Mercurial > repos > artbio > manta
comparison manta_macros.xml @ 3:d648e40c6da9 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"
author | artbio |
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date | Sun, 07 Jun 2020 16:43:54 -0400 |
parents | 6a69e5d7c21f |
children | d09254e37c68 |
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2:6a69e5d7c21f | 3:d648e40c6da9 |
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1 <macros> | 1 <macros> |
2 | 2 |
3 <token name="@VERSION@">1.6</token> | 3 <token name="@VERSION@">1.6</token> |
4 <token name="@WRAPPER_VERSION@">@VERSION@+galaxy4</token> | 4 <token name="@WRAPPER_VERSION@">@VERSION@+galaxy5</token> |
5 <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> | 5 <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> |
6 | 6 |
7 <token name="@set_reference_fasta_filename@"><![CDATA[ | 7 <token name="@set_reference_fasta_filename@"><![CDATA[ |
8 #set $reference_fasta_filename = "localref.fa" | 8 #set $reference_fasta_filename = "localref.fa" |
9 | 9 |
10 #if str( $reference_source.reference_source_selector ) == "history": | 10 #if str( $reference_source.reference_source_selector ) == "history": |
11 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' && | 11 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' && |
12 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for Manta" >&2 && | 12 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for Manta" >&2 && |
13 #else: | 13 #else: |
14 #set $reference_fasta_filename = str( $reference_source.index.fields.path ) | 14 #set $reference_fasta_filename = str( $reference_source.index.fields.path ) |
15 #end if | 15 #end if |
16 ]]></token> | 16 ]]></token> |
19 #if str( $configuration.configuration_switch ) == "Custom_config_file": | 19 #if str( $configuration.configuration_switch ) == "Custom_config_file": |
20 #set $config_file = '$configuration.CustomConfigFile' | 20 #set $config_file = '$configuration.CustomConfigFile' |
21 #else if str( $configuration.configuration_switch )== "Customized": | 21 #else if str( $configuration.configuration_switch )== "Customized": |
22 #set $config_file = '$configuration.Customized' | 22 #set $config_file = '$configuration.Customized' |
23 #else: | 23 #else: |
24 #set $config_file = $__tool_directory__ + '/configManta.py.ini' | 24 #set $config_file = 'configManta.py.ini' |
25 #end if | 25 #end if |
26 ]]></token> | 26 ]]></token> |
27 | 27 |
28 | 28 |
29 <xml name="requirements"> | 29 <xml name="requirements"> |