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comparison emboss_fuzznuc.xml @ 0:de3a45e9ccce draft

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"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
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-1:000000000000 0:de3a45e9ccce
1 <tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="6.6.0">
2 <description>Nucleic acid pattern search</description>
3 <expand macro="bio_tools" />
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <code file="emboss_format_corrector.py" />
9 <command><![CDATA[
10 fuzznuc
11
12 -sequence '$input1'
13 $seq_qualifiers.sreverse1 $seq_qualifiers.snucleotide1 $seq_qualifiers.sprotein1 $seq_qualifiers.slower1 $seq_qualifiers.supper1 $seq_qualifiers.scircular1
14 #if $seq_qualifiers.sbegin1
15 -sbegin1 '$seq_qualifiers.sbegin1'
16 #end if
17 #if $seq_qualifiers.send1
18 -send1 '$seq_qualifiers.send1'
19 #end if
20 #if $seq_qualifiers.ioffset1
21 -ioffset1 '$seq_qualifiers.ioffset1'
22 #end if
23
24 -outfile '$out_file1'
25 $out_qualifiers.raccshow2 $out_qualifiers.rdesshow2 $out_qualifiers.rscoreshow2 $out_qualifiers.rusashow2 $out_qualifiers.rstrandshow2
26 #if $out_qualifiers.rmaxall2
27 -rmaxall2 '$out_qualifiers.rmaxall2'
28 #end if
29 #if $out_qualifiers.rmaxseq2
30 -rmaxseq2 '$out_qualifiers.rmaxseq2'
31 #end if
32
33 -pattern '$pattern' -pmismatch '$mismatch' -rformat2 '$out_format1' -auto
34
35 -complement '$complement'
36 ]]></command>
37 <inputs>
38 <param name="input1" type="data" format="fasta" label="Sequences" />
39 <param name="pattern" type="text" value="" label="Search pattern">
40 <sanitizer>
41 <valid initial="string.printable">
42 <remove value="&apos;"/>
43 </valid>
44 <mapping initial="none">
45 <add source="&apos;" target=""/>
46 </mapping>
47 </sanitizer>
48 </param>
49 <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
50 <param name="complement" type="select" label="Search complementary strand">
51 <option value="no">No</option>
52 <option value="yes">Yes</option>
53 </param>
54 <param name="out_format1" type="select" label="Output report file format">
55 <option value="seqtable">SeqTable</option>
56 <option value="embl">EMBL</option>
57 <option value="genbank">GENBANK</option>
58 <option value="gff">GFF</option>
59 <option value="pir">PIR</option>
60 <option value="swiss">SwissProt</option>
61 <option value="dbmotif">DbMotif</option>
62 <option value="diffseq">Diffseq</option>
63 <option value="excel">Excel (tab delimited)</option>
64 <option value="feattable">FeatTable</option>
65 <option value="motif">Motif</option>
66 <option value="regions">Regions</option>
67 <option value="simple">SRS Simple</option>
68 <option value="fuzznuc">Fuzznuc Output File</option>
69 <option value="srs">SRS</option>
70 <option value="table">Table</option>
71 <option value="tagseq">TagSeq</option>
72 </param>
73
74 <section name="seq_qualifiers" title="Sequence associated qualifiers">
75 <param type="integer" argument="-sbegin1" optional="true" label="Start of each sequence to be used"/>
76 <param type="integer" argument="-send1" optional="true" label="End of each sequence to be used"/>
77 <param type="integer" argument="-ioffset1" optional="true" label="Input start position offset"/>
78 <param type="boolean" argument="-sreverse1" truevalue="-sreverse1 Y" falsevalue="" label="Reverse (if DNA)"/>
79 <param type="boolean" argument="-snucleotide1" truevalue="-snucleotide1 Y" falsevalue="" label="Sequence is nucleotide"/>
80 <param type="boolean" argument="-sprotein1" truevalue="-sprotein1 Y" falsevalue="" label="Sequence is protein"/>
81 <param type="boolean" argument="-slower1" truevalue="-slower1 Y" falsevalue="" label="Make lower case"/>
82 <param type="boolean" argument="-supper1" truevalue="-supper1 Y" falsevalue="" label="Make upper case"/>
83 <param type="boolean" argument="-scircular1" truevalue="-scircular1 Y" falsevalue="" label="Sequence is circular"/>
84 </section>
85
86 <section name="out_qualifiers" title="Outfile associated qualifiers">
87 <param type="boolean" argument="-raccshow2" truevalue="-raccshow2 Y" falsevalue="" label="Show accession number in the report"/>
88 <param type="boolean" argument="-rdesshow2" truevalue="-rdesshow2 Y" falsevalue="" label="Show description in the report"/>
89 <param type="boolean" argument="-rscoreshow2" truevalue="-rscoreshow2 Y" falsevalue="" label="Show the score in the report"/>
90 <param type="boolean" argument="-rstrandshow2" truevalue="-rstrandshow2 Y" falsevalue="" label="Show the nucleotide strand in the report"/>
91 <param type="boolean" argument="-rusashow2" truevalue="-rusashow2 Y" falsevalue="" label="Show the full USA in the report"/>
92 <param type="integer" argument="-rmaxall2" optional="true" label="Maximum total hits to report"/>
93 <param type="integer" argument="-rmaxseq2" optional="true" label="Maximum hits to report for one sequence"/>
94 </section>
95
96 </inputs>
97 <outputs>
98 <data name="out_file1" format="fuzznuc" />
99 </outputs>
100 <tests>
101 <test>
102 <param name="input1" value="2.fasta"/>
103 <param name="pattern" value="AA"/>
104 <param name="mismatch" value="0"/>
105 <param name="complement" value="no"/>
106 <param name="out_format1" value="excel"/>
107 <output name="out_file1" file="emboss_fuzznuc_out.tabular"/>
108 </test>
109 <test>
110 <param name="input1" value="2.fasta"/>
111 <param name="pattern" value="AA"/>
112 <param name="mismatch" value="0"/>
113 <param name="complement" value="no"/>
114 <param name="out_format1" value="excel"/>
115 <param name="seq_qualifiers|supper1" value="true"/>
116 <param name="seq_qualifiers|sbegin1" value="100"/>
117 <param name="out_qualifiers|rmaxseq2" value="5"/>
118 <output name="out_file1" file="emboss_fuzznuc_out2.tabular"/>
119 </test>
120 </tests>
121 <help>
122 .. class:: warningmark
123
124 The input dataset needs to be sequences.
125
126 -----
127
128 You can view the original documentation here_.
129
130 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzznuc.html
131 </help>
132 <expand macro="citations" />
133 </tool>