annotate multiqc.xml @ 9:919983d780e0 draft

Updated from github
author engineson
date Fri, 07 Jul 2017 07:54:00 -0400
parents c503e1c1fbad
children e17597fc06fb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
1 <tool id="multiqc" name="multiqc" version="1.0.0.0">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
2 <description>aggregate results from bioinformatics analyses into a single report</description>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
3 <requirements>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
4 <requirement type="package" version="1.0.0">multiqc</requirement>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
5 </requirements>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
6 <stdio>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
7 <exit_code range="1:" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
8 </stdio>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
9 <command>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
10 mkdir multiqc_WDir;
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
11
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
12 #for $i, $repeat in enumerate( $results )
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
13 mkdir multiqc_WDir/${repeat.software}_${i};
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
14
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
15 #if str($repeat.software) == "fastqc":
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
16 ## Searches for files named "fastqc_data.txt"
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
17 #for $k, $file in enumerate($repeat.input_file):
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
18 mkdir multiqc_WDir/${repeat.software}_${i}/file_${k};
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
19 ln -s '${file}' multiqc_WDir/fastqc_${i}/file_${k}/fastqc_data.txt;
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
20 #end for
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
21 #else if str($repeat.software) == "tophat":
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
22 ## Searches for files ending in "align_summary.txt"
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
23 #for $file in $repeat.input_file:
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
24 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}align_summary.txt';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
25 #end for
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
26 #else if str($repeat.software) == "bowtie2":
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
27 ## Searches for files containing 'reads; of these;'
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
28 #for $file in $repeat.input_file:
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
29 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
30 #end for
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
31 #else if str($repeat.software) == "cutadapt":
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
32 ## Searches for files containing 'This is cutadapt'
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
33 #for $file in $repeat.input_file:
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
34 cat '${file}' > 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
35 ## replace header for old cutadapt release
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
36 sed -i .old 's/You are running/This is/' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
37 #end for
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
38 #else if str($repeat.software) == "featurecounts":
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
39 ## Checks for files ending in '.summary'
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
40 #for $k, $file in enumerate($repeat.input_file):
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
41 mkdir multiqc_WDir/${repeat.software}_${i}/file_${k};
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
42 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/file_${k}/${file.display_name}.summary';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
43 #end for
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
44 #else if str($repeat.software) == "bismark":
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
45 ## Checks for files ending in _SE_report.txt
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
46 #for $file in $repeat.input_file
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
47 ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}_SE_report.txt';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
48 #end for
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
49 #else if str($repeat.software) == "samtools":
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
50 ## Checks for files containing 'This file was produced by samtools stats'
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
51 #for $file in $repeat.input_file
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
52 ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
53 #end for
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
54 #else if str($repeat.software) == "picard":
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
55 #for $file in $repeat.input_file
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
56 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
57 #end for
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
58 #else if str($repeat.software) == "samtools_idxstats":
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
59 ## Checks for files containing "idxstats" in the name
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
60 #for $file in $repeat.input_file
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
61 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}_idxstats.txt';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
62 #end for
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
63 #else if str($repeat.software) == "htseq":
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
64 ## Checks for files containing "__too_low_aQual"
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
65 #for $file in $repeat.input_file
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
66 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
67 #end for
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
68 #else if str($repeat.software) == "rnastar_log":
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
69 ## Checks for files named Log.final.out
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
70 #for $k, $file in enumerate($repeat.input_file):
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
71 mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
72 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}/Log.final.out';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
73 #end for
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
74 #else if str($repeat.software) == "rnastar_counts":
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
75 ## Checks for files named ReadsPerGene.out.tab
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
76 #for $k, $file in enumerate($repeat.input_file):
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
77 mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
78 ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.display_name}/ReadsPerGene.out.tab';
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
79 #end for
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
80 #end if
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
81 #end for
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
82
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
83 multiqc multiqc_WDir;
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
84
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
85 </command>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
86 <inputs>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
87 <repeat name="results" title="Results" min="1">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
88 <param name="software" type="select" label="Software name" help="Which tool was used generate logs?">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
89 <option value="fastqc">FastQC</option>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
90 <option value="cutadapt">Cutadapt/Trim Galore!</option>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
91 <option value="tophat">Tophat2</option>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
92 <option value="featurecounts">FeatureCounts (Summary file)</option>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
93 <option value="samtools">Samtools (Stats, Flagstat)</option>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
94 <option value="samtools_idxstats">Samtools (Idxstats)</option>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
95 <option value="picard">Picard</option>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
96 <option value="bismark">Bismark</option>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
97 <option value="bowtie2">Bowtie2</option>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
98 <option value="htseq">HTSeq-Count</option>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
99 <option value="rnastar_log">RNA STAR (log)</option>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
100 <option value="rnastar_counts">RNA STAR (reads per gene)</option>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
101 </param>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
102 <param name="input_file" type="data" format="txt, tabular" multiple="true" label="Result file" help="Select input datasets"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
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."/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
104 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
105 </inputs>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
106 <outputs>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
107 <data format="html" from_work_dir="multiqc_report.html" name="html_file" label="${tool.name} on ${on_string}: Webpage" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
108 <data format="txt" name="text_file" from_work_dir="multiqc_data/multiqc.log" label="${tool.name} on ${on_string}: Log">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
109 <filter>saveLog is True</filter>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
110 </data>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
111 </outputs>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
112 <tests>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
113 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
114 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
115 <param name="software" value="fastqc" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
116 <param name="input_file" value="fastqc_data.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
117 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
118 <param name="saveLog" value="True"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
119 <output name="html_file" file="report_fastqc.html" compare="sim_size" delta="1000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
120 <output name="text_file" file="log_fastqc.txt" compare="sim_size" delta="1000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
121 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
122 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
123 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
124 <param name="software" value="fastqc" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
125 <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
126 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
127 <output name="html_file" file="report_fastqc_2.html" compare="sim_size" delta="1000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
128 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
129 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
130 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
131 <param name="software" value="cutadapt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
132 <param name="input_file" value="cutadapt.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
133 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
134 <output name="html_file" file="report_cutadapt.html" compare="sim_size" delta="1000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
135 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
136 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
137 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
138 <param name="software" value="tophat" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
139 <param name="input_file" value="tophat_data.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
140 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
141 <output name="html_file" file="report_tophat.html" compare="sim_size" delta="1000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
142 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
143 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
144 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
145 <param name="software" value="bowtie2" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
146 <param name="input_file" value="bowtie2SE1.txt,bowtie2SE2.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
147 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
148 <output name="html_file" file="report_bowtie2SE.html" compare="sim_size" delta="1000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
149 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
150 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
151 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
152 <param name="software" value="featurecounts" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
153 <param name="input_file" value="featurecounts_data.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
154 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
155 <output name="html_file" file="report_featurecounts.html" compare="sim_size" delta="1000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
156 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
157 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
158 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
159 <param name="software" value="picard" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
160 <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt,picard_CollectBaseDistributionByCycle.txt,picard_CollectRnaSeqMetrics.txt,picard_CollectAlignmentSummaryMetrics.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
161 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
162 <output name="html_file" file="report_picard.html" compare="sim_size" delta="10000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
163 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
164 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
165 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
166 <param name="software" value="htseq" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
167 <param name="input_file" value="htseq_data.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
168 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
169 <output name="html_file" file="report_htseq.html" compare="sim_size" delta="1000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
170 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
171 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
172 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
173 <param name="software" value="rnastar_log" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
174 <param name="input_file" value="rnastar_log.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
175 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
176 <output name="html_file" file="report_rnastar_log.html" compare="sim_size" delta="1000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
177 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
178 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
179 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
180 <param name="software" value="rnastar_counts" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
181 <param name="input_file" value="rnastar_counts.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
182 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
183 <output name="html_file" file="report_rnastar_counts.html" compare="sim_size" delta="1000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
184 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
185 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
186 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
187 <param name="software" value="bismark" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
188 <param name="input_file" value="bismark_data.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
189 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
190 <output name="html_file" file="report_bismark.html" compare="sim_size" delta="1000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
191 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
192 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
193 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
194 <param name="software" value="samtools" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
195 <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
196 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
197 <output name="html_file" file="report_samtools.html" compare="sim_size" delta="1000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
198 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
199 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
200 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
201 <param name="software" value="samtools_idxstats" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
202 <param name="input_file" value="samtools_idxstats.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
203 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
204 <output name="html_file" file="report_samtools_idxstats.html" compare="sim_size" delta="1000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
205 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
206 <test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
207 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
208 <param name="software" value="fastqc" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
209 <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
210 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
211 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
212 <param name="software" value="cutadapt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
213 <param name="input_file" value="cutadapt.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
214 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
215 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
216 <param name="software" value="tophat" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
217 <param name="input_file" value="tophat_data.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
218 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
219 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
220 <param name="software" value="featurecounts" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
221 <param name="input_file" value="featurecounts_data.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
222 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
223 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
224 <param name="software" value="picard" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
225 <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
226 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
227 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
228 <param name="software" value="bismark" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
229 <param name="input_file" value="bismark_data.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
230 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
231 <repeat name="results">
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
232 <param name="software" value="samtools" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
233 <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" />
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
234 </repeat>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
235 <output name="html_file" file="report_all.html" compare="sim_size" delta="5000"/>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
236 </test>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
237 </tests>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
238
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
239 <help>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
240 **What it does**
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
241
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
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.
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
243
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
244 **Inputs**
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
245
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
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:
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
247
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
248 - Fastqc
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
249 - Cutadapt / Trim Galore!
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
250 - Tophat2
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
251 - FeatureCounts
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
252 - Samtools (stats, flagstat, dxstats)
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
253 - Picard (MarkDuplicatesMetrics, CollectGCBiasMetrics, CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics, CollectRnaSeqMetrics)
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
254 - Bismark (Alignment report file)
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
255 - Bowtie2 (Metrics file)
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
256 - HTSeq-count ("no feature" file; although the "Assigned" metric is always 0)
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
257 - RNA STAR (Alignment from Log.final.out, Gene counts from ReadsPerGene.out.tab)
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
258
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
259 ----
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
260
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
261 **Integrated by**
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
262
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
263 Cyril Monjeaud and Yvan Le Bras
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
264
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
265 `EnginesOn &lt;http://engineson.fr/&gt;`_ and Rennes GenOuest Bio-informatics Core Facility
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
266
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
267 </help>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
268 <citations>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
269 <citation type="doi">10.1093/bioinformatics/btw354</citation>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
270 </citations>
c503e1c1fbad Uploaded
engineson
parents:
diff changeset
271 </tool>