Mercurial > repos > devteam > ncbi_blast_plus
comparison tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml @ 15:c16c30e9ad5b draft
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
author | peterjc |
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date | Sun, 05 Jul 2015 10:37:27 -0400 |
parents | 2fe07f50a41e |
children | b5f1f599d1fb |
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14:2fe07f50a41e | 15:c16c30e9ad5b |
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1 <tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.01"> | 1 <tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.03"> |
2 <description>low-complexity regions in protein sequences</description> | 2 <description>low-complexity regions in protein sequences</description> |
3 <macros> | 3 <macros> |
4 <token name="@BINARY@">segmasker</token> | 4 <token name="@BINARY@">segmasker</token> |
5 <import>ncbi_macros.xml</import> | 5 <import>ncbi_macros.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements" /> | 7 <expand macro="preamble" /> |
8 <command> | 8 <command> |
9 ## The command is a Cheetah template which allows some Python based syntax. | 9 ## The command is a Cheetah template which allows some Python based syntax. |
10 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces | 10 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
11 segmasker | 11 segmasker |
12 #if $db_opts.db_opts_selector == "db": | 12 #if $db_opts.db_opts_selector == "db": |
13 -in "${db_opts.database.fields.path}" -infmt blastdb | 13 -in "${db_opts.database.fields.path}" -infmt blastdb |
14 #elif $db_opts.db_opts_selector == "histdb": | 14 #elif $db_opts.db_opts_selector == "histdb": |
15 -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb | 15 -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb |
16 #else: | 16 #else: |
17 -in "$subject" -infmt fasta | 17 -in "$subject" -infmt fasta |
18 #end if | 18 #end if |
19 -out "$outfile" | 19 -out "$outfile" |
20 -window $window | 20 -window $window |
21 -locut $locut | 21 -locut $locut |
22 -hicut $hicut | 22 -hicut $hicut |
23 -outfmt $outformat | 23 -outfmt $outformat |
24 </command> | 24 </command> |
25 <expand macro="stdio" /> | |
26 <inputs> | 25 <inputs> |
27 <expand macro="input_conditional_protein_db" /> | 26 <expand macro="input_conditional_protein_db" /> |
28 <param name="window" type="integer" value="12" label="SEG window length" help="(-window)" /> | 27 <param name="window" type="integer" value="12" label="SEG window length" help="(-window)" /> |
29 <param name="locut" type="float" value="2.2" label="SEG low cutoff" help="(-locut)" /> | 28 <param name="locut" type="float" value="2.2" label="SEG low cutoff" help="(-locut)" /> |
30 <param name="hicut" type="float" value="2.5" label="SEG high cutoff" help="(-hicut)" /> | 29 <param name="hicut" type="float" value="2.5" label="SEG high cutoff" help="(-hicut)" /> |
92 .. _SEG: http://www.ncbi.nlm.nih.gov/pubmed/8743706 | 91 .. _SEG: http://www.ncbi.nlm.nih.gov/pubmed/8743706 |
93 | 92 |
94 **References** | 93 **References** |
95 | 94 |
96 If you use this Galaxy tool in work leading to a scientific publication please | 95 If you use this Galaxy tool in work leading to a scientific publication please |
97 cite the following papers (a more specific paper covering this wrapper is planned): | 96 cite the following papers: |
98 | 97 |
99 @REFERENCES@ | 98 @REFERENCES@ |
100 </help> | 99 </help> |
101 <expand macro="blast_citations" /> | 100 <expand macro="blast_citations" /> |
102 </tool> | 101 </tool> |