Mercurial > repos > da-intersect > oldap11
changeset 17:eb1e67dae7b6 draft
Updated all config and scripts
| author | da-intersect |
|---|---|
| date | Thu, 11 Apr 2013 10:15:23 +1000 |
| parents | 956779875d03 |
| children | 926bb99cd83c |
| files | protein_merger.xml result_analyser.xml samifier.xml |
| diffstat | 3 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/protein_merger.xml Wed Apr 10 03:13:51 2013 -0400 +++ b/protein_merger.xml Thu Apr 11 10:15:23 2013 +1000 @@ -1,17 +1,17 @@ <tool id="protmerger" name="Protein Merger" version="0.0.1"> <description>Virtual Protein Merger</description> <command interpreter="bash"> - protein_merger.sh virtual_protein_merger.jar -g "$genomeFile" -o "$output1" + protein_merger.sh virtual_protein_merger.jar $chromosome_tar -g "$genomeFile" -o "$output1" -r "$searchResultsFile" #if $trans_tab_file -t "$trans_tab_file" #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"/> - </inputs> <outputs> <data format="sam" name="output1" />
--- a/result_analyser.xml Wed Apr 10 03:13:51 2013 -0400 +++ b/result_analyser.xml Thu Apr 11 10:15:23 2013 +1000 @@ -1,7 +1,7 @@ <tool id="resanalyser" name="Result Analyser" version="0.0.1"> <description>Result Analyser</description> <command interpreter="bash"> - result_analyser.sh results_analyser.jar -g "$genomeFile" -m "$mapping" -o "$output1" -r "$searchResultsFile" + result_analyser.sh results_analyser.jar $chromosome_tar -g "$genomeFile" -m "$mapping" -o "$output1" -r "$searchResultsFile" #if $reportId -rep "$reportId" #end if @@ -13,6 +13,7 @@ #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="mapping" type="data" format="txt" label="Select file mapping" help="File mapping protein identifier to ordered locus name" />
--- a/samifier.xml Wed Apr 10 03:13:51 2013 -0400 +++ b/samifier.xml Thu Apr 11 10:15:23 2013 +1000 @@ -13,7 +13,7 @@ #end if </command> <inputs> - <param name="chromosome_tar" type="data" format="tar" label="Select chromosome zip files" help="A zip file containing all the chromosome files" /> + <param name="chromosome_tar" type="data" format="tar" label="Select chromosome tar file" help="A Tar file containing all the chromosome files" /> <param name="genome" type="data" format="gff" label="Select genome file" help="Genome file in gff format" /> <param name="mascot" type="data" format="txt" label="Select Mascot search result" help="Mascot search results file in txt format" /> <param name="mapping" type="data" format="txt" label="Select file mapping" help="File mapping protein identifier to ordered locus name" />