Mercurial > repos > iuc > parse_mito_blast

annotate parse_mito_blast.xml @ 0:f172b1f77d6c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
author iuc
date Thu, 12 May 2022 10:45:45 +0000
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f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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1 <tool id="parse_mito_blast" name="Parse mitochondrial blast" version="@TOOL_VERSION@" profile="21.05">
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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2 <description>overlap-conscious coverage calculation between scaffold-accession number pairs from blast output</description>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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3 <macros>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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4 <token name="@TOOL_VERSION@">1.0.1</token>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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5 </macros>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">parse_mito_blast</requirement>
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8 </requirements>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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9 <command detect_errors="exit_code"><![CDATA[
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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10 parse_mito_blast.py
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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11 --blastout '$blastout'
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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12 ]]>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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13 </command>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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14 <inputs>
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15 <param argument="blastout" type="data" format="tabular" label="Tabular file generated by mito-blast"/>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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16 </inputs>
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17 <outputs>
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18 <data name="cov_report" format="tabular" from_work_dir="cov_report.tsv" label="${tool.name} on ${on_string}" />
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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19 <data name="mito_scaff_names" format="txt" from_work_dir="mito_scaff_names.txt" label="contaminant scaffolds on ${on_string}" />
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20 </outputs>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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21 <tests>
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22 <test>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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23 <param name="blastout" value="test_input.tsv" />
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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24 <output name="cov_report" file="test_cov_report.tsv" ftype="tabular" />
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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25 <output name="mito_scaff_names" file="test_mito_scaff_names.txt" ftype="txt" />
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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26 </test>
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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27 </tests>
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28 <help><![CDATA[
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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29
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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30 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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31 all the alignments it generates. Often there are multiple overlapping alignments for a unique query sequence-accession number pair. This tool \
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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32 collects all alignments between a given pair and calculates the total coverage between the query and accession number, taking into /
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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33 account overlapping alignments. Therefore a user can figure out how much of their query sequence actually identifies with a subject /
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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34 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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35 (sequence) is of mitochondrial origin. Parse_mito_blast generates a synthesized, tabular report of coverage for scaffolds with >95% /
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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36 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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37
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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38 NOTE: This tool is currently designed for use with the blast headers 'qseqid','sseqid','qlen','length','qcovhsp','eval','qstart','qend','qcovs' /
f172b1f77d6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
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39 and will be sensitive to this order.
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40 ]]>
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41 </help>
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42 <citations>
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43 <citation type="bibtex">
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44 @misc{Danecek_et_al,
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45 Author={Danecek, P., Schiffels, S., Durbin, R.},
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46 title={Multiallelic calling model in bcftools (-m)},
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47 url = {http://samtools.github.io/bcftools/call-m.pdf},}
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48 </citation>
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49 </citations>
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50 </tool>