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comparison antismash.xml @ 5:bc88856eddab draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit dc45770442ff516d6f3733e4bdb284be3163de67
author bgruening
date Tue, 05 Jul 2022 10:37:38 +0000
parents e78e25d3b4bd
children
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4:e78e25d3b4bd 5:bc88856eddab
21 ln -s '$infile' input_tempfile.$file_extension && 21 ln -s '$infile' input_tempfile.$file_extension &&
22 #if $genefinding_gff3 22 #if $genefinding_gff3
23 ln -s $genefinding_gff3 annotation.gff3 && 23 ln -s $genefinding_gff3 annotation.gff3 &&
24 #end if 24 #end if
25 25
26 #if $sideload.file
27 #if $sideload.format == 'harmonize'
28 python '$__tool_directory__/harmonize2antismash.py' '$sideload.file' sideload.json &&
29 #else
30 ln -s '$sideload.file' sideload.json &&
31 #end if
32 #end if
26 33
27 ## create html folder 34 ## create html folder
28 mkdir -p '$htmloutputfolder' && 35 mkdir -p '$htmloutputfolder' &&
29 36
30 antismash 37 antismash
59 --hmmdetection-strictness $advanced_options.hmmdetection_strictness 66 --hmmdetection-strictness $advanced_options.hmmdetection_strictness
60 --cb-nclusters $advanced_options.cb_nclusters 67 --cb-nclusters $advanced_options.cb_nclusters
61 --cb-min-homology-scale $advanced_options.cb_min_homology_scale 68 --cb-min-homology-scale $advanced_options.cb_min_homology_scale
62 --rre-cutoff $advanced_options.rre_cutoff 69 --rre-cutoff $advanced_options.rre_cutoff
63 --rre-minlength $advanced_options.rre_minlength 70 --rre-minlength $advanced_options.rre_minlength
71
72 #if $sideload.file
73 --sideload 'sideload.json'
74 #end if
64 75
65 input_tempfile.$file_extension && 76 input_tempfile.$file_extension &&
66 77
67 ## copy all content to html folder 78 ## copy all content to html folder
68 cp input_tempfile/index.html '${html}' 2> /dev/null && 79 cp input_tempfile/index.html '${html}' 2> /dev/null &&
147 for the query BGC in ClusterBlast results. Default: 0" /> 158 for the query BGC in ClusterBlast results. Default: 0" />
148 <param argument="--rre-cutoff" type="float" min="0" max="100" value="25" label="RRE cutoff" help="Bitscore cutoff for RRE pHMM detection. Default: 25.0" /> 159 <param argument="--rre-cutoff" type="float" min="0" max="100" value="25" label="RRE cutoff" help="Bitscore cutoff for RRE pHMM detection. Default: 25.0" />
149 <param argument="--rre-minlength" type="integer" min="0" max="100" value="50" label="RRE minlength" help="Minimum amino acid length of RRE domains. Default: 50" /> 160 <param argument="--rre-minlength" type="integer" min="0" max="100" value="50" label="RRE minlength" help="Minimum amino acid length of RRE domains. Default: 50" />
150 </section> 161 </section>
151 162
163 <section name="sideload" title="Sideloading" help="Sideloading allows you to load external datasets into AntiSMASH">
164 <param argument="--sideload" name="file" type="data" format="json" optional="true" label="sideload json file" help="Sideload json file to add to your report" />
165 <param name="format" type="select" label="Sideload Format">
166 <option value="harmonize">hAMRonize summarize JSON</option>
167 <option value="native">AntiSMASH JSON</option>
168 </param>
169 </section>
170
152 <param name="outputs" type="select" multiple="true" label="Outputs"> 171 <param name="outputs" type="select" multiple="true" label="Outputs">
153 <option value="html" selected="True">HTML file</option> 172 <option value="html" selected="True">HTML file</option>
154 <option value="all">All results</option> 173 <option value="all">All results</option>
155 <option value="embl">EMBL files</option> 174 <option value="embl">EMBL files</option>
156 <option value="gb">GenBank files</option> 175 <option value="gb">GenBank files</option>
234 <has_text text="HMM detection using strictness: strict"/> 253 <has_text text="HMM detection using strictness: strict"/>
235 </assert_contents> 254 </assert_contents>
236 </output> 255 </output>
237 </test> 256 </test>
238 257
258 <test expect_num_outputs="1">
259 <param name="infile" value="sequence.fasta"/>
260 <section name="sideload">
261 <param name="format" value="native"/>
262 <param name="file" value="sideload.json"/>
263 </section>
264 <output name="html" file="index.4.html"/>
265 </test>
266
267 <test expect_num_outputs="1">
268 <param name="infile" value="sequence.fasta"/>
269 <section name="sideload">
270 <param name="format" value="harmonize"/>
271 <param name="file" value="harmonize.json"/>
272 </section>
273 <output name="html" file="index.5.html"/>
274 </test>
239 </tests> 275 </tests>
240 <help> 276 <help>
241 <![CDATA[ 277 <![CDATA[
242 278
243 **What it does** 279 **What it does**