Mercurial > repos > iuc > umi_tools_dedup

comparison umi-tools_dedup.xml @ 16:c5a2ee07c4e1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a
author iuc
date Sat, 05 Oct 2024 13:08:04 +0000
parents 04e09969d376
children
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15:04e09969d376 16:c5a2ee07c4e1
1 <tool id="umi_tools_dedup" name="UMI-tools deduplicate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="umi_tools_dedup" name="UMI-tools deduplicate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Extract UMI from fastq files</description> 2 <description>Extract UMI from fastq files</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="1.21">samtools</requirement> 8 <requirement type="package" version="1.21">samtools</requirement>
9 </expand> 9 </expand>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 @LINK_SAM_BAM_INPUT@ 11 @LINK_SAM_BAM_INPUT@
20 @UMI_GROUPING_OPTIONS@ 20 @UMI_GROUPING_OPTIONS@
21 @SAMBAM_OPTIONS@ 21 @SAMBAM_OPTIONS@
22 @FULLSC_OPTIONS@ 22 @FULLSC_OPTIONS@
23 @ADVANCED_OPTIONS@ 23 @ADVANCED_OPTIONS@
24 -I '$input_file' -S deduped.bam 24 -I '$input_file' -S deduped.bam
25 ## TODO using samtools sort is a workaround, for the following error that appears when Galaxy 25 ## using samtools sort is a workaround, for the following error that appears when Galaxy
26 ## compares the generated file with the one in test-data 26 ## compares the generated file with the one in test-data
27 ## `Converting history BAM to SAM failed: 'samtools returned with error 1: stdout=None, stderr=[main_samview] fail to read the header from "/tmp/tmpd8o61jykdedup_out6.bam".\n'. Will compare BAM files` 27 ## `Converting history BAM to SAM failed: 'samtools returned with error 1: stdout=None, stderr=[main_samview] fail to read the header from "/tmp/tmpd8o61jykdedup_out6.bam".\n'. Will compare BAM files`
28 ## problem seems to be the BAM file generated with pysam 28 ## problem seems to be the BAM file generated with pysam
29 ## may be dropped in the future 29 ## may be dropped in the future
30 --no-sort-output 30 --no-sort-output