Mercurial > repos > iuc > seqkit_locate

comparison seqkit_locate.xml @ 1:592e41e46dad 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 17:45:43 +0000
parents e4c45e798464
children 03b29dff91e4
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0:e4c45e798464 1:592e41e46dad
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**