comparison draw_features.xml @ 6:d5a5d145cfce draft

Uploaded

5:c318e520dca1

mkdir feature_hits_dir &&
mkdir output_dir &&

#for $i in $feature_hits:
    #set file_name = $i.file_name
    #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
    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' &&
#end for

python '$__tool_directory__/draw_features.py'
--contigs 'contigs.fasta'
--feature_hits_dir 'feature_hits_dir'

                </collection>
            </param>
            <output_collection name="features_bed" type="list" count="1">
                <element name="amr_cds.bed" ftype="bed">
                    <assert_contents>
                        <has_size value="129" delta="10"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="features_png" type="list" count="1">
                <element name="contig_1" ftype="png">

6:d5a5d145cfce

mkdir feature_hits_dir &&
mkdir output_dir &&

#for $i in $feature_hits:
    #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
    ln -s $i 'feature_hits_dir/$identifier' &&
#end for

python '$__tool_directory__/draw_features.py'
--contigs 'contigs.fasta'
--feature_hits_dir 'feature_hits_dir'

                </collection>
            </param>
            <output_collection name="features_bed" type="list" count="1">
                <element name="amr_cds.bed" ftype="bed">
                    <assert_contents>
                        <has_size value="610" delta="10"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="features_png" type="list" count="1">
                <element name="contig_1" ftype="png">