Mercurial > repos > iuc > umi_tools_group

comparison umi-tools_group.xml @ 17:428735be9764 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 13:08:51 +0000
parents 257be15474a7
children
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16:257be15474a7 17:428735be9764
1 <tool id="umi_tools_group" name="UMI-tools group" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="umi_tools_group" name="UMI-tools group" 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@
21 @SAMBAM_OPTIONS@ 21 @SAMBAM_OPTIONS@
22 @FULLSC_OPTIONS@ 22 @FULLSC_OPTIONS@
23 -I '$input_file' -S grouped.bam 23 -I '$input_file' -S grouped.bam
24 @ADVANCED_OPTIONS@ 24 @ADVANCED_OPTIONS@
25 @LOG@ 25 @LOG@
26 ## TODO using samtools sort is a workaround, for the following error that appears when Galaxy 26 ## using samtools sort is a workaround, for the following error that appears when Galaxy
27 ## compares the generated file with the one in test-data 27 ## compares the generated file with the one in test-data
28 ## `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 ## `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`
29 ## may be dropped in the future 29 ## may be dropped in the future
30 --no-sort-output 30 --no-sort-output
31 && samtools sort --no-PG grouped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM 31 && samtools sort --no-PG grouped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM
40 <expand macro="fullsc_options_macro"/> 40 <expand macro="fullsc_options_macro"/>
41 <expand macro="advanced_options_macro"/> 41 <expand macro="advanced_options_macro"/>
42 <expand macro="log_input_macro"/> 42 <expand macro="log_input_macro"/>
43 </inputs> 43 </inputs>
44 <outputs> 44 <outputs>
45 <data format="bam" name="output" /> 45 <data format="bam" name="output" label="${tool.name} on ${on_string}: Tagged BAM"/>
46 <data format="tabular" name="group_out"> 46 <data format="tabular" name="group_out" label="${tool.name} on ${on_string}: Read groups">
47 <filter>group_output</filter> 47 <filter>group_output</filter>
48 </data> 48 </data>
49 <expand macro="log_output_macro"/> 49 <expand macro="log_output_macro"/>
50 </outputs> 50 </outputs>
51 <tests> 51 <tests>