Mercurial > repos > greg > call_insertions
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author | greg |
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date | Tue, 07 Feb 2023 21:43:42 +0000 |
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<tool id="call_insertions" name="PIMA: call insertions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ grep AvgIdentity '$dnadiff_report' | head -1 | awk '{print $2}' > reference_identity && grep AlignedBases '$dnadiff_report' | head -1 | awk '{sub(/\(.*/, "", $2); print $2 * 100}' > reference_aligned_bases && cat '$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' && 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' ]]></command> <inputs> <param argument="--dnadiff_report" type="data" format="txt" label="DNAdiff report file"/> <param argument="--dnadiff_1coords" type="data" format="tabular" label="DNAdiff 1coords file"/> <param argument="--reference_identity_min" type="float" value="98.0" min="0" label="Minimum reference identity"/> <param argument="--reference_alignment_min" type="float" value="97.0" min="0" label="Minimum reference alignment"/> </inputs> <outputs> <data name="reference_aligned" format="bed" label="${tool.name} on ${on_string} (reference alignment)"/> <data name="genome_aligned" format="bed" label="${tool.name} on ${on_string} (genome alignment)"/> </outputs> <tests> <test> <param name="dnadiff_report" value="dnadiff_report.txt" ftype="txt"/> <param name="dnadiff_1coords" value="dnadiff_1coords.tsv" ftype="tsv"/> <output name="reference_aligned" value="reference_aligned.bed" ftype="bed"/> <output name="genome_aligned" value="genome_aligned.bed" ftype="bed"/> </test> </tests> <help> **What it does** Accepts DNAdiff report and DNAdiff 1coords files and extracts the aligned regions of the two genomes, producing reference alignment and genome alignment BED files. </help> <expand macro="citations"/> </tool>