Mercurial > repos > engineson > multiqc
comparison multiqc.xml @ 8:c503e1c1fbad draft
Uploaded
author | engineson |
---|---|
date | Thu, 25 May 2017 17:51:17 -0400 |
parents | |
children | e17597fc06fb |
comparison
equal
deleted
inserted
replaced
7:4612d775965f | 8:c503e1c1fbad |
---|---|
1 <tool id="multiqc" name="multiqc" version="1.0.0.0"> | |
2 <description>aggregate results from bioinformatics analyses into a single report</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.0.0">multiqc</requirement> | |
5 </requirements> | |
6 <stdio> | |
7 <exit_code range="1:" /> | |
8 </stdio> | |
9 <command> | |
10 mkdir multiqc_WDir; | |
11 | |
12 #for $i, $repeat in enumerate( $results ) | |
13 mkdir multiqc_WDir/${repeat.software}_${i}; | |
14 | |
15 #if str($repeat.software) == "fastqc": | |
16 ## Searches for files named "fastqc_data.txt" | |
17 #for $k, $file in enumerate($repeat.input_file): | |
18 mkdir multiqc_WDir/${repeat.software}_${i}/file_${k}; | |
19 ln -s '${file}' multiqc_WDir/fastqc_${i}/file_${k}/fastqc_data.txt; | |
20 #end for | |
21 #else if str($repeat.software) == "tophat": | |
22 ## Searches for files ending in "align_summary.txt" | |
23 #for $file in $repeat.input_file: | |
24 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}align_summary.txt'; | |
25 #end for | |
26 #else if str($repeat.software) == "bowtie2": | |
27 ## Searches for files containing 'reads; of these;' | |
28 #for $file in $repeat.input_file: | |
29 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt'; | |
30 #end for | |
31 #else if str($repeat.software) == "cutadapt": | |
32 ## Searches for files containing 'This is cutadapt' | |
33 #for $file in $repeat.input_file: | |
34 cat '${file}' > 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt'; | |
35 ## replace header for old cutadapt release | |
36 sed -i .old 's/You are running/This is/' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt'; | |
37 #end for | |
38 #else if str($repeat.software) == "featurecounts": | |
39 ## Checks for files ending in '.summary' | |
40 #for $k, $file in enumerate($repeat.input_file): | |
41 mkdir multiqc_WDir/${repeat.software}_${i}/file_${k}; | |
42 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/file_${k}/${file.display_name}.summary'; | |
43 #end for | |
44 #else if str($repeat.software) == "bismark": | |
45 ## Checks for files ending in _SE_report.txt | |
46 #for $file in $repeat.input_file | |
47 ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}_SE_report.txt'; | |
48 #end for | |
49 #else if str($repeat.software) == "samtools": | |
50 ## Checks for files containing 'This file was produced by samtools stats' | |
51 #for $file in $repeat.input_file | |
52 ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}'; | |
53 #end for | |
54 #else if str($repeat.software) == "picard": | |
55 #for $file in $repeat.input_file | |
56 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}'; | |
57 #end for | |
58 #else if str($repeat.software) == "samtools_idxstats": | |
59 ## Checks for files containing "idxstats" in the name | |
60 #for $file in $repeat.input_file | |
61 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}_idxstats.txt'; | |
62 #end for | |
63 #else if str($repeat.software) == "htseq": | |
64 ## Checks for files containing "__too_low_aQual" | |
65 #for $file in $repeat.input_file | |
66 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}'; | |
67 #end for | |
68 #else if str($repeat.software) == "rnastar_log": | |
69 ## Checks for files named Log.final.out | |
70 #for $k, $file in enumerate($repeat.input_file): | |
71 mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}'; | |
72 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}/Log.final.out'; | |
73 #end for | |
74 #else if str($repeat.software) == "rnastar_counts": | |
75 ## Checks for files named ReadsPerGene.out.tab | |
76 #for $k, $file in enumerate($repeat.input_file): | |
77 mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}'; | |
78 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}/ReadsPerGene.out.tab'; | |
79 #end for | |
80 #end if | |
81 #end for | |
82 | |
83 multiqc multiqc_WDir; | |
84 | |
85 </command> | |
86 <inputs> | |
87 <repeat name="results" title="Results" min="1"> | |
88 <param name="software" type="select" label="Software name" help="Which tool was used generate logs?"> | |
89 <option value="fastqc">FastQC</option> | |
90 <option value="cutadapt">Cutadapt/Trim Galore!</option> | |
91 <option value="tophat">Tophat2</option> | |
92 <option value="featurecounts">FeatureCounts (Summary file)</option> | |
93 <option value="samtools">Samtools (Stats, Flagstat)</option> | |
94 <option value="samtools_idxstats">Samtools (Idxstats)</option> | |
95 <option value="picard">Picard</option> | |
96 <option value="bismark">Bismark</option> | |
97 <option value="bowtie2">Bowtie2</option> | |
98 <option value="htseq">HTSeq-Count</option> | |
99 <option value="rnastar_log">RNA STAR (log)</option> | |
100 <option value="rnastar_counts">RNA STAR (reads per gene)</option> | |
101 </param> | |
102 <param name="input_file" type="data" format="txt, tabular" multiple="true" label="Result file" help="Select input datasets"/> | |
103 <param name="saveLog" type="boolean" checked="false" label="Save log file" help="Save the multiQC log file to the history. This is mostly useful for debugging purposes."/> | |
104 </repeat> | |
105 </inputs> | |
106 <outputs> | |
107 <data format="html" from_work_dir="multiqc_report.html" name="html_file" label="${tool.name} on ${on_string}: Webpage" /> | |
108 <data format="txt" name="text_file" from_work_dir="multiqc_data/multiqc.log" label="${tool.name} on ${on_string}: Log"> | |
109 <filter>saveLog is True</filter> | |
110 </data> | |
111 </outputs> | |
112 <tests> | |
113 <test> | |
114 <repeat name="results"> | |
115 <param name="software" value="fastqc" /> | |
116 <param name="input_file" value="fastqc_data.txt" /> | |
117 </repeat> | |
118 <param name="saveLog" value="True"/> | |
119 <output name="html_file" file="report_fastqc.html" compare="sim_size" delta="1000"/> | |
120 <output name="text_file" file="log_fastqc.txt" compare="sim_size" delta="1000"/> | |
121 </test> | |
122 <test> | |
123 <repeat name="results"> | |
124 <param name="software" value="fastqc" /> | |
125 <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" /> | |
126 </repeat> | |
127 <output name="html_file" file="report_fastqc_2.html" compare="sim_size" delta="1000"/> | |
128 </test> | |
129 <test> | |
130 <repeat name="results"> | |
131 <param name="software" value="cutadapt" /> | |
132 <param name="input_file" value="cutadapt.txt" /> | |
133 </repeat> | |
134 <output name="html_file" file="report_cutadapt.html" compare="sim_size" delta="1000"/> | |
135 </test> | |
136 <test> | |
137 <repeat name="results"> | |
138 <param name="software" value="tophat" /> | |
139 <param name="input_file" value="tophat_data.txt" /> | |
140 </repeat> | |
141 <output name="html_file" file="report_tophat.html" compare="sim_size" delta="1000"/> | |
142 </test> | |
143 <test> | |
144 <repeat name="results"> | |
145 <param name="software" value="bowtie2" /> | |
146 <param name="input_file" value="bowtie2SE1.txt,bowtie2SE2.txt" /> | |
147 </repeat> | |
148 <output name="html_file" file="report_bowtie2SE.html" compare="sim_size" delta="1000"/> | |
149 </test> | |
150 <test> | |
151 <repeat name="results"> | |
152 <param name="software" value="featurecounts" /> | |
153 <param name="input_file" value="featurecounts_data.txt" /> | |
154 </repeat> | |
155 <output name="html_file" file="report_featurecounts.html" compare="sim_size" delta="1000"/> | |
156 </test> | |
157 <test> | |
158 <repeat name="results"> | |
159 <param name="software" value="picard" /> | |
160 <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt,picard_CollectBaseDistributionByCycle.txt,picard_CollectRnaSeqMetrics.txt,picard_CollectAlignmentSummaryMetrics.txt" /> | |
161 </repeat> | |
162 <output name="html_file" file="report_picard.html" compare="sim_size" delta="10000"/> | |
163 </test> | |
164 <test> | |
165 <repeat name="results"> | |
166 <param name="software" value="htseq" /> | |
167 <param name="input_file" value="htseq_data.txt" /> | |
168 </repeat> | |
169 <output name="html_file" file="report_htseq.html" compare="sim_size" delta="1000"/> | |
170 </test> | |
171 <test> | |
172 <repeat name="results"> | |
173 <param name="software" value="rnastar_log" /> | |
174 <param name="input_file" value="rnastar_log.txt" /> | |
175 </repeat> | |
176 <output name="html_file" file="report_rnastar_log.html" compare="sim_size" delta="1000"/> | |
177 </test> | |
178 <test> | |
179 <repeat name="results"> | |
180 <param name="software" value="rnastar_counts" /> | |
181 <param name="input_file" value="rnastar_counts.txt" /> | |
182 </repeat> | |
183 <output name="html_file" file="report_rnastar_counts.html" compare="sim_size" delta="1000"/> | |
184 </test> | |
185 <test> | |
186 <repeat name="results"> | |
187 <param name="software" value="bismark" /> | |
188 <param name="input_file" value="bismark_data.txt" /> | |
189 </repeat> | |
190 <output name="html_file" file="report_bismark.html" compare="sim_size" delta="1000"/> | |
191 </test> | |
192 <test> | |
193 <repeat name="results"> | |
194 <param name="software" value="samtools" /> | |
195 <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" /> | |
196 </repeat> | |
197 <output name="html_file" file="report_samtools.html" compare="sim_size" delta="1000"/> | |
198 </test> | |
199 <test> | |
200 <repeat name="results"> | |
201 <param name="software" value="samtools_idxstats" /> | |
202 <param name="input_file" value="samtools_idxstats.txt" /> | |
203 </repeat> | |
204 <output name="html_file" file="report_samtools_idxstats.html" compare="sim_size" delta="1000"/> | |
205 </test> | |
206 <test> | |
207 <repeat name="results"> | |
208 <param name="software" value="fastqc" /> | |
209 <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" /> | |
210 </repeat> | |
211 <repeat name="results"> | |
212 <param name="software" value="cutadapt" /> | |
213 <param name="input_file" value="cutadapt.txt" /> | |
214 </repeat> | |
215 <repeat name="results"> | |
216 <param name="software" value="tophat" /> | |
217 <param name="input_file" value="tophat_data.txt" /> | |
218 </repeat> | |
219 <repeat name="results"> | |
220 <param name="software" value="featurecounts" /> | |
221 <param name="input_file" value="featurecounts_data.txt" /> | |
222 </repeat> | |
223 <repeat name="results"> | |
224 <param name="software" value="picard" /> | |
225 <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt" /> | |
226 </repeat> | |
227 <repeat name="results"> | |
228 <param name="software" value="bismark" /> | |
229 <param name="input_file" value="bismark_data.txt" /> | |
230 </repeat> | |
231 <repeat name="results"> | |
232 <param name="software" value="samtools" /> | |
233 <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" /> | |
234 </repeat> | |
235 <output name="html_file" file="report_all.html" compare="sim_size" delta="5000"/> | |
236 </test> | |
237 </tests> | |
238 | |
239 <help> | |
240 **What it does** | |
241 | |
242 MultiQC aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools. | |
243 | |
244 **Inputs** | |
245 | |
246 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 the following Galaxy tools produce logs that can used with MultiQC. There are: | |
247 | |
248 - Fastqc | |
249 - Cutadapt / Trim Galore! | |
250 - Tophat2 | |
251 - FeatureCounts | |
252 - Samtools (stats, flagstat, dxstats) | |
253 - Picard (MarkDuplicatesMetrics, CollectGCBiasMetrics, CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics, CollectRnaSeqMetrics) | |
254 - Bismark (Alignment report file) | |
255 - Bowtie2 (Metrics file) | |
256 - HTSeq-count ("no feature" file; although the "Assigned" metric is always 0) | |
257 - RNA STAR (Alignment from Log.final.out, Gene counts from ReadsPerGene.out.tab) | |
258 | |
259 ---- | |
260 | |
261 **Integrated by** | |
262 | |
263 Cyril Monjeaud and Yvan Le Bras | |
264 | |
265 `EnginesOn <http://engineson.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility | |
266 | |
267 </help> | |
268 <citations> | |
269 <citation type="doi">10.1093/bioinformatics/btw354</citation> | |
270 </citations> | |
271 </tool> |