Mercurial > repos > abims-sbr > pogs
annotate POGs.xml @ 0:b2895c835ea8 draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
| author | abims-sbr |
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| date | Thu, 13 Apr 2017 05:46:54 -0400 |
| parents | |
| children | be2128ad0030 |
| rev | line source |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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1 <tool name="POGs" id="POGs" version="1.0"> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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2 |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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3 <description> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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4 Find orthologous groups |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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5 </description> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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6 |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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7 <macros> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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8 <import>macros.xml</import> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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9 </macros> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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10 |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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11 <requirements> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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12 <expand macro="python_required" /> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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13 <!-- <requirement type="package" version="1.3.1">samtools</requirement> --> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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14 </requirements> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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15 |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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16 <command> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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17 <![CDATA[ |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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18 python $__tool_directory__/scripts/S01_get_locus_ortholog_part1.py ${zip_file} |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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19 > ${output} && |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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20 |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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21 python $__tool_directory__/scripts/S02_get_locus_ortholog_part2.py ${zip} |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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22 >> ${output}; |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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23 ]]> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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24 </command> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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25 |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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26 <inputs> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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27 <param name="zip" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file" help="Contains the files filter after the tool oase" /> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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28 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file " help="Contains homologous sequences in PROTEIC format, ONLY A ZIP FILE" /> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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29 </inputs> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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30 |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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31 <outputs> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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32 <data format="txt" name="output" label="POGs" /> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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33 <data format="no_unzip.zip" name="output_zip" label="POGs_locus_orthologs_unaligned" from_work_dir="POGs_locus_orthologs_unaligned.zip" /> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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parents:
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34 </outputs> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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35 |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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parents:
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36 <tests> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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37 <test> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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38 <param name="zip" ftype="zip" value="filter_oase_results_for_pogs.zip" /> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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39 <param name="zip_file" ftype="zip" value="test_03_output_Pairwise_PROT_inputPOGS.zip" /> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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40 <output name="output" value="test_03.out" /> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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41 </test> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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42 </tests> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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43 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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44 <help> |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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45 ============ |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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46 What it does |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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47 ============ |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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48 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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49 | This tool takes a zip archive containing nucleic fasta sequence files and a zip archive containing a file per pairwise with the homologous sequences (in proteic format). It searches for orthologous sequences. |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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50 | There are 2 outputs. |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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51 | |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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52 | The script was written by **Eric Fontanillas**. |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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53 | The wrapper was written by **Julie Baffard**. |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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54 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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55 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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56 -------- |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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57 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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58 ====== |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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59 Inputs |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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60 ====== |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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61 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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62 option **Select a zip file containing the input files** : |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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63 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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64 | the input zip file must have the extension .ort.zip |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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65 | At the beginning, when you upload your input, you have to change the extension .zip to .ort.zip |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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66 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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67 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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68 -------- |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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69 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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70 ======= |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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71 Outputs |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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72 ======= |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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73 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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74 This tool, produces the following files : |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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75 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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76 **POGs** : |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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77 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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78 | is the general output. It gives different informations : number of locus, each locus, ... |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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79 | it gives for example, all the locus containing 2 species : |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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80 | 2_sp : [[name_of_sequence,name_of_squence],...,[name_of_sequence, name_of_sequence]] |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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81 | it's the same for locus containing 3 species, 4 species, ... |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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82 | |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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83 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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84 **POGs_locus_orthologs_unaligned** : |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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85 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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86 | is the output (in zip format) which contains each locus. |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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87 | one file corresponding to one locus. |
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88 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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89 the sequences of each locus are in nucleic format. |
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90 |
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91 .. class:: warningmark |
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92 |
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93 The zip output has to be downloaded (and extracts the files with a file archiver software), you cannot visualize them with the "eye icon" through the interface. |
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94 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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95 -------- |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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96 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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97 =============== |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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98 Working Example |
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99 =============== |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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100 |
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101 --------------- |
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102 The input files |
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103 --------------- |
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104 |
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105 |
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106 | 3 files with 200 nucleic sequences each : Ac.fasta Ap.fasta Pf.fasta. |
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107 | a zip file with 3 files containing the homologous sequences of each pairwise. |
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108 | |
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109 |
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110 ---------------- |
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111 The output files |
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112 ---------------- |
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113 |
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114 **POGs** |
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115 |
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116 | Number of locus = 56 |
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117 | |
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118 | NUMBER OF REMAINING LOCUS AFTER 1RST TREATMENT [INTRA LOCUS] = 55 |
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119 |
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120 NUMBER OF REMAINING LOCUS AFTER 2ND TREATMENT [INTER LOCUS] = 53 |
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121 |
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122 | 2_sp : [['>Ac111_5/5_0.688_714', '>Ap70_3/8_0.688_1127'], ['>Ac99_4/4_0.571_7188', '>Ap74_6/9_0.406_9467'], ['>Ac200_7/8_0.694_1836', '>Ap53_1/1_1.000_938'], |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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123 | ['>Ac181_6/10_0.432_8240', '>Ap103_3/10_0.420_9102'], ['>Ac4_2/2_1.000_230', '>Ap27_4/6_0.556_8404'], ['>Ac189_9/10_0.839_7194', '>Ap97_3/4_0.452_3023'], |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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124 | ['>Ac145_4/5_0.538_1334', '>Ap168_5/6_0.824_2007'], ['>Ac178_1/1_1.000_758', '>Ap202_3/3_0.905_2656'], ['>Ac100_1/2_1.000_2338', '>Ap77_5/8_0.405_866'], |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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125 | ['>Ac86_3/5_0.780_4131', '>Ap41_5/10_0.362_5218'], ['>Ac140_4/4_0.886_637', '>Ap62_1/3_0.667_482'], ['>Ac144_1/1_1.000_4240', '>Ap162_1/1_1.000_4925'], |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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126 | ['>Ac34_3/8_0.548_7600', '>Ap144_6/10_0.690_9671'], ['>Ac187_1/7_0.618_12870', '>Ap73_7/10_0.343_2424'], ['>Ac120_1/1_1.000_522', '>Pf74_1/1_1.000_506'], |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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127 | ['>Ac108_2/10_0.395_1982', '>Pf26_1/1_1.000_1717'], ['>Ac88_4/4_0.833_906', '>Pf102_1/1_1.000_1876'], ['>Ac202_1/1_1.000_247', '>Pf36_2/3_0.800_1482'], |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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128 | ['>Ac121_1/1_1.000_659', '>Pf7_1/1_1.000_2255'], ['>Ac129_1/5_0.636_1798', '>Pf100_2/4_0.625_1698'], ['>Ac172_1/1_1.000_348', '>Pf118_1/1_1.000_1108'], |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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129 | ['>Ac66_3/4_0.462_1465', '>Pf229_1/1_1.000_1541'], ['>Ac47_2/7_0.412_1703', '>Pf1_1/2_1.000_1890'], ['>Ac171_3/3_0.926_338', '>Pf4_1/1_1.000_1337'], |
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130 | ['>Ac194_1/5_0.875_275', '>Pf106_1/2_1.000_994'], ['>Ap2_1/2_1.000_264', '>Pf19_1/1_1.000_1879'], ['>Ap35_1/1_1.000_2505', '>Pf70_1/1_1.000_1462'], |
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131 | ['>Ap116_3/4_0.600_1380', '>Pf78_1/1_1.000_1409'], ['>Ap193_8/9_0.614_1707', '>Pf21_1/8_0.630_1314'], ['>Ap51_1/2_1.000_4292', '>Pf164_1/1_1.000_1021'], |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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132 | ['>Ap170_1/3_0.778_1303', '>Pf87_2/4_0.700_773'], ['>Ap186_6/10_0.521_4506', '>Pf72_1/1_1.000_2344'],['>Ap114_1/2_1.000_859', '>Pf192_1/1_1.000_957'], |
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133 | ['>Ap65_3/7_0.278_914', '>Pf94_1/1_1.000_1135'], ['>Ap164_4/5_0.560_219', '>Pf163_4/4_0.556_866'], ['>Ap199_3/3_0.846_958', '>Pf58_1/3_0.667_1387'], |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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134 | ['>Ap183_7/8_0.326_2702', '>Pf166_1/2_1.000_2528'], ['>Ap89_3/3_0.905_211', '>Pf3_4/4_0.688_1776'], ['>Ap34_1/1_1.000_2528', '>Pf76_3/3_0.500_1714'], |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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135 | ['>Ap16_1/3_0.714_734', '>Pf139_1/1_1.000_508'], ['>Ap119_9/9_0.595_3402', '>Pf108_1/1_1.000_1932'], ['>Ap120_5/10_0.223_8988', '>Pf57_1/1_1.000_2461'], |
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136 | ['>Ap43_1/3_0.778_644', '>Pf2_1/1_1.000_582']] |
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137 | |
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138 | 3_sp : [['>Ac112_1/2_1.000_2711', '>Ap90_7/10_0.397_2604', '>Pf79_1/1_1.000_4515'], ['>Ac148_1/1_1.000_596', '>Ap32_1/1_1.000_664', '>Pf180_1/2_1.000_2336'], |
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139 | ['>Ac177_1/2_1.000_1664', '>Ap147_1/2_1.000_1728', '>Pf178_1/1_1.000_1671'], ['>Ac124_3/3_0.375_1572', '>Ap177_1/3_0.667_625', '>Pf115_1/1_1.000_557'], |
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140 | ['>Ac53_3/4_0.375_999', '>Ap40_1/1_1.000_1011', '>Pf201_1/1_1.000_908'], ['>Ac65_1/2_0.812_306', '>Ap59_7/10_0.227_2379', '>Pf32_3/3_0.818_1014'], |
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141 | ['>Ac190_7/10_0.319_2573', '>Ap166_7/10_0.279_1859', '>Pf13_7/7_0.514_1779'], ['>Ac1_1/2_1.000_6683', '>Ap55_1/9_1.000_267', '>Pf6_1/2_1.000_3095'], |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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142 | ['>Ac91_2/2_0.696_4298', '>Ap75_5/5_0.810_1434', '>Pf69_1/1_1.000_1712'], ['>Ac29_6/9_0.639_3877', '>Ap124_4/8_0.267_1557', '>Pf18_43/95_1.000_2422']] |
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143 | |
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144 | |
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145 |
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146 **POGs_locus_orthologs_unaligned** |
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147 |
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148 | Save as *Galaxy{number}-[POGs_locus_orthologs_unaligned].zip* |
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149 | If you unzip the file, a number of files are extracted (depends on the number of locus) : locus{nb}_sp{nb_of_species}.fasta |
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150 | For example the file locus1_sp2.fasta : |
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151 | |
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152 | >Ac111_5/5_0.688_714 |
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153 | ATCCGGAATGACCTTCGGCGGAGCCAGACACGCTGCTGACATCCGGGCAGACGACATGCACCAGTCGAGTGCCGGAGTGATCAACCTGCAGATGGGCACCAACCAGGGAGCGACCCAAAGCGGCATGTCCATGGGAGGTCGTCGGGACATCAGTT |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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154 | AAAAGGGGGCGTTTCACATTTCGTCCAGGATTCTGGAACTGTCCGGATCACAGTGCCACTATCCGTGTTTGATCAATTCAAATCGCTAACTTAAAACGGCCTGTATATAGCTACACTTCATTAACAAAACATTTAGCAATGCCTTATTCTATAACAAGCTACTG |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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155 | TATCAGCATAATTATGACTTTCCAATACTTCTTTTTAGCAGATCTTTAATTCTTATTCTTTCTTGTTCGCTGCGTACACTTTTTAACAATAACGTAACATTCTGTATTCATTGATCTATGCAGTTTTATATATTTGGAGTACTTGTTAACTTTAAATATCTGTTGAATGTTA |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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156 | CTTTTGAAATGTTGTCTCTAAATATTCGCATTAATTAACGTCGTGTTCTTCATCACAGTCAATGTTAACAGCAGCCATAGCACTTTAATTTATTTTGTTACTTTGTTTATTACGCATGTTTCTAAAATTATTCTTTCATTAAAGCTATTGTTCGTTGCACGTTGATAAGT |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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157 |
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158 ATTGTTGTTGCGTTTCGTGATTCTATACATAATATATTCAAAACAATTAAAAA |
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159 |
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160 | >Ap70_3/8_0.688_1127 |
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161 | GCAGGCCGGACCAACAAGGGCGCTAGCCAATCCGGAATGACCTTCGGCGGAGCCAGACACGCTGCTGACATCCGGGCAGACGACATGCACCAGTCGAGTGCCGGAGTGATCAACCTACAGATGGGCACCAACCAGGGGGCGTCCCAAAGCGGCA |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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162 | TGTCCATGGGAGGCCGTCGGGACATCAGTTAAAAGGGGGCGTTTCACATTTCGTGCCAGCGTTCTGGAACTGTCCGGATCACAGTGCCACCATCCGAGTGTTTGGTCAATTCAAATCGCTAACTTAAAACGGCCTGTATATAGCTACATTTCATTAACAAA |
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b2895c835ea8
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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163 | ACATTTAGCGATGCCTTGTTCTATAACAAATTATTGTATCAGCATAATTATTACTTTCCAGTACTTCTTTATAGCAGATCTTTAATTATTGTTCTTTCTTGTTCGCTGCGTACTTTTTAAAAAGAATACAACATTCTGTATTCATTGATCTATGCAGTTTTATATATTTGGA |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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164 |
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165 GTACTTGTTAACTTTAAATATATGTTAAATGTTACTTTTGAAATGTTGTCTCTAAATATTCGCATTAATTAACGTCGTGCTCTTCATCACAGTCAAAGTTAACATTTAACATATATTTAAAGTTAACAAGTACTCCAAATATATAAAACTGCATAGATCAATGAATACAGA |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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166 ATGTTGTATTCTTTTTAAAAAGTACGCAGCGAACAAGAAAGAACAATAATTAAAGATCTGCTATAAAGAAGTACTGGAAAGTAATAATTATGCTGATACAATAATTTGTTATAGAACAAGGCATCGCTAAATGTTTTGTTAATGAAATGTAGCTATATACAGGCCGTTT |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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167 TAAGTTAGCGATTTGAATTGACCAAACACTCGGATGGTGGCACTGTGATCCGGACAGTTCCAGAACGCTGGCACGAAATGTGAAACGCCCCCTTTTAACTGATGTCCCGACGGCCTCCCATGGACATGCCGCTTTGGGACGCCCCCTGGTTGGTGCCCA |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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168 TCTGTAGGTTGATCACTCCGGCACTCGACTGGTGCATGTCGTCTGCCCGGATGTCAGCAGCGTGTCTGGCTCCGCCGAAGGTCATTCCGGATTGGCTAGCGCCCTTGTTGGATCCAGCTTGCAGACCGATACGGCCTGGCC |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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169 |
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170 | |
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171 | An other example, the file locus_3_sp_5.fasta |
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172 | |
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173 |
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174 >Ac53_3/4_0.375_999 |
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175 CCGATCTTGTCTGGTGTTTTGCTGCCCCCTAGCGAGTGACGACAAACTCGTTGGTACCTTGCTTAGCGCGATAGAAGGGTTGAACATGTTGGCTGCTGGGCTAAGAACTCTAAAAAGCCTTGCCCCTCGGGGTTGCGTAGCGTGGTCGTGTACTTCGGT |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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176 GCATGCCAAGCATACCCTACCAGACTTACCATATGATTACAATGCCCTGGAGCCACACATCAGTGCTGAAATCATGCTGCTGCATCACACCAAGCATCACCAGACGTATGTCAACAACCTGAATGTTGCAGAGGAGAAGTTTCATGAGGCTACAGAGAAA |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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177 GGTGATGTAACCACAGCAGTATCACTGATGCCAGCCCTAAGATTTAATGGTGGTGGACACATCAACCATACTATATTTTGGAAGAACATGTCACCAAATGGTGGTGGAGAGCCATCTGGCGAACTGATGGAGGCCATCAAACGTGACTTTGGCTCATTTGAA |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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178 AACATGAAGAACATGTTGAGTACATCAACCACTGCAGTGCAAGGCTCTGGCTGGGGATGGCTTGGGTACAATAAAAAGATGAAGAAACTAGAAATTGCCACCTGTGCCAACCAAGATCCATTAGAGGGCACTACAGGTCTCGTCCCGTTGTTTGGCATAG |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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179 ATGTCTGGGAACATGCCTATTACTTGCAGTACAAGAATGTTCGTCCAGACTATGTAAAGGCTATTTGGAATGTGGCCAACTGGGATGACATCATGGAACGTTACAACAATGCCAGAAAATAAACTGTTAAACAAATAATTAATATATTAATGTGTTGCAATTTTTG |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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180 TCAATTGGTACATACACAATTTTGTTCATAAAGAAAATTGTGATTACTTTCTGGCAACTAGTTCCCAGTGAATACAGCAATTGTTCTGCCAAGGATGCATTTGGATTGAGAAGGCACCCAGAATGGGTTATCCGTGAATGTCTATTGGAATGTGGCACCATACG |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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181 ATGTTTACTGTATTAGTTACAATTAAAA |
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182 |
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183 | >Ap40_1/1_1.000_1011 |
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184 | CTGATGTGTGGCCCCCTAGCGAGTGAAGACAAACTCGATAGCACCCAGACAGTTCTGTTGGTTAGATAAAAGGGAGAAACATGCTGGCTGCTGGGCTAAGAACTCTAAAAAGCCTTGCTCCTCGTGGTGGTCTAGCTTGGTCTTGTACCTCGGTACATGC |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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185 | CAAACACACACTGCCAGACTTGCCGTATGATTATAATGCTCTGGAGCCACACATCAGTGCTGAAATCATGTTGCTGCATCACACAAAACATCACCAGACGTATGTGAACAACCTGAATATTGCAGAGGAGAAGTTTCATGAGGCTACCGAGAAAGGCGATG |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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186 | TGACCACAGCAGTATCACTGATGCCAGCCCTAAGATTTAATGGTGGTGGACATATCAACCATACTATATTTTGGAAGAACATGTCACCAAATGGTGGTGGAGAACCATCTGGCGAACTGATGGAGGCCATCAAACGTGACTTTGGTTCATTTGAAAACATGA |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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187 | AGAACATGCTGAGTACAGCAACCACTGCAGTACAAGGCTCTGGCTGGGGATGGCTTGGGTACAATAAAAAGATGAAGAAACTAGAAATTGCCACCTGTGCCAACCAAGATCCATTAGAGGGCACTACAGGTCTTGTCCCACTGTTTGGTATCGATGTCTG |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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188 | GGAACATGCCTATTATTTACAGTACAAGAATGTTCGTCCAGACTATGTAAAGGCTATTTGGAATGTGGCTAACTGGGATGATATCATGGAGCGTTACAACAATGCCAGAAAATAAACTTAAATACATCATTATTTAGTTAATGTGCGACTTTTGTTTGTTAATCAGT |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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189 | TCACACACCATTCTATTCACAAAGAAAATGGTGTATTTGCTTTCTGTTCAACTGGTTCCCGGTGAATACAGCAGTTGTTCTGCCAAGGATGTATTTGGATTGAGAAGGCACCAAGAATGGGCTGTCACTGAATGTCAATTGGAATGTAGCCTCAATGTTTACT |
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190 |
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191 GTATTACCTACAATTAAAATGATTATGATATAACCAAG |
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192 |
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193 | >Pf201_1/1_1.000_908 |
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194 | CTTCTGGAACGATGTTGGCTGGGTATAGAACTTTGGCGAGGGTTATCCCACGTGGTGTCAGCTCCGCTTGGGCAAGTACAATAGTACATAACAAGCACACCTTGCCAGATTTACCATATGATTATAATGCCTTGGAACCACACATCAGTGCTGAAATAATGC |
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195 |
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196 TCCTTCATCATACAAAGCATCACCAGACATATGTGAACAATCTGAATGTAGCTGAAGAAAAGTTTCATGAAGCCACGGAGAAAGGTGATGTCACTACAGCTGTGTCGCTAATGCCAGCACTAAGATTTAATGGCGGAGGACACATCAATCACACCATTTTCT |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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197 GGAAGAACATGTCTCCTAATGGCGGAGGAGAGCCTTCTGGCGAGTTGATGGAAGCCATTAAACGTGATTTTGGTTCATTTGAGAATATGAAAAACATGTTAAGTACAGCTACAACAGCTGTCCAAGGATCTGGCTGGGGATGGCTTGGTTATAACAAAAAG |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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198 ATGAAAAAGCTCGAGATAGCCACTTGTGCCAACCAGGATCCACTGGAAGGAACAACAGGATTAATTCCACTGTTTGGTATTGACGTCTGGGAGCATGCTTACTATCTGCAATATAAAAATGTACGTCCAGATTATGTTAAAGCTATCTGGAATGTGGCCAACT |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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199 GGGATGATATTACAGAGCGCTACAACAATGCGAAGAAATAGATTTGCTGGGACATATGAATAGTGCTTGGCAGAGCCTAATGTTGTGTTTATTTCTGTGTTTCTTATCAATCAGTTGATGTATTAGCCCGGTGTATTGACATGAAGAATTGGACAATGATTTCAAA |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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200 TACATTTGAACAATAAATGTATCATGATCAAGCATTATTTTGTTAGTTGTCTCCTCCACTGAGAAGACCAAGTTTAATAAACAACAAACACAGA |
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201 </help> |
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202 |
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203 <expand macro="citations" /> |
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204 |
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205 </tool> |