-) [+] |
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--- a/protein_merger.xml Sun Apr 14 18:57:15 2013 -0400 +++ b/protein_merger.xml Fri Apr 19 01:51:12 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="protmerger" name="Protein Merger" version="1.0.1"> +<tool id="protmerger" name="Protein Merger" version="1.0.2"> <description>Virtual Protein Merger</description> <command interpreter="bash"> protein_merger.sh virtual_protein_merger.jar $chromosome_tar -g "$genomeFile" -o "$output1" @@ -6,13 +6,16 @@ #if $trans_tab_file -t "$trans_tab_file" #end if + #if $confidence_score + -s "$confidence_score" + #end if </command> <inputs> <param name="chromosome_tar" type="data" format="tar" label="Select chromosome tar file" help="A Tar file containing all the chromosome files" /> <param name="genomeFile" type="data" format="gff" label="Select genome file" help="Genome file in gff format" /> <param name="searchResultsFile" type="data" format="txt" label="Select Mascot search result" help="Mascot search results file in txt format" /> <param name="trans_tab_file" type="data" format="txt" label="Select Translation Table File" help="File containing a mapping of codons to amino acids, in the format used by NCBI." optional="True"/> - + <param name="confidence_score" type="integer" label="Confidence score thresold" help="Minimum confidence score for peptides to be included" optional="True"> </inputs> <outputs> <data format="sam" name="output1" />