Mercurial > repos > brinkmanlab > emboss

annotate emboss_fuzznuc.xml @ 0:de3a45e9ccce draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
author brinkmanlab
date Tue, 25 Jan 2022 03:26:28 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
1 <tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="6.6.0">
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
2 <description>Nucleic acid pattern search</description>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
3 <expand macro="bio_tools" />
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
4 <macros>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
5 <import>macros.xml</import>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
6 </macros>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
7 <expand macro="requirements" />
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
8 <code file="emboss_format_corrector.py" />
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
9 <command><![CDATA[
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
10 fuzznuc
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
11
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
12 -sequence '$input1'
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
13 $seq_qualifiers.sreverse1 $seq_qualifiers.snucleotide1 $seq_qualifiers.sprotein1 $seq_qualifiers.slower1 $seq_qualifiers.supper1 $seq_qualifiers.scircular1
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
14 #if $seq_qualifiers.sbegin1
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
15 -sbegin1 '$seq_qualifiers.sbegin1'
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
16 #end if
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
17 #if $seq_qualifiers.send1
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
18 -send1 '$seq_qualifiers.send1'
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
19 #end if
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
20 #if $seq_qualifiers.ioffset1
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
21 -ioffset1 '$seq_qualifiers.ioffset1'
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
22 #end if
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
23
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
24 -outfile '$out_file1'
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
25 $out_qualifiers.raccshow2 $out_qualifiers.rdesshow2 $out_qualifiers.rscoreshow2 $out_qualifiers.rusashow2 $out_qualifiers.rstrandshow2
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
26 #if $out_qualifiers.rmaxall2
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
27 -rmaxall2 '$out_qualifiers.rmaxall2'
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
28 #end if
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
29 #if $out_qualifiers.rmaxseq2
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
30 -rmaxseq2 '$out_qualifiers.rmaxseq2'
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
31 #end if
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
32
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
33 -pattern '$pattern' -pmismatch '$mismatch' -rformat2 '$out_format1' -auto
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
34
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
35 -complement '$complement'
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
36 ]]></command>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
37 <inputs>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
38 <param name="input1" type="data" format="fasta" label="Sequences" />
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
39 <param name="pattern" type="text" value="" label="Search pattern">
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
40 <sanitizer>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
41 <valid initial="string.printable">
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
42 <remove value="&apos;"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
43 </valid>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
44 <mapping initial="none">
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
45 <add source="&apos;" target=""/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
46 </mapping>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
47 </sanitizer>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
48 </param>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
49 <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
50 <param name="complement" type="select" label="Search complementary strand">
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
51 <option value="no">No</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
52 <option value="yes">Yes</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
53 </param>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
54 <param name="out_format1" type="select" label="Output report file format">
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
55 <option value="seqtable">SeqTable</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
56 <option value="embl">EMBL</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
57 <option value="genbank">GENBANK</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
58 <option value="gff">GFF</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
59 <option value="pir">PIR</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
60 <option value="swiss">SwissProt</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
61 <option value="dbmotif">DbMotif</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
62 <option value="diffseq">Diffseq</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
63 <option value="excel">Excel (tab delimited)</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
64 <option value="feattable">FeatTable</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
65 <option value="motif">Motif</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
66 <option value="regions">Regions</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
67 <option value="simple">SRS Simple</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
68 <option value="fuzznuc">Fuzznuc Output File</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
69 <option value="srs">SRS</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
70 <option value="table">Table</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
71 <option value="tagseq">TagSeq</option>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
72 </param>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
73
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
74 <section name="seq_qualifiers" title="Sequence associated qualifiers">
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
75 <param type="integer" argument="-sbegin1" optional="true" label="Start of each sequence to be used"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
76 <param type="integer" argument="-send1" optional="true" label="End of each sequence to be used"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
77 <param type="integer" argument="-ioffset1" optional="true" label="Input start position offset"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
78 <param type="boolean" argument="-sreverse1" truevalue="-sreverse1 Y" falsevalue="" label="Reverse (if DNA)"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
79 <param type="boolean" argument="-snucleotide1" truevalue="-snucleotide1 Y" falsevalue="" label="Sequence is nucleotide"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
80 <param type="boolean" argument="-sprotein1" truevalue="-sprotein1 Y" falsevalue="" label="Sequence is protein"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
81 <param type="boolean" argument="-slower1" truevalue="-slower1 Y" falsevalue="" label="Make lower case"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
82 <param type="boolean" argument="-supper1" truevalue="-supper1 Y" falsevalue="" label="Make upper case"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
83 <param type="boolean" argument="-scircular1" truevalue="-scircular1 Y" falsevalue="" label="Sequence is circular"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
84 </section>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
85
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
86 <section name="out_qualifiers" title="Outfile associated qualifiers">
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
87 <param type="boolean" argument="-raccshow2" truevalue="-raccshow2 Y" falsevalue="" label="Show accession number in the report"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
88 <param type="boolean" argument="-rdesshow2" truevalue="-rdesshow2 Y" falsevalue="" label="Show description in the report"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
89 <param type="boolean" argument="-rscoreshow2" truevalue="-rscoreshow2 Y" falsevalue="" label="Show the score in the report"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
90 <param type="boolean" argument="-rstrandshow2" truevalue="-rstrandshow2 Y" falsevalue="" label="Show the nucleotide strand in the report"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
91 <param type="boolean" argument="-rusashow2" truevalue="-rusashow2 Y" falsevalue="" label="Show the full USA in the report"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
92 <param type="integer" argument="-rmaxall2" optional="true" label="Maximum total hits to report"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
93 <param type="integer" argument="-rmaxseq2" optional="true" label="Maximum hits to report for one sequence"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
94 </section>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
95
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
96 </inputs>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
97 <outputs>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
98 <data name="out_file1" format="fuzznuc" />
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
99 </outputs>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
100 <tests>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
101 <test>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
102 <param name="input1" value="2.fasta"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
103 <param name="pattern" value="AA"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
104 <param name="mismatch" value="0"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
105 <param name="complement" value="no"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
106 <param name="out_format1" value="excel"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
107 <output name="out_file1" file="emboss_fuzznuc_out.tabular"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
108 </test>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
109 <test>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
110 <param name="input1" value="2.fasta"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
111 <param name="pattern" value="AA"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
112 <param name="mismatch" value="0"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
113 <param name="complement" value="no"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
114 <param name="out_format1" value="excel"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
115 <param name="seq_qualifiers|supper1" value="true"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
116 <param name="seq_qualifiers|sbegin1" value="100"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
117 <param name="out_qualifiers|rmaxseq2" value="5"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
118 <output name="out_file1" file="emboss_fuzznuc_out2.tabular"/>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
119 </test>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
120 </tests>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
121 <help>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
122 .. class:: warningmark
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
123
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
124 The input dataset needs to be sequences.
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
125
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
126 -----
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
127
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
128 You can view the original documentation here_.
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
129
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
130 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzznuc.html
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
131 </help>
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
132 <expand macro="citations" />
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
brinkmanlab
parents:
diff changeset
133 </tool>