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annotate dnds.xml @ 0:1f1214983a1c draft default tip

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planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:05:57 +0000
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1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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1 <tool id="dnds" name="dNdS Report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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2 <description>Calculate the dN/dS value for each region in a bed file</description>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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3 <macros>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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4 <import>macros.xml</import>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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5 </macros>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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6 <expand macro="requirements"/>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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7 <command detect_errors="exit_code"><![CDATA[
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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8
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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9 quasitools dnds $csv_file $ref_file $offset -o output.csv
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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11 ]]></command>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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12 <inputs>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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13 <param name="csv_file" type="data" format="csv" optional="false" label="CSV file" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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14 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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15 <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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16 </inputs>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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17 <outputs>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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18 <data format="csv" name="output" from_work_dir="output.csv" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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19 </outputs>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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20 <tests>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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21 <test>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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22 <param name="csv_file" value="mutant_types.csv" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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23 <param name="ref_file" value="hxb2_pol.fas" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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24 <output name="output" ftype="csv" >
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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25 <assert_contents>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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26 <has_text_matching expression="#gene,pn,ps,pn_sites,ps_sites,dn/ds"/>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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27 <has_text text="RT,0.0334,0.0111,1,1,3.0539" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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28 </assert_contents>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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29 </output>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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30 </test>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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31 </tests>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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32 <help><![CDATA[
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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34 dNdS Report
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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35 ===================
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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37 Determines the dNdS ratio for each codon variant in a supplied csv file (codon variants).
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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38
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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39 ]]></help>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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40 <expand macro="citations" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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41 </tool>