annotate parse_mito_blast.xml @ 1:3c9ad4adf8d2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 9c9689f095805b738f654eed152900339753f6fd
author iuc
date Thu, 09 Jun 2022 18:07:51 +0000
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3c9ad4adf8d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 9c9689f095805b738f654eed152900339753f6fd
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1 <tool id="parse_mito_blast" name="Parse mitochondrial blast" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>overlap-conscious coverage calculation between scaffold-accession number pairs from blast output</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.0.2</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">parse_mito_blast</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 parse_mito_blast.py
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12 --blastout '$blastout'
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param argument="blastout" type="data" format="tabular" label="Tabular file generated by mito-blast"/>
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17 </inputs>
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18 <outputs>
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19 <data name="cov_report" format="tabular" from_work_dir="cov_report.tsv" label="${tool.name} on ${on_string}" />
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20 <data name="mito_scaff_names" format="txt" from_work_dir="mito_scaff_names.txt" label="contaminant scaffolds on ${on_string}" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="blastout" value="test_input.tsv" />
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25 <output name="cov_report" file="test_cov_report.tsv" ftype="tabular" />
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26 <output name="mito_scaff_names" file="test_mito_scaff_names.txt" ftype="txt" />
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30
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31 This tool is intended for use on the tabular (format 6) output generated by blastn. Depending on filtering choices, blast will output \
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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32 all the alignments it generates. Often there are multiple overlapping alignments for a unique query sequence-accession number pair. This tool \
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33 collects all alignments between a given pair and calculates the total coverage between the query and accession number, taking into /
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34 account overlapping alignments. Therefore a user can figure out how much of their query sequence actually identifies with a subject /
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35 sequence (acc #). This tool was designed for use in the VGP decontamination pipeline - in particular for deciding whether a scaffold /
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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36 (sequence) is of mitochondrial origin. Parse_mito_blast generates a synthesized, tabular report of coverage for scaffolds with >95% /
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37 identity to a mitochondrial subject sequence. To use, pass a format 6 blast output (--blastout) and the desired name of the report.
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38
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39 NOTE: This tool is currently designed for use with the blast headers 'qseqid','sseqid','qlen','length','qcovhsp','eval','qstart','qend','qcovs' /
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40 and will be sensitive to this order.
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41 ]]>
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42 </help>
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43 <citations>
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44 <citation type="bibtex">
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45 @misc{Danecek_et_al,
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46 Author={Danecek, P., Schiffels, S., Durbin, R.},
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47 title={Multiallelic calling model in bcftools (-m)},
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48 url = {http://samtools.github.io/bcftools/call-m.pdf},}
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49 </citation>
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50 </citations>
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51 </tool>