Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_macros.xml @ 11:4c4a0da938ff draft
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
Supports $GALAXY_SLOTS.
Includes more tests and heavy use of macros.
author | peterjc |
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date | Thu, 05 Dec 2013 06:55:59 -0500 |
parents | |
children | 623f727cdff1 |
rev | line source |
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11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
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1 <macros> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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2 <xml name="output_change_format"> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
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3 <change_format> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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4 <when input="out_format" value="0" format="txt"/> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
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5 <when input="out_format" value="0 -html" format="html"/> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
|
6 <when input="out_format" value="2" format="txt"/> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
|
7 <when input="out_format" value="2 -html" format="html"/> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
|
8 <when input="out_format" value="4" format="txt"/> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
|
9 <when input="out_format" value="4 -html" format="html"/> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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10 <when input="out_format" value="5" format="blastxml"/> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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11 </change_format> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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12 </xml> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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13 <xml name="input_out_format"> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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14 <param name="out_format" type="select" label="Output format"> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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15 <option value="6">Tabular (standard 12 columns)</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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16 <option value="ext" selected="True">Tabular (extended 25 columns)</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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17 <option value="5">BLAST XML</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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18 <option value="0">Pairwise text</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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19 <option value="0 -html">Pairwise HTML</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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20 <option value="2">Query-anchored text</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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21 <option value="2 -html">Query-anchored HTML</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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22 <option value="4">Flat query-anchored text</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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23 <option value="4 -html">Flat query-anchored HTML</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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24 <!-- |
4c4a0da938ff
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peterjc
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25 <option value="-outfmt 11">BLAST archive format (ASN.1)</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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26 --> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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27 </param> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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28 </xml> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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29 <xml name="input_scoring_matrix"> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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30 <param name="matrix" type="select" label="Scoring matrix"> |
4c4a0da938ff
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peterjc
parents:
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31 <option value="BLOSUM90">BLOSUM90</option> |
4c4a0da938ff
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peterjc
parents:
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32 <option value="BLOSUM80">BLOSUM80</option> |
4c4a0da938ff
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peterjc
parents:
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33 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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34 <option value="BLOSUM50">BLOSUM50</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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35 <option value="BLOSUM45">BLOSUM45</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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36 <option value="PAM250">PAM250</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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37 <option value="PAM70">PAM70</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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38 <option value="PAM30">PAM30</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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39 </param> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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40 </xml> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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41 <xml name="stdio"> |
4c4a0da938ff
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peterjc
parents:
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42 <stdio> |
4c4a0da938ff
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peterjc
parents:
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43 <!-- Anything other than zero is an error --> |
4c4a0da938ff
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peterjc
parents:
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44 <exit_code range="1:" /> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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45 <exit_code range=":-1" /> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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46 <!-- In case the return code has not been set propery check stderr too --> |
4c4a0da938ff
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peterjc
parents:
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47 <regex match="Error:" /> |
4c4a0da938ff
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peterjc
parents:
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48 <regex match="Exception:" /> |
4c4a0da938ff
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peterjc
parents:
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49 </stdio> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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50 </xml> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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51 <xml name="input_query_gencode"> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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52 <param name="query_gencode" type="select" label="Query genetic code"> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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53 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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54 <option value="1" select="True">1. Standard</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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55 <option value="2">2. Vertebrate Mitochondrial</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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56 <option value="3">3. Yeast Mitochondrial</option> |
4c4a0da938ff
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peterjc
parents:
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57 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> |
4c4a0da938ff
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peterjc
parents:
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58 <option value="5">5. Invertebrate Mitochondrial</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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59 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> |
4c4a0da938ff
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peterjc
parents:
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60 <option value="9">9. Echinoderm Mitochondrial</option> |
4c4a0da938ff
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peterjc
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61 <option value="10">10. Euplotid Nuclear</option> |
4c4a0da938ff
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peterjc
parents:
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62 <option value="11">11. Bacteria and Archaea</option> |
4c4a0da938ff
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peterjc
parents:
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63 <option value="12">12. Alternative Yeast Nuclear</option> |
4c4a0da938ff
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peterjc
parents:
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64 <option value="13">13. Ascidian Mitochondrial</option> |
4c4a0da938ff
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peterjc
parents:
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65 <option value="14">14. Flatworm Mitochondrial</option> |
4c4a0da938ff
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peterjc
parents:
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66 <option value="15">15. Blepharisma Macronuclear</option> |
4c4a0da938ff
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peterjc
parents:
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67 <option value="16">16. Chlorophycean Mitochondrial Code</option> |
4c4a0da938ff
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peterjc
parents:
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68 <option value="21">21. Trematode Mitochondrial Code</option> |
4c4a0da938ff
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peterjc
parents:
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69 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> |
4c4a0da938ff
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peterjc
parents:
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70 <option value="23">23. Thraustochytrium Mitochondrial Code</option> |
4c4a0da938ff
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peterjc
parents:
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71 <option value="24">24. Pterobranchia mitochondrial code</option> |
4c4a0da938ff
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peterjc
parents:
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72 </param> |
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peterjc
parents:
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73 </xml> |
4c4a0da938ff
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peterjc
parents:
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74 <xml name="input_db_gencode"> |
4c4a0da938ff
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peterjc
parents:
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75 <param name="db_gencode" type="select" label="Database/subject genetic code"> |
4c4a0da938ff
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peterjc
parents:
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76 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> |
4c4a0da938ff
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peterjc
parents:
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77 <option value="1" select="True">1. Standard</option> |
4c4a0da938ff
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peterjc
parents:
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78 <option value="2">2. Vertebrate Mitochondrial</option> |
4c4a0da938ff
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peterjc
parents:
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79 <option value="3">3. Yeast Mitochondrial</option> |
4c4a0da938ff
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peterjc
parents:
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80 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> |
4c4a0da938ff
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peterjc
parents:
diff
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81 <option value="5">5. Invertebrate Mitochondrial</option> |
4c4a0da938ff
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peterjc
parents:
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82 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> |
4c4a0da938ff
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peterjc
parents:
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83 <option value="9">9. Echinoderm Mitochondrial</option> |
4c4a0da938ff
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peterjc
parents:
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84 <option value="10">10. Euplotid Nuclear</option> |
4c4a0da938ff
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peterjc
parents:
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85 <option value="11">11. Bacteria and Archaea</option> |
4c4a0da938ff
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peterjc
parents:
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86 <option value="12">12. Alternative Yeast Nuclear</option> |
4c4a0da938ff
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peterjc
parents:
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87 <option value="13">13. Ascidian Mitochondrial</option> |
4c4a0da938ff
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peterjc
parents:
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88 <option value="14">14. Flatworm Mitochondrial</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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89 <option value="15">15. Blepharisma Macronuclear</option> |
4c4a0da938ff
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peterjc
parents:
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90 <option value="16">16. Chlorophycean Mitochondrial Code</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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91 <option value="21">21. Trematode Mitochondrial Code</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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92 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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93 <option value="23">23. Thraustochytrium Mitochondrial Code</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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94 <option value="24">24. Pterobranchia mitochondrial code</option> |
4c4a0da938ff
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peterjc
parents:
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95 </param> |
4c4a0da938ff
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peterjc
parents:
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96 </xml> |
4c4a0da938ff
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97 <xml name="input_conditional_nucleotide_db"> |
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98 <conditional name="db_opts"> |
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99 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
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100 <option value="db" selected="True">Locally installed BLAST database</option> |
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101 <option value="histdb">BLAST database from your history</option> |
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102 <option value="file">FASTA file from your history (see warning note below)</option> |
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103 </param> |
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104 <when value="db"> |
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105 <param name="database" type="select" label="Nucleotide BLAST database"> |
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106 <options from_file="blastdb.loc"> |
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107 <column name="value" index="0"/> |
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108 <column name="name" index="1"/> |
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109 <column name="path" index="2"/> |
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110 </options> |
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111 </param> |
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112 <param name="histdb" type="hidden" value="" /> |
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113 <param name="subject" type="hidden" value="" /> |
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114 </when> |
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115 <when value="histdb"> |
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116 <param name="database" type="hidden" value="" /> |
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117 <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> |
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118 <param name="subject" type="hidden" value="" /> |
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119 </when> |
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120 <when value="file"> |
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121 <param name="database" type="hidden" value="" /> |
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122 <param name="histdb" type="hidden" value="" /> |
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123 <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> |
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124 </when> |
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125 </conditional> |
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126 </xml> |
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127 <xml name="input_conditional_protein_db"> |
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128 <conditional name="db_opts"> |
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129 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
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130 <option value="db" selected="True">Locally installed BLAST database</option> |
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131 <option value="histdb">BLAST database from your history</option> |
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132 <option value="file">FASTA file from your history (see warning note below)</option> |
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133 </param> |
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134 <when value="db"> |
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135 <param name="database" type="select" label="Protein BLAST database"> |
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136 <options from_file="blastdb_p.loc"> |
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137 <column name="value" index="0"/> |
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138 <column name="name" index="1"/> |
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139 <column name="path" index="2"/> |
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140 </options> |
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141 </param> |
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142 <param name="histdb" type="hidden" value="" /> |
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143 <param name="subject" type="hidden" value="" /> |
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144 </when> |
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145 <when value="histdb"> |
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146 <param name="database" type="hidden" value="" /> |
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147 <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> |
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148 <param name="subject" type="hidden" value="" /> |
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149 </when> |
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150 <when value="file"> |
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151 <param name="database" type="hidden" value="" /> |
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152 <param name="histdb" type="hidden" value="" /> |
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153 <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> |
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154 </when> |
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155 </conditional> |
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156 </xml> |
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157 <xml name="input_conditional_pssm"> |
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158 <conditional name="db_opts"> |
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159 <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)"> |
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160 <option value="db" selected="True">Locally installed BLAST database</option> |
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161 <!-- TODO - define new datatype |
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162 <option value="histdb">BLAST protein domain database from your history</option> |
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163 --> |
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164 </param> |
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165 <when value="db"> |
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166 <param name="database" type="select" label="Protein domain database"> |
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167 <options from_file="blastdb_d.loc"> |
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168 <column name="value" index="0"/> |
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169 <column name="name" index="1"/> |
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170 <column name="path" index="2"/> |
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171 </options> |
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172 </param> |
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173 <param name="histdb" type="hidden" value="" /> |
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174 <param name="subject" type="hidden" value="" /> |
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175 </when> |
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176 <!-- TODO - define new datatype |
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177 <when value="histdb"> |
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178 <param name="database" type="hidden" value="" /> |
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179 <param name="histdb" type="data" format="blastdbd" label="Protein domain database" /> |
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180 <param name="subject" type="hidden" value="" /> |
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181 </when> |
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182 --> |
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183 </conditional> |
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184 </xml> |
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185 <xml name="input_conditional_choose_db_type"> |
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186 <conditional name="db_opts"> |
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187 <param name="db_type" type="select" label="Type of BLAST database"> |
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188 <option value="nucl" selected="True">Nucleotide</option> |
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189 <option value="prot">Protein</option> |
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190 </param> |
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191 <when value="nucl"> |
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192 <param name="database" type="select" label="Nucleotide BLAST database"> |
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193 <options from_file="blastdb.loc"> |
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194 <column name="value" index="0"/> |
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195 <column name="name" index="1"/> |
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196 <column name="path" index="2"/> |
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197 </options> |
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198 </param> |
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199 </when> |
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200 <when value="prot"> |
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201 <param name="database" type="select" label="Protein BLAST database"> |
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202 <options from_file="blastdb_p.loc"> |
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203 <column name="value" index="0"/> |
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204 <column name="name" index="1"/> |
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205 <column name="path" index="2"/> |
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206 </options> |
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207 </param> |
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208 </when> |
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209 </conditional> |
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210 </xml> |
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211 <xml name="input_parse_deflines"> |
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212 <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> |
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213 </xml> |
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214 <xml name="input_filter_query_default_false"> |
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215 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> |
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216 </xml> |
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217 <xml name="input_filter_query_default_true"> |
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218 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> |
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219 </xml> |
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220 <xml name="input_max_hits"> |
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221 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> |
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222 <validator type="in_range" min="0" /> |
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223 </param> |
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224 </xml> |
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225 <xml name="input_evalue"> |
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226 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> |
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227 </xml> |
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228 <xml name="input_word_size"> |
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229 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> |
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230 <validator type="in_range" min="0" /> |
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231 </param> |
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232 </xml> |
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233 <xml name="input_strand"> |
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234 <param name="strand" type="select" label="Query strand(s) to search against database/subject"> |
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235 <option value="-strand both">Both</option> |
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236 <option value="-strand plus">Plus (forward)</option> |
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237 <option value="-strand minus">Minus (reverse complement)</option> |
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238 </param> |
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239 </xml> |
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240 <xml name="requirements"> |
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241 <requirements> |
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242 <requirement type="binary">@BINARY@</requirement> |
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243 <requirement type="package" version="2.2.28">blast+</requirement> |
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244 </requirements> |
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245 <version_command>@BINARY@ -version</version_command> |
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246 </xml> |
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247 <xml name="advanced_options"> |
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248 <conditional name="adv_opts"> |
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249 <param name="adv_opts_selector" type="select" label="Advanced Options"> |
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250 <option value="basic" selected="True">Hide Advanced Options</option> |
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251 <option value="advanced">Show Advanced Options</option> |
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252 </param> |
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253 <when value="basic" /> |
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254 <when value="advanced"> |
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255 <yield /> |
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256 </when> |
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257 </conditional> |
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258 </xml> |
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259 <token name="@THREADS@">-num_threads "\${GALAXY_SLOTS:-8}"</token> |
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260 <token name="@BLAST_DB_SUBJECT@"> |
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261 #if $db_opts.db_opts_selector == "db": |
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262 -db "${db_opts.database.fields.path}" |
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263 #elif $db_opts.db_opts_selector == "histdb": |
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264 -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" |
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265 #else: |
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266 -subject "$db_opts.subject" |
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267 #end if |
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268 </token> |
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269 <token name="@BLAST_OUTPUT@">-out "$output1" |
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270 ##Set the extended list here so when we add things, saved workflows are not affected |
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271 #if str($out_format)=="ext": |
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272 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles" |
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273 #else: |
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274 -outfmt $out_format |
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275 #end if |
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276 </token> |
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277 <token name="@ADVANCED_OPTIONS@">$adv_opts.filter_query |
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278 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string |
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279 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments |
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280 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): |
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281 -max_target_seqs $adv_opts.max_hits |
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282 #end if |
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283 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): |
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284 -word_size $adv_opts.word_size |
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285 #end if |
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286 $adv_opts.parse_deflines |
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287 </token> |
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288 <!-- @ON_DB_SUBJECT@ is for use with @BLAST_DB_SUBJECT@ --> |
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289 <token name="@ON_DB_SUBJECT@">#if str($db_opts.db_opts_selector)=='db' |
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290 ${db_opts.database} |
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291 #elif str($db_opts.db_opts_selector)=='histdb' |
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292 ${db_opts.histdb.name} |
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293 #else |
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294 ${db_opts.subject.name} |
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295 #end if</token> |
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296 <token name="@REFERENCES@"> |
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297 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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298 Galaxy tools and workflows for sequence analysis with applications |
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299 in molecular plant pathology. PeerJ 1:e167 |
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300 http://dx.doi.org/10.7717/peerj.167 |
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301 |
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302 Christiam Camacho et al. (2009). |
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303 BLAST+: architecture and applications. |
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304 BMC Bioinformatics. 15;10:421. |
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305 http://dx.doi.org/10.1186/1471-2105-10-421 |
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306 |
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307 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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308 Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus |
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309 </token> |
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310 <token name="@OUTPUT_FORMAT@">**Output format** |
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311 |
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312 Because Galaxy focuses on processing tabular data, the default output of this |
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313 tool is tabular. The standard BLAST+ tabular output contains 12 columns: |
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314 |
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315 ====== ========= ============================================ |
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316 Column NCBI name Description |
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317 ------ --------- -------------------------------------------- |
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318 1 qseqid Query Seq-id (ID of your sequence) |
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319 2 sseqid Subject Seq-id (ID of the database hit) |
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320 3 pident Percentage of identical matches |
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321 4 length Alignment length |
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322 5 mismatch Number of mismatches |
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323 6 gapopen Number of gap openings |
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324 7 qstart Start of alignment in query |
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325 8 qend End of alignment in query |
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326 9 sstart Start of alignment in subject (database hit) |
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327 10 send End of alignment in subject (database hit) |
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328 11 evalue Expectation value (E-value) |
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329 12 bitscore Bit score |
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330 ====== ========= ============================================ |
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331 |
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332 The BLAST+ tools can optionally output additional columns of information, |
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333 but this takes longer to calculate. Most (but not all) of these columns are |
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334 included by selecting the extended tabular output. The extra columns are |
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335 included *after* the standard 12 columns. This is so that you can write |
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336 workflow filtering steps that accept either the 12 or 25 column tabular |
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337 BLAST output. Galaxy now uses this extended 25 column output by default. |
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338 |
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339 ====== ============= =========================================== |
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340 Column NCBI name Description |
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341 ------ ------------- ------------------------------------------- |
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342 13 sallseqid All subject Seq-id(s), separated by ';' |
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343 14 score Raw score |
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344 15 nident Number of identical matches |
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345 16 positive Number of positive-scoring matches |
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346 17 gaps Total number of gaps |
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347 18 ppos Percentage of positive-scoring matches |
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348 19 qframe Query frame |
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349 20 sframe Subject frame |
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350 21 qseq Aligned part of query sequence |
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351 22 sseq Aligned part of subject sequence |
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352 23 qlen Query sequence length |
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353 24 slen Subject sequence length |
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354 25 salltitles All subject title(s), separated by '<>' |
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355 ====== ============= =========================================== |
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356 |
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357 The third option is BLAST XML output, which is designed to be parsed by |
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358 another program, and is understood by some Galaxy tools. |
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359 |
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360 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). |
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361 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. |
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362 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. |
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363 The two query anchored outputs show a multiple sequence alignment between the query and all the matches, |
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364 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). |
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365 </token> |
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366 <token name="@FASTA_WARNING@">.. class:: warningmark |
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367 |
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368 You can also search against a FASTA file of subject (target) |
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369 sequences. This is *not* advised because it is slower (only one |
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370 CPU is used), but more importantly gives e-values for pairwise |
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371 searches (very small e-values which will look overly signficiant). |
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372 In most cases you should instead turn the other FASTA file into a |
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373 database first using *makeblastdb* and search against that. |
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374 </token> |
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375 <token name="@SEARCH_TIME_WARNING@">.. class:: warningmark |
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376 |
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377 **Note**. Database searches may take a substantial amount of time. |
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378 For large input datasets it is advisable to allow overnight processing. |
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379 |
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380 ----- |
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381 </token> |
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382 </macros> |