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comparison callntvar.xml @ 9:18aad692772a draft default tip

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planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:06:36 +0000
parents 9def47f3c1e4
children
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8:9def47f3c1e4 9:18aad692772a
1 <tool id="callntvar" name="Nucleotide Variants" version="0.7.0"> 1 <tool id="callntvar" name="Nucleotide Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Identifies nucleotide variants</description> 2 <description>Identifies nucleotide variants</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.7.0">quasitools</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements"/>
6 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
7 8
8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && 9 ln -s $input_bam '${input_bam.name}' &&
9 quasitools call ntvar $input_bam $ref_file 10 ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
11
12 quasitools call ntvar '${input_bam.name}' $ref_file
10 13
11 #if $error_rate: 14 #if $error_rate:
12 -e $error_rate 15 -e $error_rate
13 #end if 16 #end if
14 17
43 =================== 46 ===================
44 47
45 Call nucleotide variants for a given BAM file and a supplied reference file. 48 Call nucleotide variants for a given BAM file and a supplied reference file.
46 49
47 ]]></help> 50 ]]></help>
48 <citations> 51 <expand macro="citations" />
49 <citation type="bibtex">
50 @misc{GitHubquasitoolscallntvar,
51 title = {quasitools callntvar},
52 publisher = {phac-nml},
53 journal = {GitHub repository},
54 url = {https://github.com/phac-nml/quasitools},
55 }
56 </citation>
57 </citations>
58 </tool> 52 </tool>