Mercurial > repos > devteam > picard
comparison picard_CollectGcBiasMetrics.xml @ 8:e417b1d6288d draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
| author | devteam |
|---|---|
| date | Tue, 06 Dec 2016 10:04:26 -0500 |
| parents | 08f69add4d06 |
| children | 41b8d087a2d2 |
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| 7:08f69add4d06 | 8:e417b1d6288d |
|---|---|
| 6 <expand macro="requirements"> | 6 <expand macro="requirements"> |
| 7 <requirement type="package" version="3.3.1">r</requirement> | 7 <requirement type="package" version="3.3.1">r</requirement> |
| 8 </expand> | 8 </expand> |
| 9 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
| 10 @java_options@ | 10 @java_options@ |
| 11 @symlink_element_identifier@ | |
| 11 ##set up input files | 12 ##set up input files |
| 12 | 13 |
| 13 #set $reference_fasta_filename = "localref.fa" | 14 #set $reference_fasta_filename = "localref.fa" |
| 14 | 15 |
| 15 #if str( $reference_source.reference_source_selector ) == "history": | 16 #if str( $reference_source.reference_source_selector ) == "history": |
| 18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | 19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) |
| 19 #end if | 20 #end if |
| 20 | 21 |
| 21 picard | 22 picard |
| 22 CollectGcBiasMetrics | 23 CollectGcBiasMetrics |
| 23 INPUT="${inputFile}" | 24 INPUT='$inputFile.element_identifier' |
| 24 OUTPUT="${outFile}" | 25 OUTPUT="${outFile}" |
| 25 CHART_OUTPUT="${pdfFile}" | 26 CHART_OUTPUT="${pdfFile}" |
| 26 SUMMARY_OUTPUT="${summaryFile}" | 27 SUMMARY_OUTPUT="${summaryFile}" |
| 27 WINDOW_SIZE="${window_size}" | 28 WINDOW_SIZE="${window_size}" |
| 28 MINIMUM_GENOME_FRACTION="${minimum_genome_fraction}" | 29 MINIMUM_GENOME_FRACTION="${minimum_genome_fraction}" |