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comparison blat.xml @ 13:820f68ad34a7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ commit f38778f3a25020809c3f6cf17aafb8dbfc54b2e8
author iuc
date Sat, 28 Sep 2024 16:29:35 +0000
parents e79965d0351c
children
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12:e79965d0351c 13:820f68ad34a7
1 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>BLAST-like sequence alignment tool</description> 2 <description>BLAST-like sequence alignment tool</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">377</token> 4 <token name="@TOOL_VERSION@">469</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 6
7 <xml name="mask_cond" tokens="maskarg,label,help"> 7 <xml name="mask_cond" tokens="maskarg,label,help">
8 <conditional name="@MASKARG@_type"> 8 <conditional name="@MASKARG@_type">
9 <param argument="-@MASKARG@" type="select" label="@LABEL@" help="@HELP@"> 9 <param argument="-@MASKARG@" type="select" label="@LABEL@" help="@HELP@">
10 <option value="" selected="true">No masking</option> 10 <option value="" selected="true">No masking</option>
178 </section> 178 </section>
179 <param argument="-dots" type="integer" value="" optional="true" label="Output a dot every N sequences in log" help="Dots show program's progress" /> 179 <param argument="-dots" type="integer" value="" optional="true" label="Output a dot every N sequences in log" help="Dots show program's progress" />
180 <param name="out" type="select" label="Select output file format (-out)"> 180 <param name="out" type="select" label="Select output file format (-out)">
181 <option value="psl">Tab-separated format, no sequence (psl)</option> 181 <option value="psl">Tab-separated format, no sequence (psl)</option>
182 <option value="psl -noHead">Tab-separated format, no sequence, no header (psl -noHead)</option> 182 <option value="psl -noHead">Tab-separated format, no sequence, no header (psl -noHead)</option>
183 <option value="pslx">Tab-separated format (pslx)</option>
184 <option value="pslx -noHead">Tab-separated format, no header (pslx -noHead)</option>
183 <option value="axt">Blastz-associated axt format (axt)</option> 185 <option value="axt">Blastz-associated axt format (axt)</option>
184 <option value="maf">Multiz-associated maf format (maf)</option> 186 <option value="maf">Multiz-associated maf format (maf)</option>
185 <option value="sim4">Similar to sim4 format (sim4)</option> 187 <option value="sim4">Similar to sim4 format (sim4)</option>
186 <option value="wublast">Similar to WU-BLAST format (wublast)</option> 188 <option value="wublast">Similar to WU-BLAST format (wublast)</option>
187 <option value="blast">Similar to NCBI BLAST format (blast)</option> 189 <option value="blast">Similar to NCBI BLAST format (blast)</option>
236 <section name="adv_align"> 238 <section name="adv_align">
237 <param name="tileSize" value="5"/><!--explicitly set default .. to check if it is on the CL--> 239 <param name="tileSize" value="5"/><!--explicitly set default .. to check if it is on the CL-->
238 <param name="stepSize" value="5"/><!--explicitly set default .. to check if it is on the CL--> 240 <param name="stepSize" value="5"/><!--explicitly set default .. to check if it is on the CL-->
239 </section> 241 </section>
240 <param name="out" value="psl -noHead" /> 242 <param name="out" value="psl -noHead" />
241 <output name="output" value="dbia3/dbia3.sorted.psl" ftype="tabular" sort="true"/> 243 <output name="output" value="dbia3/dbia3.sorted.psl" ftype="tabular" sort="true">
244 <assert_contents>
245 <has_n_columns n="21"/>
246 </assert_contents>
247 </output>
248 <assert_command>
249 <has_text text="-tileSize=5"/>
250 <has_text text="-mask" negate="true"/>
251 </assert_command>
252 </test>
253 <test>
254 <conditional name="reference_source">
255 <param name="reference_source_selector" value="cached"/>
256 <param name="database" value="dbdia display name"/>
257 </conditional>
258 <param name="query" value="dbia3/dmel-transcript.fa" ftype="fasta" />
259 <param name="database_type" value="dnax" />
260 <param name="query_type" value="rnax" />
261 <section name="basic_align">
262 <param name="maxIntron" value="" />
263 </section>
264 <section name="adv_align">
265 <param name="tileSize" value="5"/><!--explicitly set default .. to check if it is on the CL-->
266 <param name="stepSize" value="5"/><!--explicitly set default .. to check if it is on the CL-->
267 </section>
268 <param name="out" value="pslx -noHead" />
269 <output name="output" value="dbia3/dbia3.sorted.psl" ftype="tabular" sort="true" compare="contains">
270 <assert_contents>
271 <has_n_columns n="23"/>
272 </assert_contents>
273 </output>
242 <assert_command> 274 <assert_command>
243 <has_text text="-tileSize=5"/> 275 <has_text text="-tileSize=5"/>
244 <has_text text="-mask" negate="true"/> 276 <has_text text="-mask" negate="true"/>
245 </assert_command> 277 </assert_command>
246 </test> 278 </test>