Mercurial > repos > iuc > seqkit_locate

comparison seqkit_locate.xml @ 6:f8cdd98a4380 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
author iuc
date Fri, 26 Sep 2025 16:46:23 +0000
parents 03b29dff91e4
children
comparison
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5:a950264098be 6:f8cdd98a4380
10 10
11 #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier)) 11 #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
12 ln -s '${input}' '${input_identifier}' && 12 ln -s '${input}' '${input_identifier}' &&
13 13
14 seqkit locate 14 seqkit locate
15 --threads \${GALAXY_SLOTS:-4} 15 --threads "\${GALAXY_SLOTS:-4}"
16 #if $conditional_pattern.mode == 'expression' 16 #if $conditional_pattern.mode == 'expression'
17 --pattern '"$conditional_pattern.pattern"' 17 --pattern '"$conditional_pattern.pattern"'
18 $conditional_pattern.use_regexp 18 $conditional_pattern.use_regexp
19 #else 19 #else
20 --pattern-file '$conditional_pattern.pattern_file' 20 --pattern-file '$conditional_pattern.pattern_file'
59 <add value="\"/> 59 <add value="\"/>
60 <add value="["/> 60 <add value="["/>
61 <add value="]"/> 61 <add value="]"/>
62 <add value="."/> 62 <add value="."/>
63 <add value=","/> 63 <add value=","/>
64 <add value=":"/>
64 </valid> 65 </valid>
65 </sanitizer> 66 </sanitizer>
66 <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator> 67 <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator>
67 </param> 68 </param>
68 <param argument="--use-regexp" type="boolean" truevalue="--use-regexp" falsevalue="" checked="false" label="Pattern/motifs are regular expressions"/> 69 <param argument="--use-regexp" type="boolean" truevalue="--use-regexp" falsevalue="" checked="false" label="Pattern/motifs are regular expressions"/>
116 </test> 117 </test>
117 <test expect_num_outputs="1"> 118 <test expect_num_outputs="1">
118 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/> 119 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
119 <conditional name="conditional_pattern"> 120 <conditional name="conditional_pattern">
120 <param name="mode" value="expression"/> 121 <param name="mode" value="expression"/>
122 <param name="pattern" value="A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)"/>
123 <param name="use_regexp" value="true"/>
124 </conditional>
125 <output name="output" ftype="tabular">
126 <assert_contents>
127 <has_n_lines n="372"/>
128 <has_n_columns n="7"/>
129 </assert_contents>
130 </output>
131 </test>
132 <test expect_num_outputs="1">
133 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
134 <conditional name="conditional_pattern">
135 <param name="mode" value="expression"/>
121 <param name="pattern" value="A[TU]G"/> 136 <param name="pattern" value="A[TU]G"/>
122 <param name="use_regexp" value="true"/> 137 <param name="use_regexp" value="true"/>
123 </conditional> 138 </conditional>
124 <param name="output_mode" value="--bed"/> 139 <param name="output_mode" value="--bed"/>
125 <section name="advanced_options"> 140 <section name="advanced_options">