Mercurial > repos > da-intersect > oldap11
changeset 5:e49ba3299767 draft
Uploaded
author | da-intersect |
---|---|
date | Wed, 10 Apr 2013 03:01:01 -0400 |
parents | 13e3de458260 |
children | 417dd8d4387c |
files | protein_generator.xml |
diffstat | 1 files changed, 56 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/protein_generator.xml Wed Apr 10 03:01:01 2013 -0400 @@ -0,0 +1,56 @@ +<tool id="protgenerator" name="Protein Generator" version="0.0.1"> + <description>Protein Generator</description> + <command interpreter="bash"> + protein_generator.sh protein_generator.jar + -d "$databasename" + -f "$genomeFile" + #if $GlimmerFile + -g "$GlimmerFile" + #end if + #if $SplitInterval + -i "$SplitInterval" + #end if + -o "$output1" + #if $condition1.gffFile == "yes" + -p "$output2" + #end if + #if $condition2.accessionFile == "yes" + -q "$output3" + #end if + #if $trans_tab_file + -t "$trans_tab_file" + #end if + </command> + <inputs> + <param name="databasename" type="text" label="Database name" /> + <param name="genomeFile" type="data" format="faa" label="Select genome file" help="Genome file in gff format" /> + + <param name="GlimmerFile" type="data" format="txt" label="Select Glimmer File" help="Glimmer txt file. Can't be used with the Split Interval" optional="true" /> + <param name="SplitInterval" type="integer" label="Size of the intervals" help="Size of the intervals (number of codons) into which the genome will be split. Can't be used with the Glimmer File" optional="true" /> + + <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" /> + <conditional name="condition1"> + <param name="gffFile" type="select" help="write the GFF file"> + <option value="yes" selected="True">Yes</option> + <option value="no" selected="False">No</option> + </param> + </conditional> + <conditional name="condition2"> + <param name="accessionFile" type="select" label="Accession File" help="Write the accession file"> + <option value="yes" selected="True">Yes</option> + <option value="no" selected="False">No</option> + </param> + </conditional> + </inputs> + <outputs> + <data format="sam" name="output1" /> + <data format="gff" name="output2" label="GFF file"> + <filter>condition1['gffFile'] == "yes"</filter> + </data> + <data format="txt" name="output3" label="Accession File"> + <filter>condition2['accessionFile'] == "yes"</filter> + </data> + </outputs> + <help> + </help> +</tool>