Mercurial > repos > devteam > fastx_barcode_splitter
comparison fastx_barcode_splitter.xml @ 6:0b7ec11b3c7c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit fd099d17eceaa319fbfe429f4725328d88b18c9f
| author | iuc |
|---|---|
| date | Thu, 10 Aug 2023 06:53:42 +0000 |
| parents | 4bedca26c133 |
| children |
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| 5:4bedca26c133 | 6:0b7ec11b3c7c |
|---|---|
| 1 <tool id="cshl_fastx_barcode_splitter" version="1.0.1" name="Barcode Splitter"> | 1 <tool id="cshl_fastx_barcode_splitter" version="1.0.1+galaxy@VERSION_SUFFIX@" profile="22.05" name="Barcode Splitter"> |
| 2 <description></description> | 2 <description></description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <command detect_errors="aggressive"><![CDATA[ | 7 <command detect_errors="aggressive"><![CDATA[ |
| 8 mkdir split && | 8 mkdir split && |
| 9 @CATS@ '$__tool_directory__/fastx_barcode_splitter.pl' --bcfile '$BARCODE' | 9 @CATS@ '$__tool_directory__/fastx_barcode_splitter.pl' --bcfile '$BARCODE' |
| 10 --prefix 'split/' | 10 --prefix 'split/' |
| 11 --suffix | 11 --suffix |
| 12 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'): | 12 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'): |
| 13 '.fastqsanger' | 13 '.fastqsanger' |
| 14 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2'): | 14 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2'): |
| 15 '.fastqsolexa' | 15 '.fastqsolexa' |
| 16 #elif $input.is_of_type('fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'): | 16 #elif $input.is_of_type('fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'): |
| 76 <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" /> | 76 <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" /> |
| 77 <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" /> | 77 <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" /> |
| 78 <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" /> | 78 <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" /> |
| 79 </output_collection> | 79 </output_collection> |
| 80 </test> | 80 </test> |
| 81 | 81 |
| 82 <test> | 82 <test> |
| 83 <!-- Split a FASTQ.gz file --> | 83 <!-- Split a FASTQ.gz file --> |
| 84 <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> | 84 <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> |
| 85 <param name="input" value="fastx_barcode_splitter1.fastq.gz" ftype="fastqsolexa.gz" /> | 85 <param name="input" value="fastx_barcode_splitter1.fastq.gz" ftype="fastqsolexa.gz" /> |
| 86 <param name="barcodeLocation" value="bol" /> | 86 <param name="barcodeLocation" value="bol" /> |