Mercurial > repos > iuc > pipelign
annotate pipelign.xml @ 0:cd9d1eccda7e draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
author | iuc |
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date | Fri, 23 Aug 2019 14:47:13 -0400 |
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0
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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1 <?xml version="1.0"?> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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2 <tool id="pipelign" name="Automated multiple sequence" version="@VERSION@+galaxy0"> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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3 <description>alignment with pipelign</description> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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4 <macros> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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5 <token name="@VERSION@">0.2</token> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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6 </macros> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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7 <requirements> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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8 <requirement type="package" version="@VERSION@">pipelign</requirement> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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9 </requirements> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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10 <command detect_errors="exit_code"><![CDATA[ |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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11 pipelign |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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12 --outDir files |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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13 --clearExistingDirectory |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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14 --inFile '$inFile' |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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15 --outFile '$outFile' |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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16 --lenThr $lenThr |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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17 --alphabet $alphabet |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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18 --simPer $simPer |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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19 --merge $merge |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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20 --thread \${GALAXY_SLOTS:-1} |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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21 --mIterateLong $mIterateLong |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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22 --mIterateMerge $mIterateMerge |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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23 --ambigPer $ambigPer |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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24 $keepOrphans $keepBadSeqs $excludeClusters |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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25 ]]></command> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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26 <inputs> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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27 <param argument="--inFile" type="data" format="fasta" label="Input sequence file" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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28 <param argument="--lenThr" type="float" value="0.7" min="0" max="1" label="Length threshold for full sequences" help="Default: 0.7" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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29 <param argument="--alphabet" type="select" label="Alphabet for input sequences"> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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30 <option value="dna">DNA</option> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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31 <option value="rna">RNA</option> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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32 <option value="aa">Amino Acids</option> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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33 </param> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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34 <param argument="--keepOrphans" type="boolean" truevalue="--keepOrphans" falsevalue="" label="Add fragments without clusters" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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35 <param argument="--keepBadSeqs" type="boolean" truevalue="--keepBadSeqs" falsevalue="" label="Add long sequences with too many ambiguous residues" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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36 <param argument="--simPer" type="float" value="0.8" min="0" max="1" label="Percent sequence similarity for clustering" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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37 <param argument="--merge" type="select" label="Merge strategy"> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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38 <option value="P">Parallel</option> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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39 <option value="C">Consensus</option> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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40 </param> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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41 <param argument="--mIterateLong" type="integer" value="1" min="1" label="Number of iterations to refine long alignments" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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42 <param argument="--mIterateMerge" type="integer" value="1" min="1" label="Number of iterations to refine merged alignment" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
changeset
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43 <param argument="--ambigPer" type="float" value="0.1" min="0" max="1" label="Percent sequence similarity for clustering" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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44 <param argument="--excludeClusters" type="boolean" truevalue="--excludeClusters" falsevalue="" label="Exclude clusters from final alignment" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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45 </inputs> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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46 <outputs> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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47 <data name="outFile" format="fasta" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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48 </outputs> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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49 <tests> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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50 <test> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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51 <param name="inFile" value="pipelign-in1.fasta" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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52 <output name="outFile"> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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53 <assert_contents> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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54 <has_line line=">K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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55 <has_line line=">K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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56 <has_line line=">K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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57 <has_line line=">K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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58 <has_line line=">K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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59 <has_line line=">K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
diff
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60 <has_line line=">K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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61 <has_line line=">K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1" /> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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62 </assert_contents> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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63 </output> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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64 </test> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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65 </tests> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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66 <help><![CDATA[ |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
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67 .. class:: infomark |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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68 |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
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69 **What it does** |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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70 |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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71 ------------------- |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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72 |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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73 A pipeline for automated multiple sequence alignment, particularly of viral sequences. |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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74 |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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75 ]]> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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76 </help> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
iuc
parents:
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77 <citations> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
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78 <citation type="bibtex"> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
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79 @UNPUBLISHED{spond, |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
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80 author = "A.S.Md.M. Hossain, S.D.W.Frost", |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
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81 title = "Pipelign: an alignment pipeline for viral sequences.", |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
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82 year = "2019", |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
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83 note = "https://github.com/asmmhossain/pipelign/", |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
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84 url = "https://github.com/asmmhossain/pipelign/"} |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
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85 </citation> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
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86 </citations> |
cd9d1eccda7e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"
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87 </tool> |