annotate draw_circos.xml @ 0:b73148507037 draft default tip

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1 <tool id="draw_circos" name="PIMA: draw circos" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2     <description>plot of assembly v. reference alignment</description>
3     <macros>
4         <import>macros.xml</import>
5         <import>macros_conffiles.xml</import>
6     </macros>
7     <edam_topics>
8         <edam_topic>topic_0797</edam_topic>
9         <edam_topic>topic_0092</edam_topic>
10     </edam_topics>
11     <edam_operations>
12         <edam_operation>operation_0337</edam_operation>
13     </edam_operations>
14     <expand macro="requirements"/>
15     <command detect_errors="exit_code"><![CDATA[
16 mkdir -p circos_dir &&
17 mkdir -p output_png_dir &&
18 
19 cp '$circos_conf' 'circos_dir/circos.conf' &&
20 cp '$ideogram_conf' 'circos_dir/ideogram.conf' &&
21 cp '$tick_base_conf' 'circos_dir/tick_base.conf' &&
22 
23 #if $reference_source.reference_source_selector == 'history':
24     ln -f -s '$reference_source.ref_file' reference.fa &&
25 #else:
26     ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
27 #end if
28 
29 python '$__tool_directory__/draw_circos.py'
30 --circos_conf 'circos_dir/circos.conf'
31 --dnadiff_1coords_file '$dnadiff_1coords_file'
32 --output_png_dir 'output_png_dir'
33 --reference_file 'reference.fa'
34 --reference_sequence_lengths_file '$reference_sequence_lengths_file'
35 --tick_base_conf 'circos_dir/tick_base.conf'
36     ]]></command>
37     <configfiles>
38         <expand macro="configfile_circos_conf"/>
39         <expand macro="configfile_ideogram_conf"/>
40         <expand macro="configfile_tick_base_conf"/>
41     </configfiles>
42     <inputs>
43         <param argument="dnadiff_1coords_file" type="data" format="tabular,tsv" label="DNAdiff 1coords tabular file"/>
44         <conditional name="reference_source">
45             <param name="reference_source_selector" type="select" label="Select a reference genome from your history or use a cached genome index?">
46                 <option value="cached">Use a cached genome index</option>
47                 <option value="history">Select a genome from the history and build the index</option>
48             </param>
49             <when value="cached">
50                 <param name="ref_file" type="select" label="Using reference genome" help="Select reference genome">
51                     <options from_data_table="all_fasta">
52                         <filter type="sort_by" column="2"/>
53                         <validator type="no_options" message="No reference genomes are available"/>
54                     </options>
55                 </param>
56             </when>
57             <when value="history">
58                 <param name="ref_file" type="data" format="fasta,fastq" label="Select the reference sequence" help="You can upload a FASTA file and use it as reference"/>
59             </when>
60         </conditional>
61         <param name="reference_sequence_lengths_file" type="data" format="tabular" label="Reference sequences lengths tabular file"/>
62     </inputs>
63     <outputs>
64         <collection name="circos_png" type="list" format="png">
65             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;png)" directory="output_png_dir"/>
66         </collection>
67     </outputs>
68     <tests>
69         <test>
70             <param name="dnadiff_1coords_file" value="dnadiff_1coords.tabular" ftype="tabular"/>
71             <conditional name="reference_source">
72                 <param name="reference_source_selector" value="history"/>
73                 <param name="ref_file" value="ref_genome.fasta"/>
74             </conditional>
75             <param name="reference_sequence_lengths_file" value="ref_sequence_lengths.tabular" ftype="tabular"/>
76             <output_collection name="circos_png" type="list" count="3">
77                 <element name="chromosome" ftype="png">
78                     <assert_contents>
79                         <has_size value="121172" delta="1000"/>
80                     </assert_contents>
81                 </element>
82                 <element name="pXO1" ftype="png">
83                     <assert_contents>
84                         <has_size value="179913" delta="1000"/>
85                     </assert_contents>
86                 </element>
87                 <element name="pXO2" ftype="png">
88                     <assert_contents>
89                         <has_size value="169070" delta="1000"/>
90                     </assert_contents>
91                 </element>
92             </output_collection>
93         </test>
94         <test>
95             <param name="dnadiff_1coords_file" value="dnadiff_1coords.tabular" ftype="tabular"/>
96             <conditional name="reference_source">
97                 <param name="reference_source_selector" value="cached"/>
98                 <param name="ref_file" value="ref_genome"/>
99             </conditional>
00             <param name="reference_sequence_lengths_file" value="ref_sequence_lengths.tabular" ftype="tabular"/>
01             <output_collection name="circos_png" type="list" count="3">
02                 <element name="chromosome" ftype="png">
03                     <assert_contents>
04                         <has_size value="121172" delta="1000"/>
05                     </assert_contents>
06                 </element>
07                 <element name="pXO1" ftype="png">
08                     <assert_contents>
09                         <has_size value="179913" delta="1000"/>
10                     </assert_contents>
11                 </element>
12                 <element name="pXO2" ftype="png">
13                     <assert_contents>
14                         <has_size value="169070" delta="1000"/>
15                     </assert_contents>
16                 </element>
17             </output_collection>
18         </test>
19     </tests>
20     <help><![CDATA[
21 Renders circos plots of the PIMA assembly versus the reference alignemnt.
22     ]]></help>
23     <expand macro="citations"/>
24 </tool>