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comparison manta_macros.xml @ 7:555971edd46e draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 569d2234f8a576d5c4fdae120a32418c50436ac2
author artbio
date Tue, 20 Feb 2024 08:31:27 +0000
parents cb5691381acb
children
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equal deleted inserted replaced
6:cb5691381acb 7:555971edd46e
1 <macros> 1 <macros>
2 2
3 <token name="@TOOL_VERSION@">1.6</token> 3 <token name="@TOOL_VERSION@">1.6</token>
4 <token name="@VERSION_SUFFIX@">8</token> 4 <token name="@VERSION_SUFFIX@">9</token>
5 <token name="@PROFILE@">20.05</token>
5 <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> 6 <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
6 7
7 <token name="@set_reference_fasta_filename@"><![CDATA[ 8 <token name="@set_reference_fasta_filename@"><![CDATA[
8 #set $reference_fasta_filename = "localref.fa" 9 #set $reference_fasta_filename = "localref.fa"
9 10
10 #if str( $reference_source.reference_source_selector ) == "history": 11 #if str( $reference_source.reference_source_selector ) == "history":
11 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' && 12 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
12 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for Manta" >&2 && 13 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for Manta" >&2 &&
13 #else: 14 #else:
14 #set $reference_fasta_filename = str( $reference_source.index.fields.path ) 15 #set $reference_fasta_filename = str( $reference_source.index.fields.path )
15 #end if 16 #end if
16 ]]></token> 17 ]]></token>
17 18
18 <token name="@set_configuration_file@"><![CDATA[ 19 <token name="@set_configuration_file@"><![CDATA[
19 #if str( $configuration.configuration_switch ) == "Custom_config_file": 20 #if str( $configuration.configuration_switch ) == "Custom_config_file":
26 ]]></token> 27 ]]></token>
27 28
28 29
29 <xml name="requirements"> 30 <xml name="requirements">
30 <requirements> 31 <requirements>
32 <requirement type="package" version="@TOOL_VERSION@">manta</requirement>
31 <requirement type="package" version="1.7">samtools</requirement> 33 <requirement type="package" version="1.7">samtools</requirement>
32 <requirement type="package" version="@TOOL_VERSION@">manta</requirement>
33 </requirements> 34 </requirements>
34 </xml> 35 </xml>
35 36
36 <xml name="stdio"> 37 <xml name="stdio">
37 <stdio> 38 <stdio>