Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml @ 22:6f386c5dc4fb draft
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
author | peterjc |
---|---|
date | Mon, 18 Sep 2017 06:21:27 -0400 |
parents | 3034ce97dd33 |
children | 6f8ea4b9a2c4 |
rev | line source |
---|---|
17
697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents:
16
diff
changeset
|
1 <tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="@WRAPPER_VERSION@"> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
2 <description>Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb</description> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
3 <macros> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
4 <token name="@BINARY@">convert2blastmask</token> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
5 <import>ncbi_macros.xml</import> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
6 </macros> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
7 <expand macro="preamble" /> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
8 <command detect_errors="aggressive"> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
9 ## The command is a Cheetah template which allows some Python based syntax. |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
10 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
11 convert2blastmask |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
12 -in '$infile' |
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
13 -masking_algorithm '$masking_algorithm' |
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
14 -masking_options '$masking_options' |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
15 $parse_seqids |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
16 -out '$outfile' |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
17 -outfmt $outformat |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
18 </command> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
19 <inputs> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
20 <param name="infile" argument="-in" type="data" format="fasta" label="Masked FASTA file"/> |
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
21 <param argument="-masking_algorithm" type="select" label="Used masking algorithm"> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
22 <option value="dust">DUST</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
23 <option value="seg" selected="true">SEG</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
24 <option value="windowmasker">windowmasker</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
25 <option value="repeat">repeat</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
26 <option value="other">other</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
27 </param> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
28 <param argument="-masking_options" type="text" value="" size="20" label="Masking algorithm options to create the masked input" |
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
29 help ="Free text to describe the options used to create the masking files"> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
30 <sanitizer invalid_char=""> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
31 <valid initial="string.printable" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
32 </sanitizer> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
33 </param> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
34 <param argument="-parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="true" label="Parse Seq-ids in FASTA input" help="(-parse_seqids)" /> |
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
35 <param name="outformat" argument="-outfmt" type="select" label="Output format"> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
36 <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
37 <option value="maskinfo_asn1_text" selected="true">maskinfo ASN.1 text</option> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
38 <option value="maskinfo_xml">maskinfo_xml</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
39 </param> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
40 </inputs> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
41 <outputs> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
42 <data name="outfile" format="maskinfo-asn1" label="SEG Masked File"> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
43 <change_format> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
44 <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
45 <!-- |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
46 <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
47 --> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
48 <when input="outformat" value="maskinfo_xml" format="xml" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
49 </change_format> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
50 </data> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
51 </outputs> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
52 <tests> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
53 <test> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
54 <param name="infile" value="four_human_proteins_masked.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:
diff
changeset
|
55 <param name="masking_algorithm" value="seg" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
56 <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" /> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
57 <param name="parse_seqids" value="true" /> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
58 <param name="outformat" value="maskinfo_asn1_bin" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
59 <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1-binary" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
60 </test> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
61 <test> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
62 <param name="infile" value="four_human_proteins_masked.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:
diff
changeset
|
63 <param name="masking_algorithm" value="seg" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
64 <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" /> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
20
diff
changeset
|
65 <param name="parse_seqids" value="true" /> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
66 <param name="outformat" value="maskinfo_asn1_text" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
67 <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1" /> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
68 </test> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
69 </tests> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
70 <help> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
71 **What it does** |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
72 |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
73 Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb. |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
74 |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
75 More information about segmasker can be found in the `BLAST Command Line Applications User Manual`_. |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
76 |
20
3034ce97dd33
Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents:
17
diff
changeset
|
77 .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
78 |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
79 **References** |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
80 |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
81 If you use this Galaxy tool in work leading to a scientific publication please |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
82 cite the following papers: |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
83 |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
84 @REFERENCES@ |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
85 </help> |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
diff
changeset
|
86 <expand macro="blast_citations" /> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
diff
changeset
|
87 </tool> |