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1 <tool id="draw_features" name="PIMA: draw features" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>of annotated assemblies</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import re
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9
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10 #if $contigs.is_of_type('fasta.gz'):
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11 gunzip -c '$contigs' > 'contigs.fasta' &&
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12 #else:
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13 ln -s '$contigs' 'contigs.fasta' &&
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14 #end if
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15
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16 mkdir feature_hits_dir &&
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17 mkdir output_dir &&
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18
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19 #for $i in $feature_hits:
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20 #set file_name = $i.file_name
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21 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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2
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22 cat '$i' | awk '$7 != "."' | awk '{OFS="\t";locus=$7"\t"$8"\t"$9; if($5 > s[locus]){s[locus]=$5;id = sprintf("%.3f", $5); b[locus] = $1"\t"$2"\t"$3"\t"$4"\t"id"\t"$6}} END{for(i in b){print b[i]}}' | sort -k 1,1 -k2,2n > 'feature_hits_dir/$identifier' &&
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23 #end for
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24
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25 python '$__tool_directory__/draw_features.py'
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26 --contigs 'contigs.fasta'
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27 --feature_hits_dir 'feature_hits_dir'
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28 --output_dir 'output_dir'
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29 #if str($output_process_log) == 'yes':
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30 && mv 'process_log' '$process_log'
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31 #end if
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32 ]]></command>
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33 <inputs>
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34 <param name="contigs" type="data" format="fasta,fasta.gz" label="Fasta file of assembled contigs"/>
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35 <param name="feature_hits" format="bed" type="data_collection" collection_type="list" label="Collection of feature hits BED files"/>
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36 <param name="output_process_log" type="select" display="radio" label="Output process log file?">
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37 <option value="no" selected="true">No</option>
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38 <option value="yes">Yes</option>
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39 </param>
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40 </inputs>
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41 <outputs>
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4
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42 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
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43 <filter>output_process_log == 'yes'</filter>
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44 </data>
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4
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45 <collection name="features_bed" type="list" format="bed" label="${tool.name} on ${on_string} (best bed)">
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46 <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>bed)" directory="feature_hits_dir"/>
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47 </collection>
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48 <collection name="features_png" type="list" format="png" label="${tool.name} on ${on_string} (png)">
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49 <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>png)" directory="output_dir"/>
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50 </collection>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="contigs" value="PS01519_contigs.fasta.gz" ftype="fasta.gz"/>
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55 <param name="feature_hits">
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56 <collection type="list">
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57 <element name="amr_cds.bed" value="amr_cds.bed"/>
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58 </collection>
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59 </param>
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4
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60 <output_collection name="features_bed" type="list" count="1">
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61 <element name="amr_cds" ftype="bed">
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62 <assert_contents>
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63 <has_size value="129" delta="10"/>
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64 </assert_contents>
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65 </element>
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66 </output_collection>
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67 <output_collection name="features_png" type="list" count="1">
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68 <element name="contig_1" ftype="png">
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69 <assert_contents>
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70 <has_size value="25383" delta="100"/>
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71 </assert_contents>
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72 </element>
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73 </output_collection>
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74 </test>
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75 </tests>
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76 <help>
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77 **What it does**
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78
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79 Accepts a FASTA file of assembled contigs and a collection of 2 BED files containing the feature hits and plots
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80 the features.
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81 </help>
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82 <expand macro="citations"/>
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83 </tool>
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84
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