Mercurial > repos > nml > quasitools
annotate dnds.xml @ 3:8dacd75ca8f1 draft
planemo upload for repository https://github.com/phac-nml/quasitools commit 68f3866f4ee926abe3ec1b936e5d6166f94fed6c
author | nml |
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date | Mon, 26 Mar 2018 15:38:19 -0400 |
parents | a7093d5933a8 |
children | 8cdffc02d2e2 |
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71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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1 <tool id="dnds" name="dNdS Report" version="0.1.0"> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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2 <description>Calculate the dN/dS value for each region in a bed file</description> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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3 <requirements> |
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a7093d5933a8
planemo upload for repository https://github.com/phac-nml/quasitools commit de4309426401ce655435d6867b05c3673b9d086f
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4 <requirement type="package" version="0.2.3">quasitools</requirement> |
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71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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5 </requirements> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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6 <command detect_errors="exit_code"><![CDATA[ |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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7 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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8 quasitools dnds $csv_file $ref_file $offset -o output.csv |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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9 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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10 ]]></command> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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11 <inputs> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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12 <param name="csv_file" type="data" format="csv" optional="false" label="CSV file" /> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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13 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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14 <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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15 </inputs> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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16 <outputs> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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17 <data format="csv" name="output" from_work_dir="output.csv" /> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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18 </outputs> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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19 <tests> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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20 <test> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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21 <param name="csv_file" value="mutant_types.csv" /> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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22 <param name="ref_file" value="hxb2_pol.fas" /> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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23 <output name="output" ftype="csv" > |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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24 <assert_contents> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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25 <has_text_matching expression="#gene,pn,ps,pn_sites,ps_sites,dn/ds"/> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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26 <has_text text="RT,0.0334,0.0111,1,1,3.0539" /> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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27 </assert_contents> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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28 </output> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
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29 </test> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
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30 </tests> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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31 <help><![CDATA[ |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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32 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
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33 dNdS Report |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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34 =================== |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
parents:
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35 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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36 Determines the dNdS ratio for each codon variant in a supplied csv file (codon variants). |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
nml
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37 |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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38 ]]></help> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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39 <citations> |
71976cfc9022
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
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40 </citations> |
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a7093d5933a8
planemo upload for repository https://github.com/phac-nml/quasitools commit de4309426401ce655435d6867b05c3673b9d086f
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41 </tool> |