Mercurial > repos > iuc > multiqc
comparison macros.xml @ 22:9a913cdee30e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3"
| author | iuc |
|---|---|
| date | Wed, 03 Nov 2021 15:17:39 +0000 |
| parents | |
| children | abfd8a6544d7 |
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| 21:75c93c70d094 | 22:9a913cdee30e |
|---|---|
| 1 <macros> | |
| 2 <token name="@TOOL_VERSION@">1.11</token> | |
| 3 <token name="@VERSION_SUFFIX@">0</token> | |
| 4 <xml name="bio_tools"> | |
| 5 <xrefs> | |
| 6 <xref type="bio.tools">multiqc</xref> | |
| 7 </xrefs> | |
| 8 </xml> | |
| 9 <xml name="requirements"> | |
| 10 <requirements> | |
| 11 <requirement type="package" version="@TOOL_VERSION@">multiqc</requirement> | |
| 12 </requirements> | |
| 13 </xml> | |
| 14 | |
| 15 <token name="@ESCAPE_IDENTIFIER@"> | |
| 16 <![CDATA[ | |
| 17 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) | |
| 18 ]]></token> | |
| 19 | |
| 20 <token name="@CHECK_LN_FILE@"> | |
| 21 <![CDATA[ | |
| 22 #if $file_path in $file_paths | |
| 23 #set $file_path += '_' + str($file_paths.count($file_path)) | |
| 24 #end if | |
| 25 #set $file_paths += [$file_path] | |
| 26 grep -q '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" && | |
| 27 ln -s '$file' '$file_path' && | |
| 28 ]]></token> | |
| 29 | |
| 30 <token name="@CREATE_REPEAT_DIR_1@"> | |
| 31 <![CDATA[ | |
| 32 #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j)) | |
| 33 mkdir '$repeat_dir' && | |
| 34 ]]></token> | |
| 35 | |
| 36 <token name="@CREATE_REPEAT_DIR_1@"> | |
| 37 <![CDATA[ | |
| 38 #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j)) | |
| 39 mkdir '$repeat_dir' && | |
| 40 ]]></token> | |
| 41 <token name="@CREATE_REPEAT_DIR_2@"> | |
| 42 <![CDATA[ | |
| 43 #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j)) | |
| 44 mkdir '$repeat_dir' && | |
| 45 ]]></token> | |
| 46 <token name="@LN_FILES@"> | |
| 47 <![CDATA[ | |
| 48 #set file_paths = [] | |
| 49 #for $file in $repeat.software_cond.input | |
| 50 @ESCAPE_IDENTIFIER@ | |
| 51 #set file_path = os.path.join($software_dir, str($identifier)) | |
| 52 @CHECK_LN_FILE@ | |
| 53 #end for | |
| 54 ]]></token> | |
| 55 | |
| 56 <token name="@LN_2_FILES@"> | |
| 57 <![CDATA[ | |
| 58 #set file_paths = [] | |
| 59 @CREATE_REPEAT_DIR_1@ | |
| 60 #for $file in $repeat2.input | |
| 61 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) | |
| 62 #set file_path = os.path.join($repeat_dir, str($identifier)) | |
| 63 @CHECK_LN_FILE@ | |
| 64 #end for | |
| 65 ]]></token> | |
| 66 | |
| 67 <token name="@LN_3_FILES@"> | |
| 68 <![CDATA[ | |
| 69 #set file_paths = [] | |
| 70 #for $file in $repeat2.type.input | |
| 71 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) | |
| 72 #set file_path = os.path.join($repeat_dir, str($identifier)) | |
| 73 @CHECK_LN_FILE@ | |
| 74 #end for | |
| 75 ]]></token> | |
| 76 | |
| 77 <token name="@BISMARK_INPUT@"><![CDATA[ | |
| 78 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) | |
| 79 @CREATE_REPEAT_DIR_1@ | |
| 80 #if str($repeat2.type) == "align" | |
| 81 #for $file in $repeat2.input | |
| 82 @ESCAPE_IDENTIFIER@ | |
| 83 #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt') | |
| 84 ln -s '$file' '$file_path' && | |
| 85 #end for | |
| 86 #elif str($repeat2.type) == "dedup" | |
| 87 #for $file in $repeat2.input | |
| 88 @ESCAPE_IDENTIFIER@ | |
| 89 #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt') | |
| 90 ln -s '$file' '$file_path' && | |
| 91 #end for | |
| 92 #elif str($repeat2.type) == "meth_extract" | |
| 93 #for $file in $repeat2.input | |
| 94 @ESCAPE_IDENTIFIER@ | |
| 95 #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt') | |
| 96 ln -s '$file' '$file_path' && | |
| 97 #end for | |
| 98 #elif str($repeat2.type) == "m_bias" | |
| 99 #for $file in $repeat2.input | |
| 100 @ESCAPE_IDENTIFIER@ | |
| 101 #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt') | |
| 102 ln -s '$file' '$file_path' && | |
| 103 #end for | |
| 104 #elif str($repeat2.type) == "bam2nuc" | |
| 105 #for $file in $repeat2.input | |
| 106 @ESCAPE_IDENTIFIER@ | |
| 107 #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt') | |
| 108 ln -s '$file' '$file_path' && | |
| 109 #end for | |
| 110 #end if | |
| 111 #end for | |
| 112 ]]></token> | |
| 113 | |
| 114 <token name="@DEEPTOOLS_INPUT@"><![CDATA[ | |
| 115 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) | |
| 116 #if str($repeat2.type) == "bamPEFragmentSize" | |
| 117 #set $pattern = "Frag." | |
| 118 @LN_2_FILES@ | |
| 119 #elif str($repeat2.type) == "estimateReadFiltering" | |
| 120 #set $pattern = "Internally-determined Duplicate" | |
| 121 @LN_2_FILES@ | |
| 122 #elif str($repeat2.type) == "plotCoverageStdout" | |
| 123 #set $pattern = "sample" | |
| 124 @LN_2_FILES@ | |
| 125 #elif str($repeat2.type) == "plotCoverageOutRawCounts" | |
| 126 #set $pattern = "#plotCoverage --outRawCounts" | |
| 127 @LN_2_FILES@ | |
| 128 #elif str($repeat2.type) == "plotEnrichment" | |
| 129 #set $pattern = "featureReadCount" | |
| 130 @LN_2_FILES@ | |
| 131 #elif str($repeat2.type) == "plotFingerprintOutRawCounts" | |
| 132 #set $pattern = "#plotFingerprint --outRawCounts" | |
| 133 @LN_2_FILES@ | |
| 134 #end if | |
| 135 #end for | |
| 136 ]]></token> | |
| 137 | |
| 138 <token name="@PICCARD_INPUT@"><![CDATA[ | |
| 139 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) | |
| 140 #if str($repeat2.type) == "alignment_metrics" | |
| 141 #set $pattern = "picard.analysis.AlignmentSummaryMetrics" | |
| 142 @LN_2_FILES@ | |
| 143 #elif str($repeat2.type) == "basedistributionbycycle" | |
| 144 #set $pattern = "picard.analysis.BaseDistributionByCycleMetrics" | |
| 145 @LN_2_FILES@ | |
| 146 #elif str($repeat2.type) == "gcbias" | |
| 147 #set $pattern = "picard.analysis.GcBias" | |
| 148 @LN_2_FILES@ | |
| 149 #elif str($repeat2.type) == "hsmetrics" | |
| 150 #set $pattern = "picard.analysis.directed.HsMetrics" | |
| 151 @ @ | |
| 152 #elif str($repeat2.type) == "insertsize" | |
| 153 #set $pattern = "picard.analysis.InsertSizeMetrics" | |
| 154 @LN_2_FILES@ | |
| 155 #elif str($repeat2.type) == "markdups" | |
| 156 #set $pattern = "MarkDuplicates" | |
| 157 @LN_2_FILES@ | |
| 158 #elif str($repeat2.type) == "oxogmetrics" | |
| 159 #set $pattern = "picard.analysis.CollectOxoGMetrics" | |
| 160 @LN_2_FILES@ | |
| 161 #elif str($repeat2.type) == "pcr_metrics" | |
| 162 #set $pattern = "picard.analysis.directed.TargetedPcrMetrics" | |
| 163 @LN_2_FILES@ | |
| 164 #elif str($repeat2.type) == "rnaseqmetrics" | |
| 165 #set $pattern = "Collect" | |
| 166 @LN_2_FILES@ | |
| 167 #elif str($repeat2.type) == "rrbs_metrics" | |
| 168 #set $pattern = "picard.analysis.RrbsSummaryMetrics" | |
| 169 @LN_2_FILES@ | |
| 170 #elif str($repeat2.type) == "wgs_metrics" | |
| 171 #set $pattern = "picard.analysis.CollectWgsMetrics$WgsMetrics" | |
| 172 @LN_2_FILES@ | |
| 173 #end if | |
| 174 #end for | |
| 175 ]]></token> | |
| 176 | |
| 177 <token name="@FASTQC_INPUT@"><![CDATA[ | |
| 178 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) | |
| 179 @CREATE_REPEAT_DIR_1@ | |
| 180 #if str($repeat2.type) == "data" | |
| 181 #for $k, $file in enumerate($repeat2.input) | |
| 182 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) | |
| 183 #set file_path = os.path.join($file_dir, 'fastqc_data.txt') | |
| 184 mkdir '$file_dir' && | |
| 185 ln -s '$file' '$file_path' && | |
| 186 #end for | |
| 187 #elif str($repeat2.type) == "theoretical_gc" | |
| 188 #for $file in $repeat2.input | |
| 189 @ESCAPE_IDENTIFIER@ | |
| 190 #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc') | |
| 191 ln -s '$file' '$file_path' && | |
| 192 #end for | |
| 193 #end if | |
| 194 #end for | |
| 195 ]]></token> | |
| 196 | |
| 197 <token name="@RSEQ_INPUT@"><![CDATA[ | |
| 198 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) | |
| 199 @CREATE_REPEAT_DIR_2@ | |
| 200 #if str($repeat2.type.type) == "bam_stat" | |
| 201 #set $pattern = "Proper-paired reads map to different chrom:" | |
| 202 @LN_3_FILES@ | |
| 203 #elif str($repeat2.type.type) == "gene_body_coverage" | |
| 204 #for $k, $file in enumerate($repeat2.type.input) | |
| 205 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.geneBodyCoverage.txt') | |
| 206 ln -s '$file' '$file_path' && | |
| 207 #end for | |
| 208 #elif str($repeat2.type.type) == "inner_distance" | |
| 209 #for $k, $file in enumerate($repeat2.type.input) | |
| 210 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.inner_distance_freq.txt') | |
| 211 ln -s '${file}' '$file_path' && | |
| 212 #end for | |
| 213 #elif str($repeat2.type.type) == "junction_annotation" | |
| 214 #set $pattern = "Partial Novel Splicing Junctions:" | |
| 215 @LN_3_FILES@ | |
| 216 #elif str($repeat2.type.type) == "read_gc" | |
| 217 #for $k, $file in enumerate($repeat2.type.input) | |
| 218 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.GC.xls') | |
| 219 ln -s '$file' '$file_path' && | |
| 220 #end for | |
| 221 #elif str($repeat2.type.type) == "junction_annotation" | |
| 222 #set $pattern = "Group Total_bases Tag_count Tags/Kb" | |
| 223 @LN_3_FILES@ | |
| 224 #elif str($repeat2.type.type) == "read_distribution" | |
| 225 #set $pattern = "Group Total_bases Tag_count Tags/Kb" | |
| 226 @LN_3_FILES@ | |
| 227 #elif str($repeat2.type.type) == "read_duplication_pos" | |
| 228 #for $k, $file in enumerate($repeat2.type.input) | |
| 229 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls') | |
| 230 ln -s '$file' '$file_path' && | |
| 231 #end for | |
| 232 #elif str($repeat2.type.type) == "infer_experiment" | |
| 233 #set $pattern = "Fraction of reads explained by" | |
| 234 #for $file in $repeat2.type.input | |
| 235 @ESCAPE_IDENTIFIER@ | |
| 236 #set file_path = os.path.join($repeat_dir, str($identifier)) | |
| 237 grep -q "$pattern" $file || die "'$pattern' not found in the file" && | |
| 238 ln -s '$file' '$file_path' && | |
| 239 #end for | |
| 240 #end if | |
| 241 #end for | |
| 242 ]]></token> | |
| 243 | |
| 244 <token name="@VCFTOOLS_INPUT@"><![CDATA[ | |
| 245 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) | |
| 246 @CREATE_REPEAT_DIR_2@ | |
| 247 #if str($repeat2.type.type) == "relatedness2" | |
| 248 #for $file in $repeat2.type.input | |
| 249 @ESCAPE_IDENTIFIER@ | |
| 250 #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2') | |
| 251 ln -s '$file' '$file_path' && | |
| 252 #end for | |
| 253 #elif str($repeat2.type) == "tstv_by_count" | |
| 254 #for $file in $repeat2.type.input | |
| 255 @ESCAPE_IDENTIFIER@ | |
| 256 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count') | |
| 257 ln -s '$file' '$file_path' && | |
| 258 #end for | |
| 259 #elif str($repeat2.type) == "tstv_by_qual" | |
| 260 #for $file in $repeat2.type.input | |
| 261 @ESCAPE_IDENTIFIER@ | |
| 262 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual') | |
| 263 ln -s '$file' '$file_path' && | |
| 264 #end for | |
| 265 #elif str($repeat2.type) == "tstv_summary" | |
| 266 #for $file in $repeat2.type.input | |
| 267 @ESCAPE_IDENTIFIER@ | |
| 268 #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary') | |
| 269 ln -s '$file' '$file_path' && | |
| 270 #end for | |
| 271 #end if | |
| 272 #end for | |
| 273 ]]></token> | |
| 274 | |
| 275 <token name="@QUALIMAP_INPUT@"><![CDATA[ | |
| 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 | |
| 297 ]]></token> | |
| 298 | |
| 299 <token name="@SALMON_INPUT@"><![CDATA[ | |
| 300 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) | |
| 301 @CREATE_REPEAT_DIR_2@ | |
| 302 #if str($repeat2.type.type) == "meta" | |
| 303 #for $k, $file in enumerate($repeat2.type.input) | |
| 304 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) | |
| 305 #set file_path = os.path.join($file_dir, 'meta_info.json') | |
| 306 mkdir '$file_dir' && | |
| 307 ln -s '$file' '$file_path' && | |
| 308 #end for | |
| 309 #elif str($repeat2.type.type) == "fld" | |
| 310 #for $k, $file in enumerate($repeat2.type.input) | |
| 311 #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) | |
| 312 #set file_path = os.path.join($file_dir,'flenDist.txt') | |
| 313 mkdir '$file_dir' && | |
| 314 ln -s '$file' '$file_path' && | |
| 315 #end for | |
| 316 #end if | |
| 317 #end for | |
| 318 ]]></token> | |
| 319 | |
| 320 <token name="@SAMTOOLS_INPUT@"><![CDATA[ | |
| 321 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) | |
| 322 @CREATE_REPEAT_DIR_2@ | |
| 323 #if str($repeat2.type.type) == "stats" | |
| 324 #set $pattern = "This file was produced by samtools stats" | |
| 325 @LN_3_FILES@ | |
| 326 #elif str($repeat2.type.type) == "flagstat" | |
| 327 #set $pattern = "in total (QC-passed reads + QC-failed reads)" | |
| 328 @LN_3_FILES@ | |
| 329 #elif str($repeat2.type.type) == "idxstats" | |
| 330 #for $file in $repeat2.type.input | |
| 331 @ESCAPE_IDENTIFIER@ | |
| 332 #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat') | |
| 333 ln -s '$file' '$file_path' && | |
| 334 #end for | |
| 335 #elif str($repeat2.type.type) == "rmdup" | |
| 336 #set $pattern = "[bam_rmdup" | |
| 337 @LN_3_FILES@ | |
| 338 #end if | |
| 339 #end for | |
| 340 ]]></token> | |
| 341 | |
| 342 <token name="@STAR_INPUT@"><![CDATA[ | |
| 343 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) | |
| 344 @CREATE_REPEAT_DIR_2@ | |
| 345 #if str($repeat2.type.type) == "log" | |
| 346 #for $file in $repeat2.type.input | |
| 347 @ESCAPE_IDENTIFIER@ | |
| 348 #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out') | |
| 349 ln -s '$file' '$file_path' && | |
| 350 #end for | |
| 351 #elif str($repeat2.type.type) == "genecounts" | |
| 352 #for $file in $repeat2.type.input | |
| 353 @ESCAPE_IDENTIFIER@ | |
| 354 #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab') | |
| 355 ln -s '$file' '$file_path' && | |
| 356 #end for | |
| 357 #end if | |
| 358 #end for | |
| 359 ]]></token> | |
| 360 | |
| 361 <xml name="element_assert" token_name="" token_lines="" token_columns="" token_text=""> | |
| 362 <element name="@NAME@"> | |
| 363 <assert_contents> | |
| 364 <has_n_columns n="@COLUMNS@"/> | |
| 365 <has_n_lines n="@LINES@"/> | |
| 366 <has_text text="@TEXT@"/> | |
| 367 <yield/> | |
| 368 </assert_contents> | |
| 369 </element> | |
| 370 </xml> | |
| 371 | |
| 372 <xml name="citations"> | |
| 373 <citations> | |
| 374 <citation type="doi">10.1101/gr.244293.118</citation> | |
| 375 </citations> | |
| 376 </xml> | |
| 377 </macros> |