Mercurial > repos > iuc > seqkit_locate

annotate seqkit_locate.xml @ 1:6510652376b1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit e0bd99c950e2c5f403474fad5af0be3829c93607
author iuc
date Sun, 06 Nov 2022 17:48:00 +0000
parents 642d73815dd1
children 5fb2dc40c4de
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642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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1 <tool id="seqkit_locate" name="SeqKit locate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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2 <description>subsequences/motifs, mismatch allowed</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import re
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10
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11 #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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12 ln -s '${input}' '${input_identifier}' &&
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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13
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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14 seqkit locate
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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15 --threads \${GALAXY_SLOTS:-4}
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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16 #if $conditional_pattern.mode == 'expression'
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17 --pattern '"$conditional_pattern.pattern"'
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18 $conditional_pattern.use_regexp
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19 #else
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20 --pattern-file '$conditional_pattern.pattern_file'
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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21 #end if
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22 $output_mode
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23 --validate-seq-length $advanced_options.validate_seq_length
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24 $advanced_options.circular
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25 $advanced_options.degenerate
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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26 $advanced_options.hide_matched
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27 $advanced_options.ignore_case
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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28 #if not $advanced_options.degenerate
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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29 --max-mismatch $advanced_options.max_mismatch
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30 $advanced_options.use_fmi
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31 #end if
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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32 $advanced_options.non_greedy
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33 $advanced_options.only_positive_strand
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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34 $advanced_options.id_ncbi
1
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35 --seq-type $seq_type
0
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36 '${input_identifier}'
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37 > '$output'
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38 ]]></command>
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39 <inputs>
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40 <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/>
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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41 <conditional name="conditional_pattern">
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42 <param name="mode" type="select" label="Pattern mode"
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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43 help="Specify a pattern/motif sequence or a FASTA file with the motif of interest. Motifs could be EITHER plain sequence containing 'ACTGN' OR regular
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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44 expression like 'A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)' for ORFs">
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45 <option value="expression">Pattern/motif sequence</option>
642d73815dd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
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46 <option value="file">FASTA file with the pattern/motif of interest</option>
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47 </param>
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48 <when value="expression">
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49 <param argument="--pattern" type="text" value="" label="Pattern/motif sequence" help="Perl regular expressions are allowed">
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50 <sanitizer invalid_char="">
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51 <valid initial="string.letters,string.digits">
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52 <add value="^"/>
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53 <add value="$"/>
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54 <add value="("/>
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55 <add value=")"/>
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56 <add value="|"/>
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57 <add value="?"/>
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58 <add value="*"/>
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59 <add value="+"/>
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60 <add value="{"/>
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61 <add value="}"/>
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62 <add value="\"/>
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63 <add value="["/>
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64 <add value="]"/>
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65 <add value="."/>
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66 <add value=","/>
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67 </valid>
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68 </sanitizer>
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69 <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator>
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70 </param>
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71 <param argument="--use-regexp" type="boolean" truevalue="--use-regexp" falsevalue="" checked="false" label="Pattern/motifs are regular expressions"/>
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72 </when>
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73 <when value="file">
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74 <param argument="--pattern-file" type="data" format="fasta" label="Pattern/motif file"/>
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75 </when>
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76 </conditional>
1
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77 <param argument="--seq-type" type="select" label="Sequence type" help="For automatic detection, it automatically detect by the first sequence. Default: auto">
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78 <option value="auto">Automatic detection</option>
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79 <option value="dna">DNA</option>
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80 <option value="rna">RNA</option>
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81 <option value="protein">Protein</option>
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82 </param>
0
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83 <param name="output_mode" type="select" label="Output mode">
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84 <option value="">Tabular (default format)</option>
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85 <option value="--gtf">GTF</option>
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86 <option value="--bed">BED6</option>
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87 </param>
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88 <section name="advanced_options" title="Advanced options">
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89 <param argument="--validate-seq-length" type="integer" min="0" value="10000" label="Lenth of the sequence to validate" help="Default: 10000" />
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90 <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" checked="false" label="Circular genome"
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91 help="When using flag --circular, end position of matched subsequence that crossing genome sequence end would be greater than sequence length" />
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92 <param argument="--degenerate" type="boolean" truevalue="--degenerate" falsevalue="" checked="false" label="Pattern/motif contains degenerate bases"
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93 help="Do not use degenerate bases/residues in regular expression, you need convert them to regular expression, e.g., change 'N' or 'X' to '.'"/>
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94 <param argument="--hide-matched" type="boolean" truevalue="--hide-matched" falsevalue="" checked="false" label="Do not show matched sequences"/>
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95 <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" checked="false" label="Ignore case"/>
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96 <param argument="--max-mismatch" type="integer" min="0" value="0" label="Maximum mismatch" help="For large genomes like human genome, using mapping/alignment tools would be faster" />
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97 <param argument="--non-greedy" type="boolean" truevalue="--non-greedy" falsevalue="" checked="false" label="Non-greedy mode" help="Faster, but muy miss motifs overlapping with others" />
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98 <param argument="--only-positive-strand" type="boolean" truevalue="--only-positive-strand" falsevalue="" checked="false" label="Only search on positive strand"/>
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99 <param argument="--use-fmi" type="boolean" truevalue="--use-fmi" falsevalue="" checked="false" label="FM-index"
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100 help="Use FM-index for much faster search of lots of sequence patterns. This option is not compatible with the --degenerate option"/>
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101 <param argument="--id-ncbi" type="boolean" truevalue="--id-ncbi" falsevalue="" checked="false" label="FASTA head is NCBI stype" help="Example: >gi|110645304|ref|NC_002516.2| Pseud..." />
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102 </section>
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103 </inputs>
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104 <outputs>
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105 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
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106 <change_format>
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107 <when input="output_mode" value="--gtf" format="gtf"/>
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108 <when input="output_mode" value="--bed" format="bed"/>
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109 </change_format>
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110 </data>
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111 </outputs>
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112 <tests>
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113 <test expect_num_outputs="1">
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114 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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115 <conditional name="conditional_pattern">
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116 <param name="mode" value="expression"/>
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117 <param name="pattern" value="ATAGAT"/>
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118 </conditional>
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119 <section name="advanced_options">
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120 <param name="max_mismatch" value="1"/>
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121 </section>
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122 <output name="output" file="locate_output1.tabular" ftype="tabular"/>
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123 </test>
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124 <test expect_num_outputs="1">
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125 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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126 <conditional name="conditional_pattern">
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127 <param name="mode" value="expression"/>
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128 <param name="pattern" value="A[TU]G"/>
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129 <param name="use_regexp" value="true"/>
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130 </conditional>
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131 <param name="output_mode" value="--bed"/>
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132 <section name="advanced_options">
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133 <param name="circular" value="true"/>
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134 <param name="hide_matched" value="true"/>
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135 <param name="ignore_case" value="true"/>
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136 <param name="only_positive_strand" value="true"/>
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137 <param name="id_ncbi" value="true"/>
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138 </section>
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139 <output name="output" file="locate_output2.bed" ftype="bed"/>
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140 </test>
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141 <test expect_num_outputs="1">
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142 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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143 <conditional name="conditional_pattern">
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144 <param name="mode" value="file"/>
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145 <param name="pattern_file" value="motif_sequence.fasta"/>
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146 </conditional>
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147 <param name="output_mode" value="--gtf"/>
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148 <section name="advanced_options">
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149 <param name="use_fmi" value="true"/>
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150 </section>
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151 <output name="output" file="locate_output3.gtf" ftype="gtf"/>
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152 </test>
1
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153 <test expect_num_outputs="1">
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154 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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155 <conditional name="conditional_pattern">
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156 <param name="mode" value="expression"/>
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157 <param name="pattern" value="ATAGAT"/>
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158 </conditional>
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159 <param name="seq_type" value="dna"/>
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160 <section name="advanced_options">
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161 <param name="max_mismatch" value="1"/>
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162 </section>
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163 <output name="output" file="locate_output1.tabular" ftype="tabular"/>
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164 </test>
0
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165 </tests>
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166 <help>
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167 .. class:: infomark
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168
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169 **Purpose**
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170
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171 Locate subsequences/motifs, mismatch allowed.
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172
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173 ------
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174
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175 .. class:: infomark
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176
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177 **Attention**
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178
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179 1. Motifs could be EITHER plain sequence containing "ACTGN" OR regular
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180 expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.
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181 2. Degenerate bases/residues like "RYMM.." are also supported by flag -d.
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182 But do not use degenerate bases/residues in regular expression, you need
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183 convert them to regular expression, e.g., change "N" or "X" to ".".
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184 3. When providing search patterns (motifs) via flag '-p',
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185 please use double quotation marks for patterns containing comma,
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186 e.g., -p '"A{2,}"' or -p "\"A{2,}\"". Because the command line argument
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187 parser accepts comma-separated-values (CSV) for multiple values (motifs).
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188 Patterns in file do not follow this rule.
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189 4. Mismatch is allowed using flag "-m/--max-mismatch",
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190 you can increase the value of "-j/--threads" to accelerate processing.
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191 5. When using flag --circular, end position of matched subsequence that
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192 crossing genome sequence end would be greater than sequence length.
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193 </help>
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194 <expand macro="citations"/>
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195 </tool>
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196