Mercurial > repos > iuc > seqkit_locate
comparison seqkit_locate.xml @ 1:6510652376b1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit e0bd99c950e2c5f403474fad5af0be3829c93607
author | iuc |
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date | Sun, 06 Nov 2022 17:48:00 +0000 |
parents | 642d73815dd1 |
children | 5fb2dc40c4de |
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0:642d73815dd1 | 1:6510652376b1 |
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30 $advanced_options.use_fmi | 30 $advanced_options.use_fmi |
31 #end if | 31 #end if |
32 $advanced_options.non_greedy | 32 $advanced_options.non_greedy |
33 $advanced_options.only_positive_strand | 33 $advanced_options.only_positive_strand |
34 $advanced_options.id_ncbi | 34 $advanced_options.id_ncbi |
35 --seq-type $seq_type | |
35 '${input_identifier}' | 36 '${input_identifier}' |
36 > '$output' | 37 > '$output' |
37 ]]></command> | 38 ]]></command> |
38 <inputs> | 39 <inputs> |
39 <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/> | 40 <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/> |
71 </when> | 72 </when> |
72 <when value="file"> | 73 <when value="file"> |
73 <param argument="--pattern-file" type="data" format="fasta" label="Pattern/motif file"/> | 74 <param argument="--pattern-file" type="data" format="fasta" label="Pattern/motif file"/> |
74 </when> | 75 </when> |
75 </conditional> | 76 </conditional> |
77 <param argument="--seq-type" type="select" label="Sequence type" help="For automatic detection, it automatically detect by the first sequence. Default: auto"> | |
78 <option value="auto">Automatic detection</option> | |
79 <option value="dna">DNA</option> | |
80 <option value="rna">RNA</option> | |
81 <option value="protein">Protein</option> | |
82 </param> | |
76 <param name="output_mode" type="select" label="Output mode"> | 83 <param name="output_mode" type="select" label="Output mode"> |
77 <option value="">Tabular (default format)</option> | 84 <option value="">Tabular (default format)</option> |
78 <option value="--gtf">GTF</option> | 85 <option value="--gtf">GTF</option> |
79 <option value="--bed">BED6</option> | 86 <option value="--bed">BED6</option> |
80 </param> | 87 </param> |
141 <section name="advanced_options"> | 148 <section name="advanced_options"> |
142 <param name="use_fmi" value="true"/> | 149 <param name="use_fmi" value="true"/> |
143 </section> | 150 </section> |
144 <output name="output" file="locate_output3.gtf" ftype="gtf"/> | 151 <output name="output" file="locate_output3.gtf" ftype="gtf"/> |
145 </test> | 152 </test> |
153 <test expect_num_outputs="1"> | |
154 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/> | |
155 <conditional name="conditional_pattern"> | |
156 <param name="mode" value="expression"/> | |
157 <param name="pattern" value="ATAGAT"/> | |
158 </conditional> | |
159 <param name="seq_type" value="dna"/> | |
160 <section name="advanced_options"> | |
161 <param name="max_mismatch" value="1"/> | |
162 </section> | |
163 <output name="output" file="locate_output1.tabular" ftype="tabular"/> | |
164 </test> | |
146 </tests> | 165 </tests> |
147 <help> | 166 <help> |
148 .. class:: infomark | 167 .. class:: infomark |
149 | 168 |
150 **Purpose** | 169 **Purpose** |