Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @ 13:623f727cdff1 draft
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
author | peterjc |
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date | Fri, 14 Mar 2014 07:40:46 -0400 |
parents | 4c4a0da938ff |
children | 2fe07f50a41e |
rev | line source |
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13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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1 <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.1.00"> |
3
643338ac83c0
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peterjc
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2 <description>Search protein database with translated nucleotide query sequence(s)</description> |
643338ac83c0
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peterjc
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3 <!-- If job splitting is enabled, break up the query file into parts --> |
11
4c4a0da938ff
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peterjc
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4 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> |
4c4a0da938ff
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peterjc
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5 <macros> |
4c4a0da938ff
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6 <token name="@BINARY@">blastx</token> |
4c4a0da938ff
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peterjc
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7 <import>ncbi_macros.xml</import> |
4c4a0da938ff
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peterjc
parents:
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8 </macros> |
4c4a0da938ff
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peterjc
parents:
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9 <expand macro="requirements" /> |
4
9d5beacae92b
Uploaded v0.0.13 which uses the recently added error handling. No longer bundles the hide_stderr.py script which is now redundant.
peterjc
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10 <command> |
3
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peterjc
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11 ## The command is a Cheetah template which allows some Python based syntax. |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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12 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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13 blastx |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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14 -query "$query" |
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15 @BLAST_DB_SUBJECT@ |
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16 -query_gencode $query_gencode |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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17 -evalue $evalue_cutoff |
11
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peterjc
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18 @BLAST_OUTPUT@ |
4c4a0da938ff
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peterjc
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19 @THREADS@ |
3
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20 #if $adv_opts.adv_opts_selector=="advanced": |
643338ac83c0
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peterjc
parents:
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21 $adv_opts.strand |
643338ac83c0
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peterjc
parents:
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22 -matrix $adv_opts.matrix |
11
4c4a0da938ff
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peterjc
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23 @ADVANCED_OPTIONS@ |
3
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24 $adv_opts.ungapped |
643338ac83c0
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peterjc
parents:
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25 ## End of advanced options: |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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26 #end if |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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27 </command> |
11
4c4a0da938ff
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peterjc
parents:
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28 |
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 <expand macro="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:
10
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30 |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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31 <inputs> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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32 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> |
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:
10
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33 |
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 <expand macro="input_conditional_protein_db" /> |
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:
10
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35 <expand macro="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:
10
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36 <expand macro="input_evalue" /> |
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:
10
diff
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37 |
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:
10
diff
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38 <expand macro="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:
10
diff
changeset
|
39 <expand macro="advanced_options"> |
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:
10
diff
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40 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> |
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:
10
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41 <expand macro="input_filter_query_default_true" /> |
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:
10
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42 <expand macro="input_strand" /> |
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:
10
diff
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43 <expand macro="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:
10
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44 <expand macro="input_max_hits" /> |
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:
10
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45 <expand macro="input_word_size" /> |
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:
10
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46 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> |
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:
10
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47 <expand macro="input_parse_deflines" /> |
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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48 </expand> |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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49 </inputs> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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50 <outputs> |
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4c4a0da938ff
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peterjc
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51 <data name="output1" format="tabular" label="blastx $query.name vs @ON_DB_SUBJECT@"> |
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:
10
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52 <expand macro="output_change_format" /> |
3
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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53 </data> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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54 </outputs> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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|
55 <tests> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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56 <test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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57 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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58 <param name="db_opts_selector" value="file" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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59 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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60 <param name="database" value="" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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61 <param name="evalue_cutoff" value="1e-10" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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62 <param name="out_format" value="5" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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63 <param name="adv_opts_selector" value="basic" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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64 <output name="output1" file="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
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65 </test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
66 <test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
67 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
68 <param name="db_opts_selector" value="file" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
69 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
70 <param name="database" value="" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
71 <param name="evalue_cutoff" value="1e-10" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
72 <param name="out_format" value="6" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
73 <param name="adv_opts_selector" value="basic" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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|
74 <output name="output1" file="blastx_rhodopsin_vs_four_human.tabular" ftype="tabular" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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|
75 </test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
76 <test> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
77 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
78 <param name="db_opts_selector" value="file" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
79 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
80 <param name="database" value="" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
81 <param name="evalue_cutoff" value="1e-10" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
82 <param name="out_format" value="ext" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
83 <param name="adv_opts_selector" value="basic" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
changeset
|
84 <output name="output1" file="blastx_rhodopsin_vs_four_human_ext.tabular" ftype="tabular" /> |
643338ac83c0
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
peterjc
parents:
diff
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|
85 </test> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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86 <test> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
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|
87 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
88 <param name="db_opts_selector" value="file" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
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|
89 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
90 <param name="database" value="" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
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|
91 <param name="evalue_cutoff" value="1e-10" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
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|
92 <param name="out_format" value="cols" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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93 <param name="std_cols" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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94 <param name="ext_cols" value="sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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95 <param name="ids_cols" value="qgi,qacc,qaccver,sallseqid,sgi,sallgi,sacc,saccver,sallacc,stitle" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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96 <param name="misc_cols" value="sstrand,frames,btop,qcovs,qcovhsp" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
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97 <param name="tax_cols" value="staxids,sscinames,scomnames,sblastnames,sskingdoms" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
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|
98 <param name="adv_opts_selector" value="basic" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
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|
99 <output name="output1" file="blastx_rhodopsin_vs_four_human_all.tabular" ftype="tabular" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
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100 </test> |
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101 </tests> |
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102 <help> |
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103 |
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104 @SEARCH_TIME_WARNING@ |
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105 |
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106 **What it does** |
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107 |
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108 Search a *protein database* using a *translated nucleotide query*, |
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109 using the NCBI BLAST+ blastx command line tool. |
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110 |
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111 @FASTA_WARNING@ |
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112 |
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113 ----- |
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114 |
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115 @OUTPUT_FORMAT@ |
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116 |
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117 ------- |
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118 |
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119 **References** |
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120 |
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121 If you use this Galaxy tool in work leading to a scientific publication please |
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122 cite the following papers: |
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123 |
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124 @REFERENCES@ |
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125 </help> |
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126 </tool> |