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comparison multiqc.xml @ 8:6ef9e2d46af4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
author iuc
date Fri, 20 Apr 2018 01:06:06 -0400
parents 6b377ade9c97
children a531ae71d397
comparison
equal deleted inserted replaced
7:6b377ade9c97 8:6ef9e2d46af4
1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1"> 1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.0">
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@">1.3</token> 4 <token name="@WRAPPER_VERSION@">1.5</token>
5 <token name="@ESCAPE_IDENTIFIER@">
6 <![CDATA[
7 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
8 ]]></token>
9 <token name="@CHECK_LN_FILE@">
10 <![CDATA[
11 grep -q "$pattern" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
12 ln -s '$file' '$file_path' &&
13 ]]></token>
14 <token name="@CREATE_REPEAT_DIR_1@">
15 <![CDATA[
16 #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
17 mkdir '$repeat_dir' &&
18 ]]></token>
19 <token name="@CREATE_REPEAT_DIR_2@">
20 <![CDATA[
21 #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j))
22 mkdir '$repeat_dir' &&
23 ]]></token>
5 <token name="@LN_FILES@"> 24 <token name="@LN_FILES@">
6 <![CDATA[ 25 <![CDATA[
7 #for $file in $repeat.software_cond.input 26 #for $file in $repeat.software_cond.input
8 grep -q "$pattern" $file || die "'$pattern' not found in the file" && 27 @ESCAPE_IDENTIFIER@
9 ln -s '$file' '$software_dir/${file.element_identifier}' && 28 #set file_path = os.path.join($software_dir, str($identifier))
29 @CHECK_LN_FILE@
10 #end for 30 #end for
11 ]]></token> 31 ]]></token>
12 <token name="@LN_2_FILES@"> 32 <token name="@LN_2_FILES@">
13 <![CDATA[ 33 <![CDATA[
14 #for $file in $repeat2.input: 34 @CREATE_REPEAT_DIR_1@
15 grep -q "$pattern" $file || die "'$pattern' not found in the file" && 35 #for $file in $repeat2.input
16 ln -s '$file' '$software_dir/${repeat2.type}_${j}_${file.element_identifier}' && 36 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
37 #set file_path = os.path.join($repeat_dir, str($identifier))
38 @CHECK_LN_FILE@
17 #end for 39 #end for
18 ]]></token> 40 ]]></token>
19 <token name="@LN_3_FILES@"> 41 <token name="@LN_3_FILES@">
20 <![CDATA[ 42 <![CDATA[
21 #for $file in $repeat2.type.input: 43 #for $file in $repeat2.type.input
22 grep -q "$pattern" $file || die "'$pattern' not found in the file" && 44 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
23 ln -s '$file' '$repeat_dir/${file.element_identifier}' && 45 #set file_path = os.path.join($repeat_dir, str($identifier))
46 @CHECK_LN_FILE@
24 #end for 47 #end for
25 ]]></token> 48 ]]></token>
26 </macros> 49 </macros>
27 <requirements> 50 <requirements>
28 <requirement type="package" version="@WRAPPER_VERSION@">multiqc</requirement> 51 <requirement type="package" version="@WRAPPER_VERSION@">multiqc</requirement>
29 </requirements> 52 </requirements>
30 <version_command>multiqc --version</version_command> 53 <version_command>multiqc --version</version_command>
31 <command detect_errors="aggressive"> 54 <command detect_errors="aggressive">
32 <![CDATA[ 55 <![CDATA[
56 #import re
57 #import os
58
33 die() { echo "$@" 1>&2 ; exit 1; } && 59 die() { echo "$@" 1>&2 ; exit 1; } &&
34 60
35 mkdir multiqc_WDir && 61 mkdir multiqc_WDir &&
36 62
37 #set $configfile="F" 63 #set $configfile="F"
38 64
39 #for $i, $repeat in enumerate( $results ) 65 #for $i, $repeat in enumerate( $results )
40 #set software_dir = 'multiqc_WDir/' + str($repeat.software_cond.software) + '_' + str($i) 66 #set software_dir = os.path.join('multiqc_WDir', str($repeat.software_cond.software) + '_' + str($i))
41 mkdir $software_dir && 67 mkdir $software_dir &&
42 68
43 #if str($repeat.software_cond.software) == "bamtools" 69 #if str($repeat.software_cond.software) == "bamtools"
44 #set $pattern = "Stats for BAM file(s)" 70 #set $pattern = "Stats for BAM file(s)"
45 @LN_FILES@ 71 @LN_FILES@
46 #elif str($repeat.software_cond.software) == "bcftools" 72 #elif str($repeat.software_cond.software) == "bcftools"
47 #set $pattern = "This file was produced by bcftools stats" 73 #set $pattern = "This file was produced by bcftools stats"
48 @LN_FILES@ 74 @LN_FILES@
49 #elif str($repeat.software_cond.software) == "bismark" 75 #elif str($repeat.software_cond.software) == "bismark"
50 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) 76 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
51 #set file_prefix = $software_dir + '/' + str($repeat2.type) + '_' + str($j) 77 @CREATE_REPEAT_DIR_1@
52 #if str($repeat2.type) == "align" 78 #if str($repeat2.type) == "align"
53 #for $file in $repeat2.input 79 #for $file in $repeat2.input
54 ln -s '$file' '${file_prefix}_${file.element_identifier}_SE_report.txt' && 80 @ESCAPE_IDENTIFIER@
81 #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt')
82 ln -s '$file' '$file_path' &&
55 #end for 83 #end for
56 #elif str($repeat2.type) == "dedup" 84 #elif str($repeat2.type) == "dedup"
57 #for $file in $repeat2.input 85 #for $file in $repeat2.input
58 ln -s '$file' '${file_prefix}_${file.element_identifier}_deduplication_report.txt' && 86 @ESCAPE_IDENTIFIER@
87 #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt')
88 ln -s '$file' '$file_path' &&
59 #end for 89 #end for
60 #elif str($repeat2.type) == "meth_extract" 90 #elif str($repeat2.type) == "meth_extract"
61 #for $file in $repeat2.input 91 #for $file in $repeat2.input
62 ln -s '$file' '${file_prefix}_${file.element_identifier}_splitting_report.txt' && 92 @ESCAPE_IDENTIFIER@
93 #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt')
94 ln -s '$file' '$file_path' &&
63 #end for 95 #end for
64 #elif str($repeat2.type) == "m_bias" 96 #elif str($repeat2.type) == "m_bias"
65 #for $file in $repeat2.input 97 #for $file in $repeat2.input
66 ln -s '$file' '${file_prefix}_${file.element_identifier}_M-bias.txt' && 98 @ESCAPE_IDENTIFIER@
99 #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt')
100 ln -s '$file' '$file_path' &&
67 #end for 101 #end for
68 #elif str($repeat2.type) == "bam2nuc" 102 #elif str($repeat2.type) == "bam2nuc"
69 #for $file in $repeat2.input 103 #for $file in $repeat2.input
70 ln -s '$file' '${file_prefix}_${file.element_identifier}.nucleotide_stats.txt' && 104 @ESCAPE_IDENTIFIER@
105 #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt')
106 ln -s '$file' '$file_path' &&
71 #end for 107 #end for
72 #end if 108 #end if
73 #end for 109 #end for
74 #elif str($repeat.software_cond.software) == "bowtie2" 110 #elif str($repeat.software_cond.software) == "bowtie2"
75 #set $pattern = "reads; of these:" 111 #set $pattern = "reads; of these:"
76 @LN_FILES@ 112 @LN_FILES@
77 #elif str($repeat.software_cond.software) == "busco" 113 #elif str($repeat.software_cond.software) == "busco"
78 ## Searches for files "short_summary_[samplename].txt" 114 ## Searches for files "short_summary_[samplename].txt"
79 #for $file in $repeat.software_cond.input 115 #for $file in $repeat.software_cond.input
80 ln -s '$file' '$software_dir/short_summary_${file.element_identifier}' && 116 @ESCAPE_IDENTIFIER@
117 #set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier))
118 ln -s '$file' '$file_path' &&
81 #end for 119 #end for
82 #elif str($repeat.software_cond.software) == "cutadapt" 120 #elif str($repeat.software_cond.software) == "cutadapt"
83 #set $pattern = "This is cutadapt" 121 #set $pattern = "This is cutadapt"
84 #for $file in $repeat.software_cond.input 122 #for $file in $repeat.software_cond.input
85 #set file_path = $software_dir + '/' + str($file.element_identifier) + '.txt' 123 @ESCAPE_IDENTIFIER@
124 #set file_path = os.path.join($software_dir, str($identifier) + '.txt')
86 ln -s '$file' '$file_path' && 125 ln -s '$file' '$file_path' &&
87 ## replace header for old cutadapt release 126 ## replace header for old cutadapt release
88 sed -i.old 's/You are running/This is/' '$file_path' && 127 sed -i.old 's/You are running/This is/' '$file_path' &&
89 grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" && 128 grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" &&
90 #end for 129 #end for
130 #elif str($repeat.software_cond.software) == "deeptools"
131 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
132 #if str($repeat2.type) == "bamPEFragmentSize"
133 #set $pattern = "Frag."
134 @LN_2_FILES@
135 #elif str($repeat2.type) == "estimateReadFiltering"
136 #set $pattern = "Internally-determined Duplicate"
137 @LN_2_FILES@
138 #elif str($repeat2.type) == "plotCoverageStdout"
139 #set $pattern = "sample"
140 @LN_2_FILES@
141 #elif str($repeat2.type) == "plotCoverageOutRawCounts"
142 #set $pattern = "#plotCoverage --outRawCounts"
143 @LN_2_FILES@
144 #elif str($repeat2.type) == "plotEnrichment"
145 #set $pattern = "featureReadCount"
146 @LN_2_FILES@
147 #elif str($repeat2.type) == "plotFingerprintOutRawCounts"
148 #set $pattern = "#plotFingerprint --outRawCounts"
149 @LN_2_FILES@
150 #end if
151 #end for
91 #elif str($repeat.software_cond.software) == "fastqc" 152 #elif str($repeat.software_cond.software) == "fastqc"
92 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) 153 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
93 #set repeat_dir = $software_dir + '/' + str($repeat2.type) + '_' + str($j) 154 @CREATE_REPEAT_DIR_1@
94 mkdir '$repeat_dir' &&
95 #if str($repeat2.type) == "data" 155 #if str($repeat2.type) == "data"
96 #for $k, $file in enumerate($repeat2.input) 156 #for $k, $file in enumerate($repeat2.input)
97 #set file_dir = $repeat_dir + '/file_' + str($k) 157 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
158 #set file_path = os.path.join($file_dir, 'fastqc_data.txt')
98 mkdir '$file_dir' && 159 mkdir '$file_dir' &&
99 ln -s '$file' '$file_dir/fastqc_data.txt' && 160 ln -s '$file' '$file_path' &&
100 #end for 161 #end for
101 #elif str($repeat2.type) == "theoretical_gc" 162 #elif str($repeat2.type) == "theoretical_gc"
102 #for $file in $repeat2.input 163 #for $file in $repeat2.input
103 ln -s '$file' '$repeat_dir/${file.element_identifier}_fastqc_theoretical_gc' && 164 @ESCAPE_IDENTIFIER@
165 #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc')
166 ln -s '$file' '$file_path' &&
104 #end for 167 #end for
105 #end if 168 #end if
106 #end for 169 #end for
107 #elif str($repeat.software_cond.software) == "featureCounts" 170 #elif str($repeat.software_cond.software) == "featureCounts"
108 #for $file in $repeat.software_cond.input 171 #for $file in $repeat.software_cond.input
109 #set file_prefix = $software_dir + '/' + str($file.element_identifier) 172 @ESCAPE_IDENTIFIER@
173 #set file_prefix = os.path.join($software_dir, str($identifier))
110 if grep -qw Status '$file'; then 174 if grep -qw Status '$file'; then
111 ln -s '$file' '${file_prefix}.summary'; 175 ln -s '$file' '${file_prefix}.summary';
112 else 176 else
113 echo -e 'Status\t$file.element_identifier' > '${file_prefix}.summary'; 177 echo -e 'Status\t${identifier}' > '${file_prefix}.summary';
114 cat '$file' >> '${file_prefix}.summary'; 178 cat '$file' >> '${file_prefix}.summary';
115 fi && 179 fi &&
116 #end for 180 #end for
117 #elif str($repeat.software_cond.software) == "flexbar" 181 #elif str($repeat.software_cond.software) == "flexbar"
118 #set $pattern = "flexible barcode and adapter removal" 182 #set $pattern = "flexible barcode and adapter removal"
127 @LN_2_FILES@ 191 @LN_2_FILES@
128 #end if 192 #end if
129 #end for 193 #end for
130 #elif str($repeat.software_cond.software) == "hicup" 194 #elif str($repeat.software_cond.software) == "hicup"
131 #for $file in $repeat.software_cond.input 195 #for $file in $repeat.software_cond.input
132 ln -s '${file}' '$software_dir/HiCUP_summary_report_${file.element_identifier}' && 196 @ESCAPE_IDENTIFIER@
197 #set file_path = os.path.join($software_dir, 'HiCUP_summary_report_' + str($identifier))
198 ln -s '${file}' '$file_path' &&
133 #end for 199 #end for
134 #elif str($repeat.software_cond.software) == "hisat2" 200 #elif str($repeat.software_cond.software) == "hisat2"
135 #set $pattern = "HISAT2 summary stats:" 201 #set $pattern = "HISAT2 summary stats:"
136 @LN_FILES@ 202 @LN_FILES@
137 #elif str($repeat.software_cond.software) == "hicexplorer" 203 #elif str($repeat.software_cond.software) == "hicexplorer"
183 #elif str($repeat.software_cond.software) == "prokka" 249 #elif str($repeat.software_cond.software) == "prokka"
184 #set $pattern = "contigs:" 250 #set $pattern = "contigs:"
185 @LN_FILES@ 251 @LN_FILES@
186 #elif str($repeat.software_cond.software) == "quast" 252 #elif str($repeat.software_cond.software) == "quast"
187 #for $k, $file in enumerate($repeat.software_cond.input) 253 #for $k, $file in enumerate($repeat.software_cond.input)
188 #set file_dir = $software_dir + '/file_' + str($k) 254 #set file_dir = os.path.join($software_dir, 'file_' + str($k))
255 #set file_path = os.path.join($file_dir, 'report.tsv')
189 mkdir '$file_dir' && 256 mkdir '$file_dir' &&
190 ln -s '$file' '$file_dir/report.tsv' && 257 ln -s '$file' '$file_path' &&
191 #end for 258 #end for
192 #elif str($repeat.software_cond.software) == "rsem" 259 #elif str($repeat.software_cond.software) == "rsem"
193 #for $file in $repeat.software_cond.input 260 #for $file in $repeat.software_cond.input
194 ln -s '$file' '$software_dir/${file.element_identifier}.cnt' && 261 @ESCAPE_IDENTIFIER@
262 #set file_path = os.path.join($software_dir, str($identifier) + '.cnt')
263 ln -s '$file' '$file_path' &&
195 #end for 264 #end for
196 #elif str($repeat.software_cond.software) == "rseqc" 265 #elif str($repeat.software_cond.software) == "rseqc"
197 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) 266 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
198 #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) 267 @CREATE_REPEAT_DIR_2@
199 mkdir '$repeat_dir' &&
200 #if str($repeat2.type.type) == "bam_stat" 268 #if str($repeat2.type.type) == "bam_stat"
201 #set $pattern = "Proper-paired reads map to different chrom:" 269 #set $pattern = "Proper-paired reads map to different chrom:"
202 @LN_3_FILES@ 270 @LN_3_FILES@
203 #elif str($repeat2.type.type) == "gene_body_coverage" 271 #elif str($repeat2.type.type) == "gene_body_coverage"
204 #for $k, $file in enumerate($repeat2.type.input) 272 #for $k, $file in enumerate($repeat2.type.input)
205 ln -s '$file' '$repeat_dir/file_${k}.geneBodyCoverage.txt' && 273 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.geneBodyCoverage.txt')
274 ln -s '$file' '$file_path' &&
206 #end for 275 #end for
207 #elif str($repeat2.type.type) == "inner_distance" 276 #elif str($repeat2.type.type) == "inner_distance"
208 #for $k, $file in enumerate($repeat2.type.input) 277 #for $k, $file in enumerate($repeat2.type.input)
209 ln -s '${file}' '$repeat_dir/file_${k}.inner_distance_freq.txt' && 278 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.inner_distance_freq.txt')
279 ln -s '${file}' '$file_path' &&
210 #end for 280 #end for
211 #elif str($repeat2.type.type) == "junction_annotation" 281 #elif str($repeat2.type.type) == "junction_annotation"
212 #set $pattern = "Partial Novel Splicing Junctions:" 282 #set $pattern = "Partial Novel Splicing Junctions:"
213 @LN_3_FILES@ 283 @LN_3_FILES@
214 #elif str($repeat2.type.type) == "read_gc" 284 #elif str($repeat2.type.type) == "read_gc"
215 #for $k, $file in enumerate($repeat2.type.input) 285 #for $k, $file in enumerate($repeat2.type.input)
216 ln -s '$file' '$repeat_dir/file_${k}.GC.xls' && 286 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.GC.xls')
287 ln -s '$file' '$file_path' &&
217 #end for 288 #end for
218 #elif str($repeat2.type.type) == "junction_annotation" 289 #elif str($repeat2.type.type) == "junction_annotation"
219 #set $pattern = "Group Total_bases Tag_count Tags/Kb" 290 #set $pattern = "Group Total_bases Tag_count Tags/Kb"
220 @LN_3_FILES@ 291 @LN_3_FILES@
221 #elif str($repeat2.type.type) == "read_distribution" 292 #elif str($repeat2.type.type) == "read_distribution"
222 #set $pattern = "Group Total_bases Tag_count Tags/Kb" 293 #set $pattern = "Group Total_bases Tag_count Tags/Kb"
223 @LN_3_FILES@ 294 @LN_3_FILES@
224 #elif str($repeat2.type.type) == "read_duplication_pos" 295 #elif str($repeat2.type.type) == "read_duplication_pos"
225 #for $k, $file in enumerate($repeat2.type.input) 296 #for $k, $file in enumerate($repeat2.type.input)
226 ln -s '$file' '$repeat_dir/file_${k}.pos.DupRate.xls' && 297 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls')
298 ln -s '$file' '$file_path' &&
227 #end for 299 #end for
228 #elif str($repeat2.type.type) == "infer_experiment" 300 #elif str($repeat2.type.type) == "infer_experiment"
229 #set $pattern = "Fraction of reads explained by" 301 #set $pattern = "Fraction of reads explained by"
230 #for $k, $file in enumerate($repeat2.type.input) 302 #for $k, $file in enumerate($repeat2.type.input)
303 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '_infer_experiment.txt')
231 grep -q "$pattern" $file || die "'$pattern' not found in the file" && 304 grep -q "$pattern" $file || die "'$pattern' not found in the file" &&
232 ln -s '$file' '$repeat_dir/$file_${k}_infer_experiment.txt' && 305 ln -s '$file' '$file_path' &&
233 #end for 306 #end for
234 #end if 307 #end if
235 #end for 308 #end for
236 #elif str($repeat.software_cond.software) == "salmon" 309 #elif str($repeat.software_cond.software) == "salmon"
237 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) 310 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
238 #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) 311 @CREATE_REPEAT_DIR_2@
239 mkdir '$repeat_dir' &&
240 #if str($repeat2.type.type) == "meta" 312 #if str($repeat2.type.type) == "meta"
241 #for $k, $file in enumerate($repeat2.type.input) 313 #for $k, $file in enumerate($repeat2.type.input)
242 #set file_dir = $repeat_dir + '/file_' + str($k) 314 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
315 #set file_path = os.path.join($file_dir, 'meta_info.json')
243 mkdir '$file_dir' && 316 mkdir '$file_dir' &&
244 ln -s '$file' '$file_dir/meta_info.json' && 317 ln -s '$file' '$file_path' &&
245 #end for 318 #end for
246 #elif str($repeat2.type.type) == "fld" 319 #elif str($repeat2.type.type) == "fld"
247 #for $k, $file in enumerate($repeat2.type.input) 320 #for $k, $file in enumerate($repeat2.type.input)
248 #set file_dir = $repeat_dir + '/file_' + str($k) 321 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
322 #set file_path = os.path.join($file_dir,'flenDist.txt')
249 mkdir '$file_dir' && 323 mkdir '$file_dir' &&
250 ln -s '$file' '$file_dir/flenDist.txt' && 324 ln -s '$file' '$file_path' &&
251 #end for 325 #end for
252 #end if 326 #end if
253 #end for 327 #end for
254 #elif str($repeat.software_cond.software) == "samblaster" 328 #elif str($repeat.software_cond.software) == "samblaster"
255 #set $pattern = "samblaster: Version" 329 #set $pattern = "samblaster: Version"
256 @LN_FILES@ 330 @LN_FILES@
257 #elif str($repeat.software_cond.software) == "samtools" 331 #elif str($repeat.software_cond.software) == "samtools"
258 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) 332 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
259 #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) 333 @CREATE_REPEAT_DIR_2@
260 mkdir '$repeat_dir' &&
261 #if str($repeat2.type.type) == "stats" 334 #if str($repeat2.type.type) == "stats"
262 #set $pattern = "This file was produced by samtools stats" 335 #set $pattern = "This file was produced by samtools stats"
263 @LN_3_FILES@ 336 @LN_3_FILES@
264 #elif str($repeat2.type.type) == "flagstat" 337 #elif str($repeat2.type.type) == "flagstat"
265 #set $pattern = "in total (QC-passed reads + QC-failed reads)" 338 #set $pattern = "in total (QC-passed reads + QC-failed reads)"
266 @LN_3_FILES@ 339 @LN_3_FILES@
267 #elif str($repeat2.type.type) == "idxstats" 340 #elif str($repeat2.type.type) == "idxstats"
268 #for $file in $repeat2.type.input 341 #for $file in $repeat2.type.input
269 ln -s '$file' '$repeat_dir/${file.element_identifier}_idxstat' && 342 @ESCAPE_IDENTIFIER@
343 #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat')
344 ln -s '$file' '$file_path' &&
270 #end for 345 #end for
271 #elif str($repeat2.type.type) == "rmdup" 346 #elif str($repeat2.type.type) == "rmdup"
272 #set $pattern = "[bam_rmdup" 347 #set $pattern = "[bam_rmdup"
273 @LN_3_FILES@ 348 @LN_3_FILES@
274 #end if 349 #end if
279 #elif str($repeat.software_cond.software) == "sortmerna" 354 #elif str($repeat.software_cond.software) == "sortmerna"
280 #set $pattern = "Minimal SW score based on E-value" 355 #set $pattern = "Minimal SW score based on E-value"
281 @LN_FILES@ 356 @LN_FILES@
282 #else if str($repeat.software_cond.software) == "star": 357 #else if str($repeat.software_cond.software) == "star":
283 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) 358 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
284 #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) 359 @CREATE_REPEAT_DIR_2@
285 mkdir $repeat_dir &&
286 #if str($repeat2.type.type) == "log" 360 #if str($repeat2.type.type) == "log"
287 #for $file in $repeat2.type.input 361 #for $file in $repeat2.type.input
288 ln -s '$file' '${repeat_dir}/${file.element_identifier}_Log.final.out' && 362 @ESCAPE_IDENTIFIER@
363 #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out')
364 ln -s '$file' '$file_path' &&
289 #end for 365 #end for
290 #elif str($repeat2.type.type) == "genecounts" 366 #elif str($repeat2.type.type) == "genecounts"
291 #for $file in $repeat2.type.input 367 #for $file in $repeat2.type.input
292 ln -s '$file' '${repeat_dir}/${file.element_identifier}_ReadsPerGene.out.tab' && 368 @ESCAPE_IDENTIFIER@
369 #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab')
370 ln -s '$file' '$file_path' &&
293 #end for 371 #end for
294 #end if 372 #end if
295 #end for 373 #end for
296 #elif str($repeat.software_cond.software) == "tophat" 374 #elif str($repeat.software_cond.software) == "tophat"
297 #for $file in $repeat.software_cond.input 375 #for $file in $repeat.software_cond.input
298 ln -s '$file' '$software_dir/${file.element_identifier}align_summary.txt' && 376 @ESCAPE_IDENTIFIER@
377 #set file_path = os.path.join($software_dir, str($identifier) + 'align_summary.txt')
378 ln -s '$file' '$file_path' &&
299 #end for 379 #end for
300 #elif str($repeat.software_cond.software) == "trimmomatic" 380 #elif str($repeat.software_cond.software) == "trimmomatic"
301 #set $pattern = "Trimmomatic" 381 #set $pattern = "Trimmomatic"
302 @LN_FILES@ 382 @LN_FILES@
303 #elif str($repeat.software_cond.software) == "vcftools" 383 #elif str($repeat.software_cond.software) == "vcftools"
304 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) 384 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
305 #set file_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) 385 @CREATE_REPEAT_DIR_2@
306 mkdir $file_dir &&
307 #if str($repeat2.type.type) == "relatedness2" 386 #if str($repeat2.type.type) == "relatedness2"
308 #for $file in $repeat2.type.input 387 #for $file in $repeat2.type.input
309 ln -s '$file' '${repeat_dir}/${file.element_identifier}.relatedness2' && 388 @ESCAPE_IDENTIFIER@
389 #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2')
390 ln -s '$file' '$file_path' &&
310 #end for 391 #end for
311 #elif str($repeat2.type) == "tstv_by_count" 392 #elif str($repeat2.type) == "tstv_by_count"
312 #for $file in $repeat2.type.input 393 #for $file in $repeat2.type.input
313 ln -s '$file' '${repeat_dir}/${file.element_identifier}.TsTv.count' && 394 @ESCAPE_IDENTIFIER@
395 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count')
396 ln -s '$file' '$file_path' &&
314 #end for 397 #end for
315 #elif str($repeat2.type) == "tstv_by_qual" 398 #elif str($repeat2.type) == "tstv_by_qual"
316 #for $file in $repeat2.type.input 399 #for $file in $repeat2.type.input
317 ln -s '$file' '${repeat_dir}/${file.element_identifier}.TsTv.qual' && 400 @ESCAPE_IDENTIFIER@
401 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual')
402 ln -s '$file' '$file_path' &&
318 #end for 403 #end for
319 #elif str($repeat2.type) == "tstv_summary" 404 #elif str($repeat2.type) == "tstv_summary"
320 #for $file in $repeat2.type.input 405 #for $file in $repeat2.type.input
321 ln -s '$file' '${repeat_dir}/${file.element_identifier}.TsTv.summary' && 406 @ESCAPE_IDENTIFIER@
407 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary')
408 ln -s '$file' '$file_path' &&
322 #end for 409 #end for
323 #end if 410 #end if
324 #end for 411 #end for
325 #else if str($repeat.software_cond.software) == "custom_content": 412 #else if str($repeat.software_cond.software) == "custom_content":
326 #set $configfile = "T" 413 #set $configfile = "T"
327 #for $j, $file in enumerate( $repeat.software_cond.input ) 414 #for $j, $file in enumerate( $repeat.software_cond.input )
328 ln -s '$file' '${software_dir}/file_${i}_${j}' && 415 #set file_path = os.path.join($software_dir, 'file_' + str($i) + '_' + str($j))
416 ln -s '$file' '$file_path' &&
329 more $file && 417 more $file &&
330 #end for 418 #end for
331 #end if 419 #end if
332 #end for 420 #end for
333 421
334 multiqc multiqc_WDir 422 multiqc multiqc_WDir
423 --filename "report"
424
425 #if str($title)
426 --title "$title"
427 #end if
428 #if str($comment)
429 --comment "$comment"
430 #end if
335 431
336 #if $configfile == "T" 432 #if $configfile == "T"
337 -c '$multiqc_config' 433 --config '$multiqc_config'
338 #end if 434 #end if
339 ]]></command> 435 ]]></command>
340 <configfiles> 436 <configfiles>
341 <configfile name="multiqc_config"> 437 <configfile name="multiqc_config">
342 <![CDATA[ 438 <![CDATA[
369 <conditional name="software_cond"> 465 <conditional name="software_cond">
370 <param name="software" type="select" label="Which tool was used generate logs?" help="Software name"> 466 <param name="software" type="select" label="Which tool was used generate logs?" help="Software name">
371 <!--<option value="adapterRemoval">Adapter Removal</option>--> 467 <!--<option value="adapterRemoval">Adapter Removal</option>-->
372 <!--<option value="afterqc">AfterQC</option>--> 468 <!--<option value="afterqc">AfterQC</option>-->
373 <option value="bamtools">Bamtools</option> 469 <option value="bamtools">Bamtools</option>
470 <!--<option value="bbmap">BBMap</option>-->
374 <option value="bcftools">Bcftools</option> 471 <option value="bcftools">Bcftools</option>
375 <!--<option value="bcl2fastq">bcl2fastq</option>--> 472 <!--<option value="bcl2fastq">bcl2fastq</option>-->
376 <!--<option value="biobloomtools">BioBloom Tools</option>--> 473 <!--<option value="biobloomtools">BioBloom Tools</option>-->
377 <option value="bismark">Bismark</option> 474 <option value="bismark">Bismark</option>
378 <!--<option value="bowtie1">Bowtie 1</option>--> 475 <!--<option value="bowtie1">Bowtie 1</option>-->
379 <option value="bowtie2">Bowtie 2</option> 476 <option value="bowtie2">Bowtie 2</option>
380 <option value="busco">BUSCO</option> 477 <option value="busco">BUSCO</option>
381 <!--<option value="clusterflow">Cluster Flow</option>--> 478 <!--<option value="clusterflow">Cluster Flow</option>-->
382 <option value="cutadapt">Cutadapt/Trim Galore!</option> 479 <option value="cutadapt">Cutadapt/Trim Galore!</option>
480 <!--<option value="clipandmerge">ClipAndMerge</option>-->
383 <!--<option value="conpair">Conpair</option>--> 481 <!--<option value="conpair">Conpair</option>-->
482 <!--<option value="dedup">DeDup</option>-->
483 <option value="deeptools">deepTools</option>
384 <!--<option value="disambiguate">Disambiguate</option>--> 484 <!--<option value="disambiguate">Disambiguate</option>-->
385 <!--<option value="fastq_screen">FastQ Screen</option>--> 485 <!--<option value="fastq_screen">FastQ Screen</option>-->
386 <option value="fastqc">FastQC</option> 486 <option value="fastqc">FastQC</option>
387 <option value="featureCounts">featureCounts</option> 487 <option value="featureCounts">featureCounts</option>
388 <option value="flexbar">Flexbar</option> 488 <option value="flexbar">Flexbar</option>
389 <option value="gatk">GATK (BaseRecalibrator or VariantEval output)</option> 489 <option value="gatk">GATK</option>
390 <!--<option value="goleft_indexcov">goleft indexcov</option>--> 490 <!--<option value="goleft_indexcov">goleft indexcov</option>-->
391 <option value="hicexplorer">HiCExplorer</option> 491 <option value="hicexplorer">HiCExplorer</option>
392 <!--<option value="hicup">HiCUP</option>--> 492 <!--<option value="hicup">HiCUP</option>-->
393 <option value="hisat2">HISAT2</option> 493 <option value="hisat2">HISAT2</option>
394 <!--<option value="homer">HOMER</option>--> 494 <!--<option value="homer">HOMER</option>-->
395 <option value="htseq">HTSeq</option> 495 <option value="htseq">HTSeq</option>
496 <!--<option value="interop">InterOp</option>-->
396 <!--<option value="jellyfish">Jellyfish</option>--> 497 <!--<option value="jellyfish">Jellyfish</option>-->
397 <option value="kallisto">Kallisto</option> 498 <option value="kallisto">Kallisto</option>
398 <!--<option value="leehom">leeHom</option>--> 499 <!--<option value="leehom">leeHom</option>-->
399 <!--<option value="macs2">MACS2</option>--> 500 <!--<option value="macs2">MACS2</option>-->
400 <!--<option value="methylQA">methylQA</option>--> 501 <!--<option value="methylQA">methylQA</option>-->
405 <!--<option value="qorts">QoRTs</option>--> 506 <!--<option value="qorts">QoRTs</option>-->
406 <!--<option value="qualimap">Qualimap (BamQC or RNASeq output)</option>--> 507 <!--<option value="qualimap">Qualimap (BamQC or RNASeq output)</option>-->
407 <option value="quast">QUAST</option> 508 <option value="quast">QUAST</option>
408 <!--<option value="rna_seqc">RNA-SeQC</option>--> 509 <!--<option value="rna_seqc">RNA-SeQC</option>-->
409 <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>--> 510 <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>-->
410 <option value="rseqc">RSeQC (bam_stat, gene_body_coverage, infer_experiment, ...)</option> 511 <option value="rseqc">RSeQC</option>
411 <!--<option value="salmon">Salmon</option>--> 512 <!--<option value="salmon">Salmon</option>-->
412 <option value="samblaster">Samblaster</option> 513 <option value="samblaster">Samblaster</option>
413 <option value="samtools">Samtools</option> 514 <option value="samtools">Samtools</option>
515 <!--<option value="sargasso">Sargasso</option>-->
414 <!--<option value="skewer">Skewer</option>--> 516 <!--<option value="skewer">Skewer</option>-->
517 <!--<option value="slamdunk">Slamdunk</option>-->
518 <option value="snpeff">SnpEff</option>
415 <option value="sortmerna">SortMeRNA</option> 519 <option value="sortmerna">SortMeRNA</option>
416 <!--<option value="slamdunk">Slamdunk</option>-->
417 <!--<option value="snpeff">SnpEff</option>-->
418 <option value="star">STAR</option> 520 <option value="star">STAR</option>
521 <!--<option value="supernova">Supernova</option>-->
419 <!--<option value="theta2">THeTA2</option>--> 522 <!--<option value="theta2">THeTA2</option>-->
420 <option value="tophat">TopHat2</option> 523 <option value="tophat">TopHat2</option>
421 <option value="trimmomatic">Trimmomatic</option> 524 <option value="trimmomatic">Trimmomatic</option>
422 <option value="vcftools">VCFTools</option> 525 <option value="vcftools">VCFTools</option>
526 <!--<option value="verifybamid">VerifyBAMID</option>-->
423 <!--Custom--> 527 <!--Custom-->
424 <option value="custom_content">Custom Content</option> 528 <option value="custom_content">Custom Content</option>
425 </param> 529 </param>
426 <when value="bamtools"> 530 <when value="bamtools">
427 <param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'Stats for BAM file(s)'"/> 531 <param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'Stats for BAM file(s)'"/>
448 <param name="input" type="data" format="txt" multiple="true" label="Output of BUSCO"/> 552 <param name="input" type="data" format="txt" multiple="true" label="Output of BUSCO"/>
449 </when> 553 </when>
450 <when value="cutadapt"> 554 <when value="cutadapt">
451 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Cutadapt" help="It should contain 'This is cutadapt' or 'You are running cutadapt'"/> 555 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Cutadapt" help="It should contain 'This is cutadapt' or 'You are running cutadapt'"/>
452 </when> 556 </when>
557 <when value="deeptools">
558 <repeat name="output" title="deepTools output" min="1">
559 <param name="type" type="select" label="deepTool used to generate the output?">
560 <option value="bamPEFragmentSize">bamPEFragmentSize</option>
561 <option value="estimateReadFiltering">estimateReadFiltering</option>
562 <option value="plotCoverageStdout">plotCoverageStdout</option>
563 <option value="plotCoverageOutRawCounts">plotCoverageOutRawCounts</option>
564 <option value="plotEnrichment">plotEnrichment</option>
565 <option value="plotFingerprintOutRawCounts">plotFingerprintOutRawCounts</option>
566 <option value="plotFingerprintOutQualityMetrics">plotFingerprintOutQualityMetrics</option>
567 </param>
568 <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/>
569 </repeat>
570 </when>
453 <when value="fastqc"> 571 <when value="fastqc">
454 <repeat name="output" title="FastQC output" min="1"> 572 <repeat name="output" title="FastQC output" min="1">
455 <param name="type" type="select" label="Type of FastQC output?"> 573 <param name="type" type="select" label="Type of FastQC output?">
456 <option value="data">Raw data</option> 574 <option value="data">Raw data</option>
457 <option value="theoretical_gc">Theorectical GC</option> 575 <option value="theoretical_gc">Theorectical GC</option>
458 </param> 576 </param>
459 <param name="input" type="data" format="txt" multiple="true" label="FastQC output"/> 577 <param name="input" type="data" format="txt" multiple="true" label="FastQC output">
578 <validator type="expression" message="MultiQC does not accept the HTML report generated by FastQC, only the Raw Data">value is not None and value.extension != "html"</validator>
579 </param>
460 </repeat> 580 </repeat>
461 </when> 581 </when>
462 <when value="featureCounts"> 582 <when value="featureCounts">
463 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of FeatureCounts"/> 583 <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of FeatureCounts"/>
464 </when> 584 </when>
582 </repeat> 702 </repeat>
583 </when> 703 </when>
584 <when value="sortmerna"> 704 <when value="sortmerna">
585 <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'"/> 705 <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'"/>
586 </when> 706 </when>
707 <when value="snpeff">
708 <param name="input" type="data" format="csv" multiple="true" label="Output of SnpEff"/>
709 </when>
587 <when value="star"> 710 <when value="star">
588 <repeat name="output" title="STAR output" min="1"> 711 <repeat name="output" title="STAR output" min="1">
589 <conditional name="type"> 712 <conditional name="type">
590 <param name="type" type="select" label="Type of STAR output?"> 713 <param name="type" type="select" label="Type of STAR output?">
591 <option value="log">Log</option> 714 <option value="log">Log</option>
645 <param argument="ylab" label="Y axis label" type="text" /> 768 <param argument="ylab" label="Y axis label" type="text" />
646 <param name="input" type="data" format="tabular,tsv" multiple="true" label="Data files"/> 769 <param name="input" type="data" format="tabular,tsv" multiple="true" label="Data files"/>
647 </when> 770 </when>
648 </conditional> 771 </conditional>
649 </repeat> 772 </repeat>
773 <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"/>
774 <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"/>
775 <param name="saveLog" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/>
650 <param name="saveLog" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/> 776 <param name="saveLog" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/>
651 </inputs> 777 </inputs>
652 <outputs> 778 <outputs>
653 <data name="html_report" format="html" from_work_dir="multiqc_report.html" label="${tool.name} on ${on_string}: Webpage" /> 779 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" />
654 <data name="log" format="txt" from_work_dir="multiqc_data/multiqc.log" label="${tool.name} on ${on_string}: Log"> 780 <data name="log" format="txt" from_work_dir="report_data/multiqc.log" label="${tool.name} on ${on_string}: Log">
655 <filter>saveLog</filter> 781 <filter>saveLog</filter>
656 </data> 782 </data>
657 <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats"> 783 <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats">
658 <discover_datasets pattern="multiqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="multiqc_data" /> 784 <discover_datasets pattern="multiqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" />
659 </collection> 785 </collection>
660 </outputs> 786 </outputs>
661 <tests> 787 <tests>
662 <test> 788 <test>
663 <repeat name="results"> 789 <repeat name="results">
691 <conditional name="software_cond"> 817 <conditional name="software_cond">
692 <param name="software" value="trimmomatic" /> 818 <param name="software" value="trimmomatic" />
693 <param name="input" value="trimmomatic.txt" /> 819 <param name="input" value="trimmomatic.txt" />
694 </conditional> 820 </conditional>
695 </repeat> 821 </repeat>
822 <param name="title" value="Title of the report"/>
823 <param name="comment" value="Commment for the report"/>
696 <param name="saveLog" value="True"/> 824 <param name="saveLog" value="True"/>
697 <output name="html_report"> 825 <output name="html_report">
698 <assert_contents> 826 <assert_contents>
827 <has_text text="Title of the report" />
828 <has_text text="Commment for the report" />
699 <has_text text="cutadapt_plot" /> 829 <has_text text="cutadapt_plot" />
700 <has_text text="fastqc_seq_heatmap_key_t" /> 830 <has_text text="fastqc_seq_heatmap_key_t" />
701 <has_text text="flexbar_plot" /> 831 <has_text text="flexbar_plot" />
702 <has_text text="sortmerna-detailed-plot" /> 832 <has_text text="sortmerna-detailed-plot" />
703 <has_text text="trimmomatic_plot" /> 833 <has_text text="trimmomatic_plot" />
783 913
784 </assert_contents> 914 </assert_contents>
785 </output> 915 </output>
786 <output_collection name="stats" type="list"> 916 <output_collection name="stats" type="list">
787 <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/> 917 <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/>
788 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="0"/> 918 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/>
789 <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/> 919 <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/>
790 <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="0"/> 920 <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="20"/>
791 <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> --> 921 <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> -->
792 <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/> 922 <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/>
793 <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/> 923 <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/>
794 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/> 924 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/>
795 </output_collection> 925 </output_collection>
813 <param name="input" value="busco.txt" /> 943 <param name="input" value="busco.txt" />
814 </conditional> 944 </conditional>
815 </repeat> 945 </repeat>
816 <repeat name="results"> 946 <repeat name="results">
817 <conditional name="software_cond"> 947 <conditional name="software_cond">
948 <param name="software" value="deeptools" />
949 <repeat name="output">
950 <param name="type" value="bamPEFragmentSize"/>
951 <param name="input" value="deeptools_bamPEFragmentSize.txt"/>
952 </repeat>
953 <repeat name="output">
954 <param name="type" value="estimateReadFiltering"/>
955 <param name="input" value="deeptools_estimateReadFiltering.txt"/>
956 </repeat>
957 <repeat name="output">
958 <param name="type" value="plotCoverageStdout"/>
959 <param name="input" value="deeptools_plotCoverageStdout.txt"/>
960 </repeat>
961 <repeat name="output">
962 <param name="type" value="plotCoverageOutRawCounts"/>
963 <param name="input" value="deeptools_plotCoverageOutRawCounts.txt"/>
964 </repeat>
965 <repeat name="output">
966 <param name="type" value="plotEnrichment"/>
967 <param name="input" value="deeptools_plotEnrichment.txt"/>
968 </repeat>
969 <repeat name="output">
970 <param name="type" value="plotFingerprintOutRawCounts"/>
971 <param name="input" value="deeptools_plotFingerprintOutRawCounts.txt"/>
972 </repeat>
973 </conditional>
974 </repeat>
975 <repeat name="results">
976 <conditional name="software_cond">
818 <param name="software" value="featureCounts" /> 977 <param name="software" value="featureCounts" />
819 <param name="input" value="featureCounts.txt" /> 978 <param name="input" value="featureCounts.txt" />
820 </conditional> 979 </conditional>
821 </repeat> 980 </repeat>
822 <repeat name="results"> 981 <repeat name="results">
915 <conditional name="type"> 1074 <conditional name="type">
916 <param name="type" value="idxstats"/> 1075 <param name="type" value="idxstats"/>
917 <param name="input" value="samtools_idxstats.txt"/> 1076 <param name="input" value="samtools_idxstats.txt"/>
918 </conditional> 1077 </conditional>
919 </repeat> 1078 </repeat>
1079 </conditional>
1080 </repeat>
1081 <repeat name="results">
1082 <conditional name="software_cond">
1083 <param name="software" value="snpeff" />
1084 <param name="input" value="snpeff.csv" />
920 </conditional> 1085 </conditional>
921 </repeat> 1086 </repeat>
922 <repeat name="results"> 1087 <repeat name="results">
923 <conditional name="software_cond"> 1088 <conditional name="software_cond">
924 <param name="software" value="vcftools" /> 1089 <param name="software" value="vcftools" />
934 <output name="html_report"> 1099 <output name="html_report">
935 <assert_contents> 1100 <assert_contents>
936 <has_text text="bamtools-stats" /> 1101 <has_text text="bamtools-stats" />
937 <has_text text="bcftools_stats_indel-lengths" /> 1102 <has_text text="bcftools_stats_indel-lengths" />
938 <has_text text="busco-lineage-fungi_odb9" /> 1103 <has_text text="busco-lineage-fungi_odb9" />
1104 <has_text text="deeptools" />
939 <has_text text="featureCounts_assignment_plot" /> 1105 <has_text text="featureCounts_assignment_plot" />
940 <has_text text="gatk_varianteval_variant_plot" /> 1106 <has_text text="gatk_varianteval_variant_plot" />
941 <has_text text="htseq_assignment_plot" /> 1107 <has_text text="htseq_assignment_plot" />
942 <has_text text="picard_aligned_reads" /> 1108 <has_text text="picard_aligned_reads" />
943 <has_text text="picard-rna-assignment" /> 1109 <has_text text="picard-rna-assignment" />
946 <has_text text="picard-gcbias" /> 1112 <has_text text="picard-gcbias" />
947 <has_text text="prokka_plot" /> 1113 <has_text text="prokka_plot" />
948 <has_text text="samblaster_duplicates" /> 1114 <has_text text="samblaster_duplicates" />
949 <has_text text="quast-stats" /> 1115 <has_text text="quast-stats" />
950 <has_text text="samtools-flagstat-dp" /> 1116 <has_text text="samtools-flagstat-dp" />
951 <has_text text="bamtools-stats" /> 1117 <has_text text="snpeff" />
952 </assert_contents> 1118 </assert_contents>
953 </output> 1119 </output>
954 <output_collection name="stats" type="list"> 1120 <output_collection name="stats" type="list">
955 <element name="bamtools_stats" file="bamtools_stats.tabular" compare="sim_size" delta="0"/> 1121 <element name="bamtools_stats" file="bamtools_stats.tabular" compare="sim_size" delta="10"/>
956 <element name="bcftools_stats" file="bcftools_stats.tabular" compare="sim_size" delta="0"/> 1122 <element name="bcftools_stats" file="bcftools_stats.tabular" compare="sim_size" delta="0"/>
957 <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="0"/> 1123 <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="10"/>
958 <element name="featureCounts" file="featureCounts_stats.tabular" compare="sim_size" delta="25"/> 1124 <element name="featureCounts" file="featureCounts_stats.tabular" compare="sim_size" delta="25"/>
959 <element name="gatk_varianteval" file="gatk_varianteval_stats.tabular" compare="sim_size" delta="20"/> 1125 <element name="gatk_varianteval" file="gatk_varianteval_stats.tabular" compare="sim_size" delta="20"/>
960 <element name="general_stats" file="post_aligner_soft_stats.tabular" compare="sim_size" delta="25"/> 1126 <element name="general_stats" file="post_aligner_soft_stats.tabular" compare="sim_size" delta="25"/>
961 <element name="htseq" file="htseq_stats.tabular" compare="sim_size" delta="0"/> 1127 <element name="htseq" file="htseq_stats.tabular" compare="sim_size" delta="10"/>
962 <element name="picard_AlignmentSummaryMetrics" file="picard_AlignmentSummaryMetrics_stats.tabular" compare="sim_size" delta="0"/> 1128 <element name="picard_AlignmentSummaryMetrics" file="picard_AlignmentSummaryMetrics_stats.tabular" compare="sim_size" delta="0"/>
963 <element name="picard_RnaSeqMetrics" file="picard_RnaSeqMetrics_stats.tabular" compare="sim_size" delta="40"/> 1129 <element name="picard_RnaSeqMetrics" file="picard_RnaSeqMetrics_stats.tabular" compare="sim_size" delta="40"/>
964 <element name="picard_baseContent" file="picard_baseContent_stats.tabular" compare="sim_size" delta="50"/> 1130 <element name="picard_baseContent" file="picard_baseContent_stats.tabular" compare="sim_size" delta="50"/>
965 <element name="picard_dups" file="picard_dups_stats.tabular" compare="sim_size" delta="0"/> 1131 <element name="picard_dups" file="picard_dups_stats.tabular" compare="sim_size" delta="0"/>
966 <element name="picard_insertSize" file="picard_insertSize_stats.tabular" compare="sim_size" delta="0"/> 1132 <element name="picard_insertSize" file="picard_insertSize_stats.tabular" compare="sim_size" delta="0"/>
973 <has_text text="mapped_passed" /> 1139 <has_text text="mapped_passed" />
974 <has_text text="20689039" /> 1140 <has_text text="20689039" />
975 </assert_contents> 1141 </assert_contents>
976 </element> 1142 </element>
977 <element name="samtools_stats" file="samtools_stats_stats.tabular" compare="sim_size" delta="15"/> 1143 <element name="samtools_stats" file="samtools_stats_stats.tabular" compare="sim_size" delta="15"/>
1144 <element name="snpeff" file="snpeff_stats.tabular" compare="sim_size" delta="10"/>
978 </output_collection> 1145 </output_collection>
979 </test> 1146 </test>
980 <test> 1147 <test>
981 <repeat name="results"> 1148 <repeat name="results">
982 <conditional name="software_cond"> 1149 <conditional name="software_cond">
1003 1170
1004 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 1171 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
1005 1172
1006 ---- 1173 ----
1007 1174
1008 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). 1175 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>`_.
1009 ]]></help> 1176 ]]></help>
1010 <citations> 1177 <citations>
1011 <citation type="doi">10.1093/bioinformatics/btw354</citation> 1178 <citation type="doi">10.1093/bioinformatics/btw354</citation>
1012 </citations> 1179 </citations>
1013 </tool> 1180 </tool>