Mercurial > repos > devteam > fastx_barcode_splitter

comparison fastx_barcode_splitter.xml @ 6:8da8564e2e45 draft

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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 06:51:23 +0000
parents da00153634dc
children af6999ddeab5
comparison
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5:da00153634dc 6:8da8564e2e45
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" />