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comparison multiqc.xml @ 27:b7e8663db1ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee
author iuc
date Tue, 18 Feb 2025 23:17:45 +0000
parents 1206c725e45a
children e99aaf069191
comparison
equal deleted inserted replaced
26:1206c725e45a 27:b7e8663db1ec
21 <import>salmon_plugin.xml</import> 21 <import>salmon_plugin.xml</import>
22 <import>samtools_plugin.xml</import> 22 <import>samtools_plugin.xml</import>
23 <import>star_plugin.xml</import> 23 <import>star_plugin.xml</import>
24 <import>trimmomatic_plugin.xml</import> 24 <import>trimmomatic_plugin.xml</import>
25 <import>vcftools_plugin.xml</import> 25 <import>vcftools_plugin.xml</import>
26 <import>kraken_plugin.xml</import>
27 <import>diamond_plugin.xml</import>
28 <import>bakta_plugin.xml</import>
29 <import>freyja_plugin.xml</import>
30 <import>checkm_plugin.xml</import>
31 <import>pairtools_plugin.xml</import>
32 <import>porechop_plugin.xml</import>
33 <import>snippy_plugin.xml</import>
34 <import>metaphlan_plugin.xml</import>
35 <import>bbduk_plugin.xml</import>
36 <import>megahit_plugin.xml</import>
37 <import>nonpareil_plugin.xml</import>
38 <import>gtdbtk_plugin.xml</import>
26 <import>sambamba_plugin.xml</import> 39 <import>sambamba_plugin.xml</import>
27 </macros> 40 </macros>
28 <expand macro="bio_tools"/> 41 <expand macro="bio_tools"/>
29 <expand macro="requirements"/> 42 <expand macro="requirements"/>
30 <version_command>multiqc --version</version_command> 43 <version_command>multiqc --version</version_command>
142 #end for 155 #end for
143 #elif str($repeat.software_cond.software) == "trimmomatic" 156 #elif str($repeat.software_cond.software) == "trimmomatic"
144 @TRIMMOMATIC_COMMAND@ 157 @TRIMMOMATIC_COMMAND@
145 #elif str($repeat.software_cond.software) == "vcftools" 158 #elif str($repeat.software_cond.software) == "vcftools"
146 @VCFTOOLS_COMMAND@ 159 @VCFTOOLS_COMMAND@
160 #elif str($repeat.software_cond.software) == "kraken"
161 @KRAKEN_COMMAND@
162 #elif str($repeat.software_cond.software) == "diamond"
163 @DIAMOND_COMMAND@
164 #elif str($repeat.software_cond.software) == "bakta"
165 @BAKTA_COMMAND@
166 #elif str($repeat.software_cond.software) == "freyja"
167 @FREYJA_COMMAND@
168 #elif str($repeat.software_cond.software) == "checkm"
169 @CHECKM_COMMAND@
170 #elif str($repeat.software_cond.software) == "pairtools"
171 @PAIRTOOLS_COMMAND@
172 #elif str($repeat.software_cond.software) == "porechop"
173 @PORECHOP_COMMAND@
174 #elif str($repeat.software_cond.software) == "snippy"
175 @SNIPPY_COMMAND@
176 #elif str($repeat.software_cond.software) == "metaphlan"
177 @METAPHLAN_COMMAND@
178 #elif str($repeat.software_cond.software) == "bbduk"
179 @BBDUK_COMMAND@
180 #elif str($repeat.software_cond.software) == "megahit"
181 @MEGAHIT_COMMAND@
182 #elif str($repeat.software_cond.software) == "nonpareil"
183 @NONPAREIL_COMMAND@
184 #elif str($repeat.software_cond.software) == "gtdbtk"
185 @GTDBTK_COMMAND@
147 #elif str($repeat.software_cond.software) == "sambamba" 186 #elif str($repeat.software_cond.software) == "sambamba"
148 @SAMBAMBA_COMMAND@ 187 @SAMBAMBA_COMMAND@
149 #else if str($repeat.software_cond.software) == "custom_content": 188 #else if str($repeat.software_cond.software) == "custom_content":
150 #set $configfile = "T" 189 #set $configfile = "T"
151 #for $j, $file in enumerate( $repeat.software_cond.input ) 190 #for $j, $file in enumerate( $repeat.software_cond.input )
251 <!--<option value="supernova">Supernova</option>--> 290 <!--<option value="supernova">Supernova</option>-->
252 <!--<option value="theta2">THeTA2</option>--> 291 <!--<option value="theta2">THeTA2</option>-->
253 <option value="tophat">TopHat2 (TopHat2 is deprecated you should not use it)</option> 292 <option value="tophat">TopHat2 (TopHat2 is deprecated you should not use it)</option>
254 <option value="trimmomatic">Trimmomatic</option> 293 <option value="trimmomatic">Trimmomatic</option>
255 <option value="vcftools">VCFTools</option> 294 <option value="vcftools">VCFTools</option>
295 <option value="kraken">Kraken 1 or 2</option>
296 <option value="diamond">DIAMOND</option>
297 <option value="bakta">Bakta</option>
298 <option value="freyja">Freyja</option>
299 <option value="checkm">CheckM</option>
300 <option value="pairtools">pairtools</option>
301 <option value="porechop">Porechop</option>
302 <option value="snippy">Snippy</option>
303 <option value="metaphlan">MetaPhlAn</option>
304 <option value="bbduk">BBDuk</option>
305 <option value="megahit">MEGAHIT</option>
306 <option value="nonpareil">Nonpareil</option>
307 <option value="gtdbtk">GTDB-Tk</option>
256 <!--<option value="verifybamid">VerifyBAMID</option>--> 308 <!--<option value="verifybamid">VerifyBAMID</option>-->
257 <!--Custom--> 309 <!--Custom-->
258 <option value="custom_content">Custom Content</option> 310 <option value="custom_content">Custom Content</option>
259 </param> 311 </param>
260 <when value="bamtools"> 312 <when value="bamtools">
350 <when value="trimmomatic"> 402 <when value="trimmomatic">
351 <expand macro="trimmomatic_form"/> 403 <expand macro="trimmomatic_form"/>
352 </when> 404 </when>
353 <when value="vcftools"> 405 <when value="vcftools">
354 <expand macro="vcftools_form"/> 406 <expand macro="vcftools_form"/>
407 </when>
408 <when value="kraken">
409 <expand macro="kraken_form"/>
410 </when>
411 <when value="diamond">
412 <expand macro="diamond_form"/>
413 </when>
414 <when value="bakta">
415 <expand macro="bakta_form"/>
416 </when>
417 <when value="freyja">
418 <expand macro="freyja_form"/>
419 </when>
420 <when value="checkm">
421 <expand macro="checkm_form"/>
422 </when>
423 <when value="pairtools">
424 <expand macro="pairtools_form"/>
425 </when>
426 <when value="porechop">
427 <expand macro="porechop_form"/>
428 </when>
429 <when value="snippy">
430 <expand macro="snippy_form"/>
431 </when>
432 <when value="metaphlan">
433 <expand macro="metaphlan_form"/>
434 </when>
435 <when value="bbduk">
436 <expand macro="bbduk_form"/>
437 </when>
438 <when value="megahit">
439 <expand macro="megahit_form"/>
440 </when>
441 <when value="nonpareil">
442 <expand macro="nonpareil_form"/>
443 </when>
444 <when value="gtdbtk">
445 <expand macro="gtdbtk_form"/>
355 </when> 446 </when>
356 <when value="sambamba"> 447 <when value="sambamba">
357 <expand macro="sambamba_form"/> 448 <expand macro="sambamba_form"/>
358 </when> 449 </when>
359 <when value="custom_content"> 450 <when value="custom_content">
430 <!-- Test 20 --> 521 <!-- Test 20 -->
431 <expand macro="qualimap_test"/> 522 <expand macro="qualimap_test"/>
432 <expand macro="gatk_test"/> 523 <expand macro="gatk_test"/>
433 <expand macro="bamtools_test"/> 524 <expand macro="bamtools_test"/>
434 <expand macro="pycoqc_test"/> 525 <expand macro="pycoqc_test"/>
526 <expand macro="kraken_test"/>
527 <expand macro="diamond_test"/>
528 <expand macro="bakta_test"/>
529 <expand macro="freyja_test"/>
530 <expand macro="checkm_test"/>
531 <expand macro="pairtools_test"/>
532 <expand macro="porechop_test"/>
533 <expand macro="snippy_test"/>
534 <expand macro="metaphlan_test"/>
535 <expand macro="bbduk_test"/>
536 <expand macro="megahit_test"/>
537 <expand macro="nonpareil_test"/>
538 <expand macro="gtdbtk_test"/>
435 <expand macro="sambamba_test"/> 539 <expand macro="sambamba_test"/>
436 540
437 <!--expand macro="vcftools_test"/> Does not work, did it ever worked? --> 541 <!--expand macro="vcftools_test"/> Does not work, did it ever worked? -->
438 542
439 </tests> 543 </tests>