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comparison circos.xml @ 11:31a35811dda6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit b9ec351920dbc83fa14bd1f8cfdd0a6a19b89473"
author iuc
date Tue, 16 Nov 2021 09:20:08 +0000
parents 7f13dc906cb9
children 290a11559985
comparison
equal deleted inserted replaced
10:7f13dc906cb9 11:31a35811dda6
9 <macros> 9 <macros>
10 <import>macros.xml</import> 10 <import>macros.xml</import>
11 <import>macros_conffiles.xml</import> 11 <import>macros_conffiles.xml</import>
12 <import>macros_tests.xml</import> 12 <import>macros_tests.xml</import>
13 </macros> 13 </macros>
14 <expand macro="requirements"/>
15 <edam_topics> 14 <edam_topics>
16 <edam_topic>topic_0797</edam_topic> 15 <edam_topic>topic_0797</edam_topic>
17 <edam_topic>topic_0092</edam_topic> 16 <edam_topic>topic_0092</edam_topic>
18 </edam_topics> 17 </edam_topics>
19 <edam_operations> 18 <edam_operations>
20 <edam_operation>operation_0337</edam_operation> 19 <edam_operation>operation_0337</edam_operation>
21 </edam_operations> 20 </edam_operations>
22 <version_command>circos --version</version_command> 21 <expand macro="requirements"/>
23 <stdio> 22 <stdio>
24 <!-- Anything other than zero is an error --> 23 <!-- Anything other than zero is an error -->
25 <exit_code range="1:"/> 24 <exit_code range="1:"/>
26 <exit_code range=":-1"/> 25 <exit_code range=":-1"/>
27 <!-- In case the return code has not been set propery check stderr too --> 26 <!-- In case the return code has not been set propery check stderr too -->
28 <regex match="Circos::Error::fatal_error.* called at"/> 27 <regex match="Circos::Error::fatal_error.* called at"/>
29 </stdio> 28 </stdio>
29 <version_command>circos --version</version_command>
30 <command><![CDATA[ 30 <command><![CDATA[
31 ## Directory structure 31 ## Directory structure
32 mkdir -p circos/conf/ circos/data/ && 32 mkdir -p circos/conf/ circos/data/ &&
33 33
34 #if $reference_genome.ref.ref_source == 'history': 34 #if $reference_genome.ref.ref_source == 'history':
56 python 56 python
57 '$__tool_directory__/karyotype-from-fasta.py' 57 '$__tool_directory__/karyotype-from-fasta.py'
58 genomeref.fa 58 genomeref.fa
59 > circos/conf/karyotype.txt && 59 > circos/conf/karyotype.txt &&
60 #else if $reference_genome.ref.ref_source == 'preset': 60 #else if $reference_genome.ref.ref_source == 'preset':
61 cp '$__tool_directory__/karyotype/'${reference_genome.ref.preset_karyotype} circos/conf/karyotype.txt && 61 cp '$__tool_directory__/karyotype/${reference_genome.ref.preset_karyotype}' circos/conf/karyotype.txt &&
62 #end if 62 #end if
63 63
64 python '$__tool_directory__/karyotype-colors.py' `grep -c '^chr\s' 'circos/conf/karyotype.txt'` 64 python '$__tool_directory__/karyotype-colors.py' `grep -c '^chr\s' 'circos/conf/karyotype.txt'`
65 > 'circos/conf/karyotype-colors.conf' && 65 > 'circos/conf/karyotype-colors.conf' &&
66 66