Mercurial > repos > iuc > multiqc
comparison multiqc.xml @ 30:4981b6c4f7fa draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4
| author | iuc |
|---|---|
| date | Thu, 15 Jan 2026 20:38:43 +0000 |
| parents | ef6bd40a30d2 |
| children |
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| 29:ef6bd40a30d2 | 30:4981b6c4f7fa |
|---|---|
| 19 <import>qualimap_plugin.xml</import> | 19 <import>qualimap_plugin.xml</import> |
| 20 <import>rseqc_plugin.xml</import> | 20 <import>rseqc_plugin.xml</import> |
| 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>sylphtax_plugin.xml</import> | |
| 24 <import>trimmomatic_plugin.xml</import> | 25 <import>trimmomatic_plugin.xml</import> |
| 25 <import>vcftools_plugin.xml</import> | 26 <import>vcftools_plugin.xml</import> |
| 26 <import>kraken_plugin.xml</import> | 27 <import>kraken_plugin.xml</import> |
| 27 <import>diamond_plugin.xml</import> | 28 <import>diamond_plugin.xml</import> |
| 28 <import>bakta_plugin.xml</import> | 29 <import>bakta_plugin.xml</import> |
| 29 <import>freyja_plugin.xml</import> | 30 <import>freyja_plugin.xml</import> |
| 30 <import>checkm_plugin.xml</import> | 31 <import>checkm_plugin.xml</import> |
| 32 <import>checkm2_plugin.xml</import> | |
| 31 <import>pairtools_plugin.xml</import> | 33 <import>pairtools_plugin.xml</import> |
| 32 <import>porechop_plugin.xml</import> | 34 <import>porechop_plugin.xml</import> |
| 33 <import>snippy_plugin.xml</import> | 35 <import>snippy_plugin.xml</import> |
| 34 <import>metaphlan_plugin.xml</import> | 36 <import>metaphlan_plugin.xml</import> |
| 35 <import>bbduk_plugin.xml</import> | 37 <import>bbduk_plugin.xml</import> |
| 39 <import>sambamba_plugin.xml</import> | 41 <import>sambamba_plugin.xml</import> |
| 40 <import>image_content_plugin.xml</import> | 42 <import>image_content_plugin.xml</import> |
| 41 </macros> | 43 </macros> |
| 42 <expand macro="bio_tools"/> | 44 <expand macro="bio_tools"/> |
| 43 <expand macro="requirements"/> | 45 <expand macro="requirements"/> |
| 46 <expand macro="stdio"/> | |
| 44 <version_command>multiqc --version</version_command> | 47 <version_command>multiqc --version</version_command> |
| 45 <command detect_errors="aggressive"> | 48 <command detect_errors="aggressive"> |
| 46 <![CDATA[ | 49 <![CDATA[ |
| 47 #import re | 50 #import re |
| 48 #import os | 51 #import os |
| 146 #elif str($repeat.software_cond.software) == "sortmerna" | 149 #elif str($repeat.software_cond.software) == "sortmerna" |
| 147 #set $pattern = "Minimal SW score based on E-value" | 150 #set $pattern = "Minimal SW score based on E-value" |
| 148 @LN_FILES@ | 151 @LN_FILES@ |
| 149 #else if str($repeat.software_cond.software) == "star": | 152 #else if str($repeat.software_cond.software) == "star": |
| 150 @STAR_COMMAND@ | 153 @STAR_COMMAND@ |
| 154 #elif str($repeat.software_cond.software) == "sylphtax" | |
| 155 @SYLPHTAX_COMMAND@ | |
| 151 #elif str($repeat.software_cond.software) == "tophat" | 156 #elif str($repeat.software_cond.software) == "tophat" |
| 152 #for $file in $repeat.software_cond.input | 157 #for $file in $repeat.software_cond.input |
| 153 @ESCAPE_IDENTIFIER@ | 158 @ESCAPE_IDENTIFIER@ |
| 154 #set file_path = os.path.join($software_dir, str($identifier) + 'align_summary.txt') | 159 #set file_path = os.path.join($software_dir, str($identifier) + 'align_summary.txt') |
| 155 ln -s '$file' '$file_path' && | 160 ln -s '$file' '$file_path' && |
| 166 @BAKTA_COMMAND@ | 171 @BAKTA_COMMAND@ |
| 167 #elif str($repeat.software_cond.software) == "freyja" | 172 #elif str($repeat.software_cond.software) == "freyja" |
| 168 @FREYJA_COMMAND@ | 173 @FREYJA_COMMAND@ |
| 169 #elif str($repeat.software_cond.software) == "checkm" | 174 #elif str($repeat.software_cond.software) == "checkm" |
| 170 @CHECKM_COMMAND@ | 175 @CHECKM_COMMAND@ |
| 176 #elif str($repeat.software_cond.software) == "checkm2" | |
| 177 @CHECKM2_COMMAND@ | |
| 171 #elif str($repeat.software_cond.software) == "pairtools" | 178 #elif str($repeat.software_cond.software) == "pairtools" |
| 172 @PAIRTOOLS_COMMAND@ | 179 @PAIRTOOLS_COMMAND@ |
| 173 #elif str($repeat.software_cond.software) == "porechop" | 180 #elif str($repeat.software_cond.software) == "porechop" |
| 174 @PORECHOP_COMMAND@ | 181 @PORECHOP_COMMAND@ |
| 175 #elif str($repeat.software_cond.software) == "snippy" | 182 #elif str($repeat.software_cond.software) == "snippy" |
| 295 <!--<option value="skewer">Skewer</option>--> | 302 <!--<option value="skewer">Skewer</option>--> |
| 296 <option value="slamdunk">Slamdunk</option> | 303 <option value="slamdunk">Slamdunk</option> |
| 297 <option value="snpeff">SnpEff</option> | 304 <option value="snpeff">SnpEff</option> |
| 298 <option value="sortmerna">SortMeRNA</option> | 305 <option value="sortmerna">SortMeRNA</option> |
| 299 <option value="star">STAR</option> | 306 <option value="star">STAR</option> |
| 307 <option value="sylphtax">Sylph-tax</option> | |
| 300 <!--<option value="supernova">Supernova</option>--> | 308 <!--<option value="supernova">Supernova</option>--> |
| 301 <!--<option value="theta2">THeTA2</option>--> | 309 <!--<option value="theta2">THeTA2</option>--> |
| 302 <option value="tophat">TopHat2 (TopHat2 is deprecated you should not use it)</option> | 310 <option value="tophat">TopHat2 (TopHat2 is deprecated you should not use it)</option> |
| 303 <option value="trimmomatic">Trimmomatic</option> | 311 <option value="trimmomatic">Trimmomatic</option> |
| 304 <option value="vcftools">VCFTools</option> | 312 <option value="vcftools">VCFTools</option> |
| 305 <option value="kraken">Kraken 1 or 2</option> | 313 <option value="kraken">Kraken 1 or 2</option> |
| 306 <option value="diamond">DIAMOND</option> | 314 <option value="diamond">DIAMOND</option> |
| 307 <option value="bakta">Bakta</option> | 315 <option value="bakta">Bakta</option> |
| 308 <option value="freyja">Freyja</option> | 316 <option value="freyja">Freyja</option> |
| 309 <option value="checkm">CheckM</option> | 317 <option value="checkm">CheckM</option> |
| 318 <option value="checkm2">CheckM2</option> | |
| 310 <option value="pairtools">pairtools</option> | 319 <option value="pairtools">pairtools</option> |
| 311 <option value="porechop">Porechop</option> | 320 <option value="porechop">Porechop</option> |
| 312 <option value="snippy">Snippy</option> | 321 <option value="snippy">Snippy</option> |
| 313 <option value="metaphlan">MetaPhlAn</option> | 322 <option value="metaphlan">MetaPhlAn</option> |
| 314 <option value="bbduk">BBDuk</option> | 323 <option value="bbduk">BBDuk</option> |
| 404 <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/> | 413 <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/> |
| 405 </when> | 414 </when> |
| 406 <when value="star"> | 415 <when value="star"> |
| 407 <expand macro="star_form"/> | 416 <expand macro="star_form"/> |
| 408 </when> | 417 </when> |
| 418 <when value="sylphtax"> | |
| 419 <expand macro="sylphtax_form"/> | |
| 420 </when> | |
| 409 <when value="tophat"> | 421 <when value="tophat"> |
| 410 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of TopHat2"/> | 422 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of TopHat2"/> |
| 411 </when> | 423 </when> |
| 412 <when value="trimmomatic"> | 424 <when value="trimmomatic"> |
| 413 <expand macro="trimmomatic_form"/> | 425 <expand macro="trimmomatic_form"/> |
| 427 <when value="freyja"> | 439 <when value="freyja"> |
| 428 <expand macro="freyja_form"/> | 440 <expand macro="freyja_form"/> |
| 429 </when> | 441 </when> |
| 430 <when value="checkm"> | 442 <when value="checkm"> |
| 431 <expand macro="checkm_form"/> | 443 <expand macro="checkm_form"/> |
| 444 </when> | |
| 445 <when value="checkm2"> | |
| 446 <expand macro="checkm2_form"/> | |
| 432 </when> | 447 </when> |
| 433 <when value="pairtools"> | 448 <when value="pairtools"> |
| 434 <expand macro="pairtools_form"/> | 449 <expand macro="pairtools_form"/> |
| 435 </when> | 450 </when> |
| 436 <when value="porechop"> | 451 <when value="porechop"> |
| 551 <expand macro="bbduk_test"/> | 566 <expand macro="bbduk_test"/> |
| 552 <expand macro="megahit_test"/> | 567 <expand macro="megahit_test"/> |
| 553 <expand macro="nonpareil_test"/> | 568 <expand macro="nonpareil_test"/> |
| 554 <expand macro="gtdbtk_test"/> | 569 <expand macro="gtdbtk_test"/> |
| 555 <expand macro="sambamba_test"/> | 570 <expand macro="sambamba_test"/> |
| 571 <expand macro="checkm2_test"/> | |
| 572 <expand macro="sylphtax_test"/> | |
| 556 <!--expand macro="vcftools_test"/> Does not work, did it ever worked? --> | 573 <!--expand macro="vcftools_test"/> Does not work, did it ever worked? --> |
| 557 | 574 |
| 558 </tests> | 575 </tests> |
| 559 <help><![CDATA[ | 576 <help><![CDATA[ |
| 560 **What it does** | 577 **What it does** |