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1 <tool id="call_insertions" name="PIMA: call insertions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></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 grep AvgIdentity '$dnadiff_report' | head -1 | awk '{print $2}' > reference_identity &&
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9 grep AlignedBases '$dnadiff_report' | head -1 | awk '{sub(/\(.*/, "", $2); print $2 * 100}' > reference_aligned_bases &&
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10 cat '$dnadiff_1coords' | awk '{OFS = "\t"; if ($2 < $1){t = $2; $2 = $1; $1 = t} print $12,$1,$2}' | sort -k 1,1 -k 2,2n > '$reference_aligned' &&
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11 cat '$dnadiff_1coords' | awk '{OFS = "\t"; if ($4 < $3){t = $4; $4 = $3; $3 = t} print $13,$3,$4}' | sort -k 1,1 -k 2,2n > '$genome_aligned'
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12 ]]></command>
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13 <inputs>
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14 <param argument="--dnadiff_report" type="data" format="txt" label="DNAdiff report file"/>
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15 <param argument="--dnadiff_1coords" type="data" format="tabular" label="DNAdiff 1coords file"/>
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16 <param argument="--reference_identity_min" type="float" value="98.0" min="0" label="Minimum reference identity"/>
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17 <param argument="--reference_alignment_min" type="float" value="97.0" min="0" label="Minimum reference alignment"/>
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18 </inputs>
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19 <outputs>
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20 <data name="reference_aligned" format="bed" label="${tool.name} on ${on_string} (reference alignment)"/>
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21 <data name="genome_aligned" format="bed" label="${tool.name} on ${on_string} (genome alignment)"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="dnadiff_report" value="dnadiff_report.txt" ftype="txt"/>
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26 <param name="dnadiff_1coords" value="dnadiff_1coords.tsv" ftype="tsv"/>
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27 <output name="reference_aligned" value="reference_aligned.bed" ftype="bed"/>
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28 <output name="genome_aligned" value="genome_aligned.bed" ftype="bed"/>
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29 </test>
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30 </tests>
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31 <help>
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32 **What it does**
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33
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34 Accepts DNAdiff report and DNAdiff 1coords files and extracts the aligned regions of the two genomes, producing reference alignment
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35 and genome alignment BED files.
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36 </help>
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37 <expand macro="citations"/>
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38 </tool>
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39
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