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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit 1a6cdd455506ca8013a089fdb64b75fb39d34856"
author brinkmanlab
date Tue, 25 Jan 2022 04:02:42 +0000
parents de3a45e9ccce
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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1 <tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="6.6.0">
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2 <description>Nucleic acid pattern search</description>
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3 <expand macro="bio_tools" />
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <code file="emboss_format_corrector.py" />
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9 <command><![CDATA[
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10 fuzznuc
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11
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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12 -sequence '$input1'
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13 $seq_qualifiers.sreverse1 $seq_qualifiers.snucleotide1 $seq_qualifiers.sprotein1 $seq_qualifiers.slower1 $seq_qualifiers.supper1 $seq_qualifiers.scircular1
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14 #if $seq_qualifiers.sbegin1
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15 -sbegin1 '$seq_qualifiers.sbegin1'
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16 #end if
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17 #if $seq_qualifiers.send1
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18 -send1 '$seq_qualifiers.send1'
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19 #end if
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20 #if $seq_qualifiers.ioffset1
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21 -ioffset1 '$seq_qualifiers.ioffset1'
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22 #end if
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23
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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24 -outfile '$out_file1'
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25 $out_qualifiers.raccshow2 $out_qualifiers.rdesshow2 $out_qualifiers.rscoreshow2 $out_qualifiers.rusashow2 $out_qualifiers.rstrandshow2
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26 #if $out_qualifiers.rmaxall2
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27 -rmaxall2 '$out_qualifiers.rmaxall2'
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28 #end if
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29 #if $out_qualifiers.rmaxseq2
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30 -rmaxseq2 '$out_qualifiers.rmaxseq2'
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31 #end if
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32
de3a45e9ccce "planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/emboss commit eaefd81cf7afec08ffc570ac53d6718d62743a99"
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33 -pattern '$pattern' -pmismatch '$mismatch' -rformat2 '$out_format1' -auto
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34
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35 -complement '$complement'
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36 ]]></command>
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37 <inputs>
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38 <param name="input1" type="data" format="fasta" label="Sequences" />
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39 <param name="pattern" type="text" value="" label="Search pattern">
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40 <sanitizer>
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41 <valid initial="string.printable">
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42 <remove value="&apos;"/>
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43 </valid>
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44 <mapping initial="none">
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45 <add source="&apos;" target=""/>
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46 </mapping>
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47 </sanitizer>
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48 </param>
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49 <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
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50 <param name="complement" type="select" label="Search complementary strand">
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51 <option value="no">No</option>
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52 <option value="yes">Yes</option>
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53 </param>
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54 <param name="out_format1" type="select" label="Output report file format">
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55 <option value="seqtable">SeqTable</option>
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56 <option value="embl">EMBL</option>
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57 <option value="genbank">GENBANK</option>
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58 <option value="gff">GFF</option>
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59 <option value="pir">PIR</option>
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60 <option value="swiss">SwissProt</option>
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61 <option value="dbmotif">DbMotif</option>
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62 <option value="diffseq">Diffseq</option>
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63 <option value="excel">Excel (tab delimited)</option>
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64 <option value="feattable">FeatTable</option>
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65 <option value="motif">Motif</option>
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66 <option value="regions">Regions</option>
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67 <option value="simple">SRS Simple</option>
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68 <option value="fuzznuc">Fuzznuc Output File</option>
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69 <option value="srs">SRS</option>
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70 <option value="table">Table</option>
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71 <option value="tagseq">TagSeq</option>
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72 </param>
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73
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74 <section name="seq_qualifiers" title="Sequence associated qualifiers">
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75 <param type="integer" argument="-sbegin1" optional="true" label="Start of each sequence to be used"/>
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76 <param type="integer" argument="-send1" optional="true" label="End of each sequence to be used"/>
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77 <param type="integer" argument="-ioffset1" optional="true" label="Input start position offset"/>
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78 <param type="boolean" argument="-sreverse1" truevalue="-sreverse1 Y" falsevalue="" label="Reverse (if DNA)"/>
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79 <param type="boolean" argument="-snucleotide1" truevalue="-snucleotide1 Y" falsevalue="" label="Sequence is nucleotide"/>
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80 <param type="boolean" argument="-sprotein1" truevalue="-sprotein1 Y" falsevalue="" label="Sequence is protein"/>
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81 <param type="boolean" argument="-slower1" truevalue="-slower1 Y" falsevalue="" label="Make lower case"/>
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82 <param type="boolean" argument="-supper1" truevalue="-supper1 Y" falsevalue="" label="Make upper case"/>
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83 <param type="boolean" argument="-scircular1" truevalue="-scircular1 Y" falsevalue="" label="Sequence is circular"/>
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84 </section>
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85
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86 <section name="out_qualifiers" title="Outfile associated qualifiers">
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87 <param type="boolean" argument="-raccshow2" truevalue="-raccshow2 Y" falsevalue="" label="Show accession number in the report"/>
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88 <param type="boolean" argument="-rdesshow2" truevalue="-rdesshow2 Y" falsevalue="" label="Show description in the report"/>
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89 <param type="boolean" argument="-rscoreshow2" truevalue="-rscoreshow2 Y" falsevalue="" label="Show the score in the report"/>
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90 <param type="boolean" argument="-rstrandshow2" truevalue="-rstrandshow2 Y" falsevalue="" label="Show the nucleotide strand in the report"/>
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91 <param type="boolean" argument="-rusashow2" truevalue="-rusashow2 Y" falsevalue="" label="Show the full USA in the report"/>
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92 <param type="integer" argument="-rmaxall2" optional="true" label="Maximum total hits to report"/>
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93 <param type="integer" argument="-rmaxseq2" optional="true" label="Maximum hits to report for one sequence"/>
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94 </section>
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95
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96 </inputs>
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97 <outputs>
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98 <data name="out_file1" format="fuzznuc" />
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99 </outputs>
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100 <tests>
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101 <test>
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102 <param name="input1" value="2.fasta"/>
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103 <param name="pattern" value="AA"/>
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104 <param name="mismatch" value="0"/>
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105 <param name="complement" value="no"/>
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106 <param name="out_format1" value="excel"/>
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107 <output name="out_file1" file="emboss_fuzznuc_out.tabular"/>
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108 </test>
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109 <test>
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110 <param name="input1" value="2.fasta"/>
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111 <param name="pattern" value="AA"/>
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112 <param name="mismatch" value="0"/>
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113 <param name="complement" value="no"/>
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114 <param name="out_format1" value="excel"/>
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115 <param name="seq_qualifiers|supper1" value="true"/>
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116 <param name="seq_qualifiers|sbegin1" value="100"/>
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117 <param name="out_qualifiers|rmaxseq2" value="5"/>
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118 <output name="out_file1" file="emboss_fuzznuc_out2.tabular"/>
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119 </test>
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120 </tests>
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121 <help>
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122 .. class:: warningmark
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123
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124 The input dataset needs to be sequences.
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125
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126 -----
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127
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128 You can view the original documentation here_.
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129
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130 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzznuc.html
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131 </help>
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132 <expand macro="citations" />
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133 </tool>