Mercurial > repos > przemyslaw > samifier
comparison protein_generator.xml @ 0:cafda610cf4b draft default tip
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| author | przemyslaw |
|---|---|
| date | Thu, 27 Jun 2013 20:38:20 -0400 |
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| -1:000000000000 | 0:cafda610cf4b |
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| 1 <tool id="protgenerator" name="Protein Generator" version="1.0.8"> | |
| 2 <description>Protein Generator</description> | |
| 3 <command interpreter="bash"> | |
| 4 protein_generator.sh protein_generator.jar | |
| 5 -d "$databasename" | |
| 6 -f "$genomeFile" | |
| 7 #if $GlimmerFile | |
| 8 -g "$GlimmerFile" | |
| 9 #end if | |
| 10 #if $SplitInterval | |
| 11 -i "$SplitInterval" | |
| 12 #end if | |
| 13 -o "$output1" | |
| 14 #if $condition1.gffFile == "yes" | |
| 15 -p "$output2" | |
| 16 #end if | |
| 17 #if $condition2.accessionFile == "yes" | |
| 18 -q "$output3" | |
| 19 #end if | |
| 20 #if $trans_tab_file | |
| 21 -t "$trans_tab_file" | |
| 22 #end if | |
| 23 </command> | |
| 24 <inputs> | |
| 25 <param name="databasename" type="text" label="Database name" /> | |
| 26 <param name="genomeFile" type="data" format="faa" label="Select genome file" help="Genome file in gff format" /> | |
| 27 | |
| 28 <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" /> | |
| 29 <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" /> | |
| 30 | |
| 31 <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" /> | |
| 32 <conditional name="condition1"> | |
| 33 <param name="gffFile" type="select" help="write the GFF file"> | |
| 34 <option value="yes" selected="True">Yes</option> | |
| 35 <option value="no" selected="False">No</option> | |
| 36 </param> | |
| 37 </conditional> | |
| 38 <conditional name="condition2"> | |
| 39 <param name="accessionFile" type="select" label="Accession File" help="Write the accession file"> | |
| 40 <option value="yes" selected="True">Yes</option> | |
| 41 <option value="no" selected="False">No</option> | |
| 42 </param> | |
| 43 </conditional> | |
| 44 </inputs> | |
| 45 <outputs> | |
| 46 <data format="sam" name="output1" /> | |
| 47 <data format="gff" name="output2" label="GFF file"> | |
| 48 <filter>condition1['gffFile'] == "yes"</filter> | |
| 49 </data> | |
| 50 <data format="txt" name="output3" label="Accession File"> | |
| 51 <filter>condition2['accessionFile'] == "yes"</filter> | |
| 52 </data> | |
| 53 </outputs> | |
| 54 <help> | |
| 55 </help> | |
| 56 </tool> |