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comparison snippy-core.xml @ 9:e4d0231d8595 draft

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"planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792"
author iuc
date Mon, 27 Jan 2020 21:50:49 -0500
parents 32f2211eeec3
children 5bbf9eada9c2
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8:32f2211eeec3 9:e4d0231d8595
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy1"> 2 <tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy2">
3 <description> 3 <description>
4 Combine multiple Snippy outputs into a core SNP alignment 4 Combine multiple Snippy outputs into a core SNP alignment
5 </description> 5 </description>
6 <macros> 6 <macros>
7 <import>macros.xml</import> 7 <import>macros.xml</import>
8 </macros> 8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 @REFERENCE_SOURCE_FILE@ 11 @REFERENCE_SOURCE_FILE@
12 mkdir 'snippy_dirs' && cd 'snippy_dirs' &&
12 #for $indir in $indirs 13 #for $indir in $indirs
13 #set $sample_name = os.path.splitext(os.path.basename(str($indir.name)))[0] 14 tar -xf '$indir' -C . &&
14 mkdir '$sample_name' && tar -xf '$indir' -C '$sample_name' --strip-components=1 &&
15 #end for 15 #end for
16 #set snippy_dirs = " ".join(["'{0}'".format(os.path.splitext(os.path.basename(str($indir.name)))[0]) for $indir in $indirs]) 16 cd - &&
17 snippy-core 17 snippy-core
18 @REFERENCE_COMMAND@ 18 @REFERENCE_COMMAND@
19 ${snippy_dirs} 19 snippy_dirs/*
20 ]]></command> 20 ]]></command>
21 21
22 <inputs> 22 <inputs>
23 <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" /> 23 <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
24 <expand macro="reference_selector" /> 24 <expand macro="reference_selector" />