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comparison multiqc.xml @ 16:9c1131228d96 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"
author iuc
date Fri, 09 Oct 2020 14:56:00 +0000
parents 2091f142f7a2
children 71f3455819a0
comparison
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15:2091f142f7a2 16:9c1131228d96
1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1"> 1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy1">
2 <description>aggregate results from bioinformatics analyses into a single report</description> 2 <description>aggregate results from bioinformatics analyses into a single report</description>
3 <macros> 3 <macros>
4 <token name="@WRAPPER_VERSION@">1.7</token> 4 <token name="@WRAPPER_VERSION@">1.8</token>
5 <token name="@ESCAPE_IDENTIFIER@"> 5 <token name="@ESCAPE_IDENTIFIER@">
6 <![CDATA[ 6 <![CDATA[
7 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) 7 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
8 ]]></token> 8 ]]></token>
9 <token name="@CHECK_LN_FILE@"> 9 <token name="@CHECK_LN_FILE@">
113 ln -s '$file' '$file_path' && 113 ln -s '$file' '$file_path' &&
114 #end for 114 #end for
115 #end if 115 #end if
116 #end for 116 #end for
117 #elif str($repeat.software_cond.software) == "bowtie2" 117 #elif str($repeat.software_cond.software) == "bowtie2"
118 #set $pattern = "reads; of these:" 118 #set $pattern = "% overall alignment rate"
119 @LN_FILES@ 119 @LN_FILES@
120 #elif str($repeat.software_cond.software) == "busco" 120 #elif str($repeat.software_cond.software) == "busco"
121 ## Searches for files "short_summary_[samplename].txt" 121 ## Searches for files "short_summary_[samplename].txt"
122 #for $file in $repeat.software_cond.input 122 #for $file in $repeat.software_cond.input
123 @ESCAPE_IDENTIFIER@ 123 @ESCAPE_IDENTIFIER@
248 @LN_2_FILES@ 248 @LN_2_FILES@
249 #elif str($repeat2.type) == "insertsize" 249 #elif str($repeat2.type) == "insertsize"
250 #set $pattern = "picard.analysis.InsertSizeMetrics" 250 #set $pattern = "picard.analysis.InsertSizeMetrics"
251 @LN_2_FILES@ 251 @LN_2_FILES@
252 #elif str($repeat2.type) == "markdups" 252 #elif str($repeat2.type) == "markdups"
253 #set $pattern = "picard.sam.DuplicationMetrics" 253 #set $pattern = "MarkDuplicates"
254 @LN_2_FILES@ 254 @LN_2_FILES@
255 #elif str($repeat2.type) == "oxogmetrics" 255 #elif str($repeat2.type) == "oxogmetrics"
256 #set $pattern = "picard.analysis.CollectOxoGMetrics" 256 #set $pattern = "picard.analysis.CollectOxoGMetrics"
257 @LN_2_FILES@ 257 @LN_2_FILES@
258 #elif str($repeat2.type) == "pcr_metrics" 258 #elif str($repeat2.type) == "pcr_metrics"
270 #end if 270 #end if
271 #end for 271 #end for
272 #elif str($repeat.software_cond.software) == "prokka" 272 #elif str($repeat.software_cond.software) == "prokka"
273 #set $pattern = "contigs:" 273 #set $pattern = "contigs:"
274 @LN_FILES@ 274 @LN_FILES@
275 #elif str($repeat.software_cond.software) == "qualimap"
276 #for $file in $repeat.software_cond.input
277 #if re.search("genome_results", str($file.element_identifier))
278 sample="\$(grep 'bam file = ' $file | sed 's/bam file = //g' | sed 's: ::g')" &&
279 dir_name="$software_dir/\${sample}" &&
280 mkdir -p \${dir_name} &&
281 filepath_1="\${dir_name}/genome_results.txt" &&
282 ln -sf '$file' \${filepath_1} &&
283 #elif re.search("coverage_histogram", str($file.element_identifier))
284 nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
285 mkdir -p \${nested_dir_name} &&
286 filepath_2="\${nested_dir_name}/coverage_histogram.txt" &&
287 ln -sf '$file' \${filepath_2} &&
288 #elif re.search("gc-content_distribution", str($file.element_identifier))
289 nested_dir_name="\${dir_name}/raw_data_qualimapReport/" &&
290 mkdir -p \${nested_dir_name} &&
291 filepath_3="\${nested_dir_name}/mapped_reads_gc-content_distribution.txt" &&
292 ln -sf '$file' \${filepath_3} &&
293 #else
294 #pass
295 #end if
296 #end for
275 #elif str($repeat.software_cond.software) == "quast" 297 #elif str($repeat.software_cond.software) == "quast"
276 #for $k, $file in enumerate($repeat.software_cond.input) 298 #for $k, $file in enumerate($repeat.software_cond.input)
277 #set file_dir = os.path.join($software_dir, 'file_' + str($k)) 299 #set file_dir = os.path.join($software_dir, 'file_' + str($k))
278 #set file_path = os.path.join($file_dir, 'report.tsv') 300 #set file_path = os.path.join($file_dir, 'report.tsv')
279 mkdir '$file_dir' && 301 mkdir '$file_dir' &&
497 <!--<option value="afterqc">AfterQC</option>--> 519 <!--<option value="afterqc">AfterQC</option>-->
498 <option value="bamtools">Bamtools</option> 520 <option value="bamtools">Bamtools</option>
499 <!--<option value="bbmap">BBMap</option>--> 521 <!--<option value="bbmap">BBMap</option>-->
500 <option value="bcftools">Bcftools</option> 522 <option value="bcftools">Bcftools</option>
501 <!--<option value="bcl2fastq">bcl2fastq</option>--> 523 <!--<option value="bcl2fastq">bcl2fastq</option>-->
524 <!--<option value="biobambam2">biobambam2</option>-->
502 <!--<option value="biobloomtools">BioBloom Tools</option>--> 525 <!--<option value="biobloomtools">BioBloom Tools</option>-->
503 <option value="bismark">Bismark</option> 526 <option value="bismark">Bismark</option>
504 <!--<option value="bowtie1">Bowtie 1</option>--> 527 <!--<option value="bowtie1">Bowtie 1</option>-->
505 <option value="bowtie2">Bowtie 2</option> 528 <option value="bowtie2">Bowtie 2</option>
506 <option value="busco">BUSCO</option> 529 <option value="busco">BUSCO</option>
513 <!--<option value="disambiguate">Disambiguate</option>--> 536 <!--<option value="disambiguate">Disambiguate</option>-->
514 <!--<option value="fastq_screen">FastQ Screen</option>--> 537 <!--<option value="fastq_screen">FastQ Screen</option>-->
515 <option value="fastp">fastp</option> 538 <option value="fastp">fastp</option>
516 <option value="fastqc">FastQC</option> 539 <option value="fastqc">FastQC</option>
517 <option value="featureCounts">featureCounts</option> 540 <option value="featureCounts">featureCounts</option>
541 <!--<option value="fgbio">fgbio</option>-->
518 <option value="flexbar">Flexbar</option> 542 <option value="flexbar">Flexbar</option>
519 <option value="gatk">GATK</option> 543 <option value="gatk">GATK</option>
520 <!--<option value="goleft_indexcov">goleft indexcov</option>--> 544 <!--<option value="goleft_indexcov">goleft indexcov</option>-->
521 <option value="hicexplorer">HiCExplorer</option> 545 <option value="hicexplorer">HiCExplorer</option>
522 <!--<option value="hicup">HiCUP</option>--> 546 <!--<option value="hicup">HiCUP</option>-->
527 <!--<option value="jellyfish">Jellyfish</option>--> 551 <!--<option value="jellyfish">Jellyfish</option>-->
528 <option value="kallisto">Kallisto</option> 552 <option value="kallisto">Kallisto</option>
529 <!--<option value="leehom">leeHom</option>--> 553 <!--<option value="leehom">leeHom</option>-->
530 <option value="macs2">MACS2</option> 554 <option value="macs2">MACS2</option>
531 <!--<option value="methylQA">methylQA</option>--> 555 <!--<option value="methylQA">methylQA</option>-->
556 <!--<option value="mosdepth">mostdepth</option>-->
557 <!--<option value="mtnucratio">mtnucratio</option>-->
532 <!--<option value="peddy">Peddy</option>--> 558 <!--<option value="peddy">Peddy</option>-->
533 <option value="picard">Picard</option> 559 <option value="picard">Picard</option>
534 <!--<option value="preseq">Preseq</option>--> 560 <!--<option value="preseq">Preseq</option>-->
535 <option value="prokka">Prokka</option> 561 <option value="prokka">Prokka</option>
536 <!--<option value="qorts">QoRTs</option>--> 562 <!--<option value="qorts">QoRTs</option>-->
537 <!--<option value="qualimap">Qualimap (BamQC or RNASeq output)</option>--> 563 <option value="qualimap">Qualimap (BamQC or RNASeq output)</option>
538 <option value="quast">QUAST</option> 564 <option value="quast">QUAST</option>
539 <!--<option value="rna_seqc">RNA-SeQC</option>--> 565 <!--<option value="rna_seqc">RNA-SeQC</option>-->
540 <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>--> 566 <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>-->
541 <option value="rseqc">RSeQC</option> 567 <option value="rseqc">RSeQC</option>
542 <!--<option value="salmon">Salmon</option>--> 568 <!--<option value="salmon">Salmon</option>-->
543 <option value="samblaster">Samblaster</option> 569 <option value="samblaster">Samblaster</option>
544 <option value="samtools">Samtools</option> 570 <option value="samtools">Samtools</option>
545 <!--<option value="sargasso">Sargasso</option>--> 571 <!--<option value="sargasso">Sargasso</option>-->
572 <!--<option value="seqyclean">SeqyClean</option>-->
573 <!--<option value="sexdeterrmine">SexDetErrmine</option>-->
546 <!--<option value="skewer">Skewer</option>--> 574 <!--<option value="skewer">Skewer</option>-->
547 <option value="slamdunk">Slamdunk</option> 575 <option value="slamdunk">Slamdunk</option>
548 <option value="snpeff">SnpEff</option> 576 <option value="snpeff">SnpEff</option>
549 <option value="sortmerna">SortMeRNA</option> 577 <option value="sortmerna">SortMeRNA</option>
550 <option value="star">STAR</option> 578 <option value="star">STAR</option>
660 <param name="input" type="data" format="txt" multiple="true" label="Picard output"/> 688 <param name="input" type="data" format="txt" multiple="true" label="Picard output"/>
661 </repeat> 689 </repeat>
662 </when> 690 </when>
663 <when value="prokka"> 691 <when value="prokka">
664 <param name="input" type="data" format="txt" multiple="true" label="Output of Prokka" help="It should contain 'contigs:'"/> 692 <param name="input" type="data" format="txt" multiple="true" label="Output of Prokka" help="It should contain 'contigs:'"/>
693 </when>
694 <when value="qualimap">
695 <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report" />
665 </when> 696 </when>
666 <when value="quast"> 697 <when value="quast">
667 <param name="input" type="data" format="tabular,tsv" multiple="true" label="Output of Quast"/> 698 <param name="input" type="data" format="tabular,tsv" multiple="true" label="Output of Quast"/>
668 </when> 699 </when>
669 <when value="rseqc"> 700 <when value="rseqc">
1098 <param name="input" value="prokka_1.txt,prokka_2.txt" /> 1129 <param name="input" value="prokka_1.txt,prokka_2.txt" />
1099 </conditional> 1130 </conditional>
1100 </repeat> 1131 </repeat>
1101 <repeat name="results"> 1132 <repeat name="results">
1102 <conditional name="software_cond"> 1133 <conditional name="software_cond">
1134 <param name="software" value="qualimap" />
1135 <param name="input" value="genome_results.txt" />
1136 </conditional>
1137 </repeat>
1138 <repeat name="results">
1139 <conditional name="software_cond">
1103 <param name="software" value="quast" /> 1140 <param name="software" value="quast" />
1104 <param name="input" value="quast.tsv" /> 1141 <param name="input" value="quast.tsv" />
1105 </conditional> 1142 </conditional>
1106 </repeat> 1143 </repeat>
1107 <repeat name="results"> 1144 <repeat name="results">
1175 <has_text text="picard-rna-assignment" /> 1212 <has_text text="picard-rna-assignment" />
1176 <has_text text="picard-markduplicates" /> 1213 <has_text text="picard-markduplicates" />
1177 <has_text text="picard-insertsize" /> 1214 <has_text text="picard-insertsize" />
1178 <has_text text="picard-gcbias" /> 1215 <has_text text="picard-gcbias" />
1179 <has_text text="prokka_plot" /> 1216 <has_text text="prokka_plot" />
1217 <has_text text="qualimap" />
1180 <has_text text="samblaster_duplicates" /> 1218 <has_text text="samblaster_duplicates" />
1181 <has_text text="quast-stats" /> 1219 <has_text text="quast-stats" />
1182 <has_text text="samtools-flagstat-dp" /> 1220 <has_text text="samtools-flagstat-dp" />
1183 <has_text text="snpeff" /> 1221 <has_text text="snpeff" />
1184 </assert_contents> 1222 </assert_contents>
1195 <element name="picard_RnaSeqMetrics" file="picard_RnaSeqMetrics_stats.tabular" compare="sim_size" delta="40"/> 1233 <element name="picard_RnaSeqMetrics" file="picard_RnaSeqMetrics_stats.tabular" compare="sim_size" delta="40"/>
1196 <element name="picard_baseContent" file="picard_baseContent_stats.tabular" compare="sim_size" delta="50"/> 1234 <element name="picard_baseContent" file="picard_baseContent_stats.tabular" compare="sim_size" delta="50"/>
1197 <element name="picard_dups" file="picard_dups_stats.tabular" compare="sim_size" delta="0"/> 1235 <element name="picard_dups" file="picard_dups_stats.tabular" compare="sim_size" delta="0"/>
1198 <element name="picard_insertSize" file="picard_insertSize_stats.tabular" compare="sim_size" delta="0"/> 1236 <element name="picard_insertSize" file="picard_insertSize_stats.tabular" compare="sim_size" delta="0"/>
1199 <element name="prokka" file="prokka_stats.tabular" compare="sim_size" delta="0"/> 1237 <element name="prokka" file="prokka_stats.tabular" compare="sim_size" delta="0"/>
1238 <element name="qualimap_bamqc_genome_results" file="qualimap_bamqc_genome_results.tabular" compare="sim_size" delta="0"/>
1200 <element name="quast" file="quast_stats.tabular" compare="sim_size" delta="0"/> 1239 <element name="quast" file="quast_stats.tabular" compare="sim_size" delta="0"/>
1201 <element name="samblaster" file="samblaster_stats.tabular" compare="sim_size" delta="0"/> 1240 <element name="samblaster" file="samblaster_stats.tabular" compare="sim_size" delta="0"/>
1202 <element name="samtools_flagstat"> 1241 <element name="samtools_flagstat">
1203 <assert_contents> 1242 <assert_contents>
1204 <has_text text="samtools_flagstat" /> 1243 <has_text text="samtools_flagstat" />
1260 1299
1261 MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report. This is done using the **Software name** dropdown. At present only the Galaxy tools found in the ToolShed produce logs that can used with MultiQC 1300 MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report. This is done using the **Software name** dropdown. At present only the Galaxy tools found in the ToolShed produce logs that can used with MultiQC
1262 1301
1263 ---- 1302 ----
1264 1303
1265 The first integration of this tool was made by Cyril Monjeaud and Yvan Le Bras (`Enancio <http://enancio.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility). It is now maintained by the `Intergalactic Utilities Commission <https://galaxyproject.org/iuc>`_. 1304 The first integration of this tool was made by
1305 `@cmonjeau <https://github.com/cmonjeau>`_ and `@yvanlebras <https://github.com/yvanlebras>`_.
1306 It is now maintained by the `Intergalactic Utilities Commission <https://galaxyproject.org/iuc>`_.
1266 ]]></help> 1307 ]]></help>
1267 <citations> 1308 <citations>
1268 <citation type="doi">10.1093/bioinformatics/btw354</citation> 1309 <citation type="doi">10.1093/bioinformatics/btw354</citation>
1269 </citations> 1310 </citations>
1270 </tool> 1311 </tool>