0
+ − 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<designation>.+)\.(?P<ext>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>
+ − 100 <param name="reference_sequence_lengths_file" value="ref_sequence_lengths.tabular" ftype="tabular"/>
+ − 101 <output_collection name="circos_png" type="list" count="3">
+ − 102 <element name="chromosome" ftype="png">
+ − 103 <assert_contents>
+ − 104 <has_size value="121172" delta="1000"/>
+ − 105 </assert_contents>
+ − 106 </element>
+ − 107 <element name="pXO1" ftype="png">
+ − 108 <assert_contents>
+ − 109 <has_size value="179913" delta="1000"/>
+ − 110 </assert_contents>
+ − 111 </element>
+ − 112 <element name="pXO2" ftype="png">
+ − 113 <assert_contents>
+ − 114 <has_size value="169070" delta="1000"/>
+ − 115 </assert_contents>
+ − 116 </element>
+ − 117 </output_collection>
+ − 118 </test>
+ − 119 </tests>
+ − 120 <help><![CDATA[
+ − 121 Renders circos plots of the PIMA assembly versus the reference alignemnt.
+ − 122 ]]></help>
+ − 123 <expand macro="citations"/>
+ − 124 </tool>