Mercurial > repos > rnateam > bctools
comparison merge_pcr_duplicates.xml @ 2:de4ea3aa1090 draft
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| author | rnateam |
|---|---|
| date | Thu, 22 Oct 2015 10:26:45 -0400 |
| parents | |
| children | bf5b606f1aa7 |
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| 1:ae0f58d3318f | 2:de4ea3aa1090 |
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| 1 <tool id="merge_pcr_duplicates.py" name="merge_pcr_duplicates.py" version="1.0"> | |
| 2 <description>Merge PCR duplicates according to random barcode library.</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <version_command>python merge_pcr_duplicates.py --version</version_command> | |
| 9 <command interpreter="python"><![CDATA[merge_pcr_duplicates.py | |
| 10 #if $positional_1 and $positional_1 is not None: | |
| 11 $positional_1 | |
| 12 #end if | |
| 13 | |
| 14 #if $positional_2 and $positional_2 is not None: | |
| 15 $positional_2 | |
| 16 #end if | |
| 17 | |
| 18 > $default]]></command> | |
| 19 <inputs> | |
| 20 <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/> | |
| 21 <param area="false" label="fasta barcode library." name="positional_2" type="data" format="fasta"/> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="bed" hidden="false" name="default"/> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 <test> | |
| 28 <param name="positional_1" value="pcr_dupes_sorted_2.bed"/> | |
| 29 <param name="positional_2" value="pcr_dupes_randomdict.fa"/> | |
| 30 <output name="default" file="merged_pcr_dupes.bed"/> | |
| 31 </test> | |
| 32 </tests> | |
| 33 <help><![CDATA[ | |
| 34 Merge PCR duplicates according to random barcode library. | |
| 35 | |
| 36 Barcodes containing uncalled base 'N' are removed. | |
| 37 | |
| 38 Input: | |
| 39 * bed6 file containing alignments with fastq read-id in name field | |
| 40 * fasta library with fastq read-id as sequence ids | |
| 41 | |
| 42 Output: | |
| 43 * bed6 file with random barcode in name field and number of PCR duplicates as score, sorted by fields chrom, start, stop, strand, name | |
| 44 | |
| 45 Author: Daniel Maticzka | |
| 46 Copyright: 2015 | |
| 47 License: Apache | |
| 48 Email: maticzkd@informatik.uni-freiburg.de | |
| 49 Status: Testing | |
| 50 ]]></help> | |
| 51 <expand macro="citations" /> | |
| 52 </tool> |