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comparison draw_features.xml @ 6:d5a5d145cfce draft

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author greg
date Fri, 10 Mar 2023 18:02:00 +0000
parents c318e520dca1
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5:c318e520dca1 6:d5a5d145cfce
15 15
16 mkdir feature_hits_dir && 16 mkdir feature_hits_dir &&
17 mkdir output_dir && 17 mkdir output_dir &&
18 18
19 #for $i in $feature_hits: 19 #for $i in $feature_hits:
20 #set file_name = $i.file_name
21 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) 20 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
22 cat '$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' && 21 ln -s $i 'feature_hits_dir/$identifier' &&
23 #end for 22 #end for
24 23
25 python '$__tool_directory__/draw_features.py' 24 python '$__tool_directory__/draw_features.py'
26 --contigs 'contigs.fasta' 25 --contigs 'contigs.fasta'
27 --feature_hits_dir 'feature_hits_dir' 26 --feature_hits_dir 'feature_hits_dir'
58 </collection> 57 </collection>
59 </param> 58 </param>
60 <output_collection name="features_bed" type="list" count="1"> 59 <output_collection name="features_bed" type="list" count="1">
61 <element name="amr_cds.bed" ftype="bed"> 60 <element name="amr_cds.bed" ftype="bed">
62 <assert_contents> 61 <assert_contents>
63 <has_size value="129" delta="10"/> 62 <has_size value="610" delta="10"/>
64 </assert_contents> 63 </assert_contents>
65 </element> 64 </element>
66 </output_collection> 65 </output_collection>
67 <output_collection name="features_png" type="list" count="1"> 66 <output_collection name="features_png" type="list" count="1">
68 <element name="contig_1" ftype="png"> 67 <element name="contig_1" ftype="png">