Mercurial > repos > greg > call_insertions
comparison call_insertions.xml @ 0:5626dc2d0ef2 draft default tip
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author | greg |
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date | Tue, 07 Feb 2023 21:43:42 +0000 |
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-1:000000000000 | 0:5626dc2d0ef2 |
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1 <tool id="call_insertions" name="PIMA: call insertions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
2 <description></description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 grep AvgIdentity '$dnadiff_report' | head -1 | awk '{print $2}' > reference_identity && | |
9 grep AlignedBases '$dnadiff_report' | head -1 | awk '{sub(/\(.*/, "", $2); print $2 * 100}' > reference_aligned_bases && | |
10 cat '$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' && | |
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' | |
12 ]]></command> | |
13 <inputs> | |
14 <param argument="--dnadiff_report" type="data" format="txt" label="DNAdiff report file"/> | |
15 <param argument="--dnadiff_1coords" type="data" format="tabular" label="DNAdiff 1coords file"/> | |
16 <param argument="--reference_identity_min" type="float" value="98.0" min="0" label="Minimum reference identity"/> | |
17 <param argument="--reference_alignment_min" type="float" value="97.0" min="0" label="Minimum reference alignment"/> | |
18 </inputs> | |
19 <outputs> | |
20 <data name="reference_aligned" format="bed" label="${tool.name} on ${on_string} (reference alignment)"/> | |
21 <data name="genome_aligned" format="bed" label="${tool.name} on ${on_string} (genome alignment)"/> | |
22 </outputs> | |
23 <tests> | |
24 <test> | |
25 <param name="dnadiff_report" value="dnadiff_report.txt" ftype="txt"/> | |
26 <param name="dnadiff_1coords" value="dnadiff_1coords.tsv" ftype="tsv"/> | |
27 <output name="reference_aligned" value="reference_aligned.bed" ftype="bed"/> | |
28 <output name="genome_aligned" value="genome_aligned.bed" ftype="bed"/> | |
29 </test> | |
30 </tests> | |
31 <help> | |
32 **What it does** | |
33 | |
34 Accepts DNAdiff report and DNAdiff 1coords files and extracts the aligned regions of the two genomes, producing reference alignment | |
35 and genome alignment BED files. | |
36 </help> | |
37 <expand macro="citations"/> | |
38 </tool> | |
39 |