Mercurial > repos > iuc > seqkit_locate

annotate seqkit_locate.xml @ 7:e3ea1c01423a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit commit 3e9d74190f9a12f75b044a302ba1a70bd866831c
author iuc
date Thu, 04 Dec 2025 12:48:32 +0000
parents f8cdd98a4380
children
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1 <tool id="seqkit_locate" name="SeqKit locate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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"/>
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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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11 #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
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12 ln -s '${input}' '${input_identifier}' &&
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14 seqkit locate
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15 --threads "\${GALAXY_SLOTS:-4}"
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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'
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21 #end if
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22 $output_mode
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23 $advanced_options.circular
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24 $advanced_options.degenerate
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25 $advanced_options.hide_matched
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26 $advanced_options.ignore_case
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27 #if not $advanced_options.degenerate
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28 --max-mismatch $advanced_options.max_mismatch
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29 $advanced_options.use_fmi
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30 #end if
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31 $advanced_options.non_greedy
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32 $advanced_options.only_positive_strand
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33 $advanced_options.id_ncbi
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34 --seq-type $seq_type
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35 '${input_identifier}'
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36 > '$output'
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37 ]]></command>
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38 <inputs>
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39 <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/>
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40 <conditional name="conditional_pattern">
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41 <param name="mode" type="select" label="Pattern mode" help="Specify a pattern/motif sequence or a FASTA file with the motif of interest. Motifs could be EITHER plain sequence containing 'ACTGN' OR regular expression like 'A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)' for ORFs">
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42 <option value="expression">Pattern/motif sequence</option>
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43 <option value="file">FASTA file with the pattern/motif of interest</option>
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44 </param>
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45 <when value="expression">
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46 <param argument="--pattern" type="text" value="" label="Pattern/motif sequence" help="Perl regular expressions are allowed">
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47 <sanitizer invalid_char="">
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48 <valid initial="string.letters,string.digits">
2
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49 <add value="^"/>
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50 <add value="$"/>
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51 <add value="("/>
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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=","/>
6
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64 <add value=":"/>
0
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65 </valid>
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66 </sanitizer>
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67 <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator>
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68 </param>
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69 <param argument="--use-regexp" type="boolean" truevalue="--use-regexp" falsevalue="" checked="false" label="Pattern/motifs are regular expressions"/>
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70 </when>
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71 <when value="file">
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72 <param argument="--pattern-file" type="data" format="fasta" label="Pattern/motif file"/>
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73 </when>
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74 </conditional>
1
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75 <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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76 <option value="auto">Automatic detection</option>
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77 <option value="dna">DNA</option>
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78 <option value="rna">RNA</option>
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79 <option value="protein">Protein</option>
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80 </param>
0
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81 <param name="output_mode" type="select" label="Output mode">
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82 <option value="">Tabular (default format)</option>
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83 <option value="--gtf">GTF</option>
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84 <option value="--bed">BED6</option>
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85 </param>
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86 <section name="advanced_options" title="Advanced options">
2
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87 <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" checked="false" label="Circular genome" 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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88 <param argument="--degenerate" type="boolean" truevalue="--degenerate" falsevalue="" checked="false" label="Pattern/motif contains degenerate bases" help="Do not use degenerate bases/residues in regular expression, you need convert them to regular expression, e.g., change 'N' or 'X' to '.'"/>
0
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89 <param argument="--hide-matched" type="boolean" truevalue="--hide-matched" falsevalue="" checked="false" label="Do not show matched sequences"/>
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90 <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" checked="false" label="Ignore case"/>
2
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91 <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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92 <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"/>
0
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93 <param argument="--only-positive-strand" type="boolean" truevalue="--only-positive-strand" falsevalue="" checked="false" label="Only search on positive strand"/>
2
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94 <param argument="--use-fmi" type="boolean" truevalue="--use-fmi" falsevalue="" checked="false" label="FM-index" 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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95 <param argument="--id-ncbi" type="boolean" truevalue="--id-ncbi" falsevalue="" checked="false" label="FASTA head is NCBI stype" help="Example: &gt;gi|110645304|ref|NC_002516.2| Pseud..."/>
0
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96 </section>
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97 </inputs>
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98 <outputs>
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99 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
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100 <change_format>
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101 <when input="output_mode" value="--gtf" format="gtf"/>
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102 <when input="output_mode" value="--bed" format="bed"/>
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103 </change_format>
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104 </data>
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105 </outputs>
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106 <tests>
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107 <test expect_num_outputs="1">
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108 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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109 <conditional name="conditional_pattern">
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110 <param name="mode" value="expression"/>
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111 <param name="pattern" value="ATAGAT"/>
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112 </conditional>
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113 <section name="advanced_options">
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114 <param name="max_mismatch" value="1"/>
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115 </section>
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116 <output name="output" file="locate_output1.tabular" ftype="tabular"/>
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117 </test>
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118 <test expect_num_outputs="1">
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119 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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120 <conditional name="conditional_pattern">
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121 <param name="mode" value="expression"/>
6
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122 <param name="pattern" value="A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)"/>
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123 <param name="use_regexp" value="true"/>
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124 </conditional>
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125 <output name="output" ftype="tabular">
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126 <assert_contents>
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127 <has_n_lines n="372"/>
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128 <has_n_columns n="7"/>
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129 </assert_contents>
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130 </output>
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131 </test>
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132 <test expect_num_outputs="1">
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133 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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134 <conditional name="conditional_pattern">
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135 <param name="mode" value="expression"/>
0
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136 <param name="pattern" value="A[TU]G"/>
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137 <param name="use_regexp" value="true"/>
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138 </conditional>
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139 <param name="output_mode" value="--bed"/>
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140 <section name="advanced_options">
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141 <param name="circular" value="true"/>
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142 <param name="hide_matched" value="true"/>
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143 <param name="ignore_case" value="true"/>
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144 <param name="only_positive_strand" value="true"/>
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145 <param name="id_ncbi" value="true"/>
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146 </section>
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147 <output name="output" file="locate_output2.bed" ftype="bed"/>
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148 </test>
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149 <test expect_num_outputs="1">
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150 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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151 <conditional name="conditional_pattern">
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152 <param name="mode" value="file"/>
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153 <param name="pattern_file" value="motif_sequence.fasta"/>
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154 </conditional>
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155 <param name="output_mode" value="--gtf"/>
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156 <section name="advanced_options">
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157 <param name="use_fmi" value="true"/>
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158 </section>
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159 <output name="output" file="locate_output3.gtf" ftype="gtf"/>
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160 </test>
1
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161 <test expect_num_outputs="1">
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162 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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163 <conditional name="conditional_pattern">
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164 <param name="mode" value="expression"/>
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165 <param name="pattern" value="ATAGAT"/>
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166 </conditional>
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167 <param name="seq_type" value="dna"/>
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168 <section name="advanced_options">
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169 <param name="max_mismatch" value="1"/>
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170 </section>
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171 <output name="output" file="locate_output1.tabular" ftype="tabular"/>
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172 </test>
0
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173 </tests>
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174 <help>
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175 .. class:: infomark
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176
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177 **Purpose**
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178
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179 Locate subsequences/motifs, mismatch allowed.
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180
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181 ------
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182
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183 .. class:: infomark
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184
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185 **Attention**
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186
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187 1. Motifs could be EITHER plain sequence containing "ACTGN" OR regular
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188 expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.
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189 2. Degenerate bases/residues like "RYMM.." are also supported by flag -d.
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190 But do not use degenerate bases/residues in regular expression, you need
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191 convert them to regular expression, e.g., change "N" or "X" to ".".
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192 3. When providing search patterns (motifs) via flag '-p',
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193 please use double quotation marks for patterns containing comma,
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194 e.g., -p '"A{2,}"' or -p "\"A{2,}\"". Because the command line argument
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195 parser accepts comma-separated-values (CSV) for multiple values (motifs).
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196 Patterns in file do not follow this rule.
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197 4. Mismatch is allowed using flag "-m/--max-mismatch",
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198 you can increase the value of "-j/--threads" to accelerate processing.
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199 5. When using flag --circular, end position of matched subsequence that
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200 crossing genome sequence end would be greater than sequence length.
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201 </help>
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202 <expand macro="citations"/>
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203 </tool>