Mercurial > repos > iuc > sinto_barcode

comparison sinto_barcode.xml @ 3:fb61eb03e313 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit 4a156b17a386e1ecf13dfb2b232a1fc7d8344adc
author iuc
date Tue, 05 Nov 2024 11:51:48 +0000
parents d1b34ac42b8f
children
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2:d0f56ac6bb60 3:fb61eb03e313
1 <tool id="sinto_barcode" name="Sinto barcode" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="sinto_barcode" name="Sinto barcode" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>add cell barcodes to FASTQ read names</description> 2 <description>add cell barcodes to FASTQ read names</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
6 <requirements> 7 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">sinto</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">sinto</requirement>
8 </requirements> 9 </requirements>
9 <version_command>sinto --version</version_command> 10 <version_command>sinto --version</version_command>
10 <command><![CDATA[ 11 <command><![CDATA[
11 ln -s '$barcode_fastq' barcodes.fastq.gz && 12 ln -s '$barcode_fastq' barcodes.fastq.gz &&
12 ln -s '${fastq_input.read1_fastq}' read1.fastq.gz && 13 ln -s '${fastq_input.read1_fastq}' read1.fastq.gz &&
13 #if str( $fastq_input.fastq_input_selector ) == "paired": 14 #if str( $fastq_input.fastq_input_selector ) == "paired":
14 ln -s '${fastq_input.read2_fastq}' read2.fastq.gz && 15 ln -s '${fastq_input.read2_fastq}' read2.fastq.gz &&
15 #end if 16 #end if
16 sinto barcode 17 sinto barcode
17 --barcode_fastq barcodes.fastq.gz 18 --barcode_fastq barcodes.fastq.gz
18 --read1 read1.fastq.gz 19 --read1 read1.fastq.gz
19 #if str( $fastq_input.fastq_input_selector ) == "paired": 20 #if str( $fastq_input.fastq_input_selector ) == "paired":
20 --read2 read2.fastq.gz 21 --read2 read2.fastq.gz
21 #end if 22 #end if
22 --bases $bases 23 --bases $bases