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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 0cfd88d16b0b20a66d4b21b037ddee6a8c440d88
author iuc
date Wed, 12 Apr 2023 15:08:23 +0000
parents 7b64033fb9b1
children
comparison
equal deleted inserted replaced
12:7b64033fb9b1 13:8b1cf140bbd4
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="circos" name="Circos" version="@WRAPPER_VERSION@"> 2 <tool id="circos" name="Circos" version="@WRAPPER_VERSION@" profile="21.09">
3 <description>visualizes data in a circular layout</description> 3 <description>visualizes data in a circular layout</description>
4 <xrefs>
5 <xref type="bio.tools">galactic_circos</xref>
6 <!--<xref type="bioconda">circos</xref>-->
7 <!--<xref type="rrid">RRID:SCR_018207</xref>-->
8 </xrefs>
9 <macros> 4 <macros>
10 <import>macros.xml</import> 5 <import>macros.xml</import>
11 <import>macros_conffiles.xml</import> 6 <import>macros_conffiles.xml</import>
12 <import>macros_tests.xml</import> 7 <import>macros_tests.xml</import>
13 </macros> 8 </macros>
16 <edam_topic>topic_0092</edam_topic> 11 <edam_topic>topic_0092</edam_topic>
17 </edam_topics> 12 </edam_topics>
18 <edam_operations> 13 <edam_operations>
19 <edam_operation>operation_0337</edam_operation> 14 <edam_operation>operation_0337</edam_operation>
20 </edam_operations> 15 </edam_operations>
16 <xrefs>
17 <xref type="bio.tools">galactic_circos</xref>
18 <!--<xref type="bioconda">circos</xref>-->
19 <!--<xref type="rrid">RRID:SCR_018207</xref>-->
20 </xrefs>
21 <expand macro="requirements"/> 21 <expand macro="requirements"/>
22 <stdio> 22 <stdio>
23 <!-- Anything other than zero is an error --> 23 <!-- Anything other than zero is an error -->
24 <exit_code range="1:"/> 24 <exit_code range="1:"/>
25 <exit_code range=":-1"/> 25 <exit_code range=":-1"/>
27 <regex match="Circos::Error::fatal_error.* called at"/> 27 <regex match="Circos::Error::fatal_error.* called at"/>
28 </stdio> 28 </stdio>
29 <version_command>circos --version</version_command> 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 $reference_genome.ref.ref_source == 'history':
35 ln -s '$reference_genome.ref.genome_fasta' genomeref.fa && 35 ln -s '$reference_genome.ref.genome_fasta' genomeref.fa;
36 #end if 36 #end if
37 37
38 #if $reference_genome.ref.ref_source in ('lengths', 'cached'): 38 #if $reference_genome.ref.ref_source in ('lengths', 'cached'):
39 python '$__tool_directory__/karyotype-from-lengths.py' 39 python '$__tool_directory__/karyotype-from-lengths.py'
40 #if $reference_genome.ref.ref_source == 'lengths' 40 #if $reference_genome.ref.ref_source == 'lengths'
46 #else 46 #else
47 ## Otherwise only the reduced list, as the full list will often overwhelm circos 47 ## Otherwise only the reduced list, as the full list will often overwhelm circos
48 <(head -n 50 '${reference_genome.ref.fasta_indexes.fields.len_path}') 48 <(head -n 50 '${reference_genome.ref.fasta_indexes.fields.len_path}')
49 #end if 49 #end if
50 #end if 50 #end if
51 > circos/conf/karyotype.txt && 51 > circos/conf/karyotype.txt;
52 #else if $reference_genome.ref.ref_source == 'karyotype': 52 #else if $reference_genome.ref.ref_source == 'karyotype':
53 cp $reference_genome.ref.input_karyotype circos/conf/karyotype.txt && 53 cp '${reference_genome.ref.input_karyotype}' circos/conf/karyotype.txt;
54 #else if str($reference_genome.ref.ref_source) == 'history': 54 #else if str($reference_genome.ref.ref_source) == 'history':
55 ## Process the karyotype.txt file 55 ## Process the karyotype.txt file
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
67 touch circos/conf/karyotype-colors.conf && 67 touch circos/conf/karyotype-colors.conf;
68 68
69 ## #if $ideogram.bands.bands: 69 ## #if $ideogram.bands.bands:
70 ## #if $ideogram.bands.convert_bands: 70 ## #if $ideogram.bands.convert_bands:
71 ## python '$__tool_directory__/process-cytogenetic-bands.py' 71 ## python '$__tool_directory__/process-cytogenetic-bands.py'
72 ## '${ideogram.bands.bands}' 72 ## '${ideogram.bands.bands}'
73 ## >> circos/conf/karyotype.txt 73 ## >> circos/conf/karyotype.txt
74 ## 2> circos/conf/karyotype-colors.conf && 74 ## 2> circos/conf/karyotype-colors.conf;
75 ## #else 75 ## #else
76 ## cat '${ideogram.bands.bands}' 76 ## cat '${ideogram.bands.bands}'
77 ## >> circos/conf/karyotype.txt && 77 ## >> circos/conf/karyotype.txt;
78 ## #end if 78 ## #end if
79 ## #end if 79 ## #end if
80 80
81 #if $plot_options.colour_profile: 81 #if $plot_options.colour_profile:
82 #if str($plot_options.colour_profile) == 'cg': 82 #if str($plot_options.colour_profile) == 'cg':
83 cat '$__tool_directory__/colours/cg.conf' >> circos/conf/karyotype-colors.conf && 83 cat '$__tool_directory__/colours/cg.conf' >> circos/conf/karyotype-colors.conf;
84 #end if 84 #end if
85 #end if 85 #end if
86 86
87 cp '$circos_conf' circos/conf/circos.conf && 87 cp '$circos_conf' circos/conf/circos.conf ;
88 cp '$ticks_conf' circos/conf/ticks.conf && 88 cp '$ticks_conf' circos/conf/ticks.conf ;
89 cp '$ideogram_conf' circos/conf/ideogram.conf && 89 cp '$ideogram_conf' circos/conf/ideogram.conf ;
90 cp '$data_conf' circos/conf/data.conf && 90 cp '$data_conf' circos/conf/data.conf ;
91 cp '$links_conf' circos/conf/links.conf && 91 cp '$links_conf' circos/conf/links.conf ;
92 cp '$test_case_conf' circos/conf/galaxy_test_case.json && 92 cp '$test_case_conf' circos/conf/galaxy_test_case.json ;
93 93
94 ## 2D Data Plots 94 ## 2D Data Plots
95 #for $hi, $data in enumerate($sec_tdd.data): 95 #for $hi, $data in enumerate($sec_tdd.data):
96 cp '${data.plot_format.data_source}' circos/data/data-${hi}.txt && 96 cp '${data.plot_format.data_source}' circos/data/data-${hi}.txt ;
97 #end for 97 #end for
98 98
99 ## Link Tracks 99 ## Link Tracks
100 #for $hi, $data in enumerate($sec_links.data): 100 #for $hi, $data in enumerate($sec_links.data):
101 cp '${data.data_source}' circos/data/links-${hi}.txt && 101 cp '${data.data_source}' circos/data/links-${hi}.txt ;
102 #end for 102 #end for
103 103
104 #if $outputs.tar == "yes" 104 #if $outputs.tar == "yes"
105 tar -czf circos.tar.gz circos && 105 tar -czf circos.tar.gz circos ;
106 #end if 106 #end if
107 107
108 #if $outputs.svg == "yes" or $outputs.png == "yes": 108 #if $outputs.svg == "yes" or $outputs.png == "yes":
109 circos -conf circos/conf/circos.conf -noparanoid 109 circos -conf circos/conf/circos.conf -noparanoid
110 #end if 110 #end if
615 <param name="svg" type="boolean" truevalue="yes" falsevalue="no" label="SVG" checked="false" help="Oftentimes this will not be viewable directly in Galaxy, you may need to download this file first."/> 615 <param name="svg" type="boolean" truevalue="yes" falsevalue="no" label="SVG" checked="false" help="Oftentimes this will not be viewable directly in Galaxy, you may need to download this file first."/>
616 <param name="tar" type="boolean" truevalue="yes" falsevalue="no" label="Configuration Archive" checked="false" help="This contains all the files needed to make this plot. With the data contained within here, and a copy of Circos installed locally, you can rebuild the plot and make any manual changes that are not possible in Galaxy (e.g. colours not in the colour picker)"/> 616 <param name="tar" type="boolean" truevalue="yes" falsevalue="no" label="Configuration Archive" checked="false" help="This contains all the files needed to make this plot. With the data contained within here, and a copy of Circos installed locally, you can rebuild the plot and make any manual changes that are not possible in Galaxy (e.g. colours not in the colour picker)"/>
617 </section> 617 </section>
618 </inputs> 618 </inputs>
619 <outputs> 619 <outputs>
620 <data name="output_png" format="png" from_work_dir="circos.png" label="Circos Plot"> 620 <data name="output_png" format="png" from_work_dir="circos.png" label="Circos Plot (PNG)">
621 <filter>outputs['png']</filter> 621 <filter>outputs['png']</filter>
622 </data> 622 </data>
623 <data name="output_svg" format="svg" from_work_dir="circos.svg" label="Circos Plot"> 623 <data name="output_svg" format="svg" from_work_dir="circos.svg" label="Circos Plot (SVG)">
624 <filter>outputs['svg']</filter> 624 <filter>outputs['svg']</filter>
625 </data> 625 </data>
626 <data name="output_tar" format="tar.gz" from_work_dir="circos.tar.gz" label="Circos Conf Files"> 626 <data name="output_tar" format="tar.gz" from_work_dir="circos.tar.gz" label="Circos Conf Files">
627 <filter>outputs['tar']</filter> 627 <filter>outputs['tar']</filter>
628 </data> 628 </data>