Mercurial > repos > dfornika > medaka_consensus

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
author dfornika
date Wed, 11 Mar 2020 03:34:28 +0000
parents eecb8c891134
children
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2bcf9108d73c "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
dfornika
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1 <tool id="medaka_consensus" name="medaka_consensus" version="@VERSION@+galaxy0" profile="19.01">
0
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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2 <description>Creates a consensus sequence from an alignment generated from nanopore sequence data</description>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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3 <macros>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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4 <token name="@VERSION@">0.11.5</token>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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5 </macros>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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6 <requirements>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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7 <requirement type="package" version="@VERSION@">medaka</requirement>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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8 <requirement type="package" version="1.9">samtools</requirement>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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9 </requirements>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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10 <version_command>medaka --version</version_command>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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11 <command detect_errors="exit_code"><![CDATA[
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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12 ln -s '${input_alignment}' alignment.bam &&
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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13 samtools index alignment.bam &&
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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14 medaka consensus
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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15 --threads \${GALAXY_SLOTS:-4}
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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16 --model '${model}'
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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17 alignment.bam
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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18 '${consensus_hdf}'
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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19 > '${log}'
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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20 ]]></command>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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21 <inputs>
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22 <param name="input_alignment" type="data" format="bam" label="Input Alignment"/>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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23 <param name="model" type="select" label="Model">
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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24 <option value="r941_min_fast_g303">r941_min_fast_g303</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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25 <option value="r941_min_high_g303" selected="True">r941_min_high_g303</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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26 <option value="r941_min_high_g330">r941_min_high_g330</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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27 <option value="r941_min_high_g344">r941_min_high_g344</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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28 <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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29 <option value="r941_prom_high_g303">r941_prom_high_g303</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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30 <option value="r941_prom_high_g344">r941_prom_high_g344</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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31 <option value="r941_prom_high_g330">r941_prom_high_g330</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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32 <option value="r10_min_high_g303">r10_min_high_g303</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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33 <option value="r10_min_high_g340">r10_min_high_g340</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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34 <option value="r103_min_high_g345">r103_min_high_g345</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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35 <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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36 <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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37 <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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38 </param>
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39 </inputs>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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40 <outputs>
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41 <data name="consensus_hdf" format="binary" label="${tool.name} on ${on_string}: consensus hdf" />
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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42 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt"/>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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43 </outputs>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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44 <tests>
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45 </tests>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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46 <help><![CDATA[
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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47 ]]></help>
eecb8c891134 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
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48 </tool>