Mercurial > repos > dfornika > match_plasmid_to_reference

annotate match_plasmid_to_reference.xml @ 2:faf74a1bbd5f draft

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"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
author dfornika
date Wed, 06 Nov 2019 01:08:56 -0500
parents 3616b6eda1da
children d56b4f743779
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8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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1 <tool id="match_plasmid_to_reference" name="Match plasmid to reference" version="0.1.0">
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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2 <description>Pick plasmids containing specific genes</description>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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3 <requirements>
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4 </requirements>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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5 <command detect_errors="exit_code"><![CDATA[
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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6 '$__tool_directory__/match_plasmid_to_reference.py'
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7 --plasmid '${plasmid}'
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8 --reference_plasmids
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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9 #for $reference_plasmid in $reference_plasmids:
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10 '${reference_plasmid}'
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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11 #end for
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faf74a1bbd5f "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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12 --mob_typer_report '${concatenated_mob_typer_reports}'
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13 --outdir outdir
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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14 ]]></command>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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15 <inputs>
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16 <param name="plasmid" type="data" format="fasta" />
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17 <param name="reference_plasmids" type="data_collection" collection_type="list" format="genbank" />
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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18 <param name="concatenated_mob_typer_reports" type="data" format="tabular" />
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19 </inputs>
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20 <outputs>
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21 <data name="output_plasmid" from_work_dir="outdir/plasmid.fasta" />
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22 <data name="matched_reference_plasmid" from_work_dir="outdir/reference_plasmid.gbk" />
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23 <data name="matched_mob_typer_record" from_work_dir="outdir/mob_typer_record.tsv" />
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="plasmid" value="SRR9113487_plasmid_2719.fasta"/>
3616b6eda1da "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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28 <param name="reference_plasmids">
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29 <collection type="list">
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30 <element name="CP008719" value="CP008719.gbk" ftype="genbank" />
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31 <element name="JQ739157" value="JQ739157.gbk" ftype="genbank" />
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32 </collection>
3616b6eda1da "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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33 </param>
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34 <param name="concatenated_mob_typer_reports" value="concatenated_mob_typer_reports.tsv" />
faf74a1bbd5f "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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35 <output name="output_plasmid" file="outdir/plasmid.fasta" />
faf74a1bbd5f "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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36 <output name="matched_reference_plasmid" file="outdir/reference_plasmid.gbk" />
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37 <output name="matched_mob_typer_record" file="outdir/mob_typer_record.tsv" />
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41 ]]></help>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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42 <citations>
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43 </citations>
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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44 </tool>