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comparison multiqc.xml @ 26:d2aaac19f42f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
author iuc
date Tue, 11 Feb 2025 10:13:08 +0000
parents f7e2f1eb3a16
children 7591bce96601
comparison
equal deleted inserted replaced
25:a7e081ceb76a 26:d2aaac19f42f
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>sambamba_plugin.xml</import>
26 </macros> 27 </macros>
27 <expand macro="bio_tools"/> 28 <expand macro="bio_tools"/>
28 <expand macro="requirements"/> 29 <expand macro="requirements"/>
29 <version_command>multiqc --version</version_command> 30 <version_command>multiqc --version</version_command>
30 <command detect_errors="aggressive"> 31 <command detect_errors="aggressive">
141 #end for 142 #end for
142 #elif str($repeat.software_cond.software) == "trimmomatic" 143 #elif str($repeat.software_cond.software) == "trimmomatic"
143 @TRIMMOMATIC_COMMAND@ 144 @TRIMMOMATIC_COMMAND@
144 #elif str($repeat.software_cond.software) == "vcftools" 145 #elif str($repeat.software_cond.software) == "vcftools"
145 @VCFTOOLS_COMMAND@ 146 @VCFTOOLS_COMMAND@
147 #elif str($repeat.software_cond.software) == "sambamba"
148 @SAMBAMBA_COMMAND@
146 #else if str($repeat.software_cond.software) == "custom_content": 149 #else if str($repeat.software_cond.software) == "custom_content":
147 #set $configfile = "T" 150 #set $configfile = "T"
148 #for $j, $file in enumerate( $repeat.software_cond.input ) 151 #for $j, $file in enumerate( $repeat.software_cond.input )
149 #set file_path = os.path.join($software_dir, 'file_' + str($i) + '_' + str($j)) 152 #set file_path = os.path.join($software_dir, 'file_' + str($i) + '_' + str($j))
150 ln -s '$file' '$file_path' && 153 ln -s '$file' '$file_path' &&
234 <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>--> 237 <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>-->
235 <option value="rseqc">RSeQC</option> 238 <option value="rseqc">RSeQC</option>
236 <!--<option value="salmon">Salmon</option>--> 239 <!--<option value="salmon">Salmon</option>-->
237 <option value="samblaster">Samblaster</option> 240 <option value="samblaster">Samblaster</option>
238 <option value="samtools">Samtools</option> 241 <option value="samtools">Samtools</option>
242 <option value="sambamba">Sambamba</option>
239 <!--<option value="sargasso">Sargasso</option>--> 243 <!--<option value="sargasso">Sargasso</option>-->
240 <!--<option value="seqyclean">SeqyClean</option>--> 244 <!--<option value="seqyclean">SeqyClean</option>-->
241 <!--<option value="sexdeterrmine">SexDetErrmine</option>--> 245 <!--<option value="sexdeterrmine">SexDetErrmine</option>-->
242 <!--<option value="skewer">Skewer</option>--> 246 <!--<option value="skewer">Skewer</option>-->
243 <option value="slamdunk">Slamdunk</option> 247 <option value="slamdunk">Slamdunk</option>
346 <when value="trimmomatic"> 350 <when value="trimmomatic">
347 <expand macro="trimmomatic_form"/> 351 <expand macro="trimmomatic_form"/>
348 </when> 352 </when>
349 <when value="vcftools"> 353 <when value="vcftools">
350 <expand macro="vcftools_form"/> 354 <expand macro="vcftools_form"/>
355 </when>
356 <when value="sambamba">
357 <expand macro="sambamba_form"/>
351 </when> 358 </when>
352 <when value="custom_content"> 359 <when value="custom_content">
353 <param argument="plot_type" label="The plot type to visualise the data with" type="select"> 360 <param argument="plot_type" label="The plot type to visualise the data with" type="select">
354 <option value="linegraph">linegraph</option> 361 <option value="linegraph">linegraph</option>
355 <option value="bargraph">bargraph</option> 362 <option value="bargraph">bargraph</option>
423 <!-- Test 20 --> 430 <!-- Test 20 -->
424 <expand macro="qualimap_test"/> 431 <expand macro="qualimap_test"/>
425 <expand macro="gatk_test"/> 432 <expand macro="gatk_test"/>
426 <expand macro="bamtools_test"/> 433 <expand macro="bamtools_test"/>
427 <expand macro="pycoqc_test"/> 434 <expand macro="pycoqc_test"/>
435 <expand macro="sambamba_test"/>
428 436
429 <!--expand macro="vcftools_test"/> Does not work, did it ever worked? --> 437 <!--expand macro="vcftools_test"/> Does not work, did it ever worked? -->
430 438
431 </tests> 439 </tests>
432 <help><![CDATA[ 440 <help><![CDATA[