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comparison multiqc.xml @ 20:c1a4b5f3b432 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720"
author iuc
date Tue, 02 Mar 2021 08:02:36 +0000
parents f7985e0479b9
children 75c93c70d094
comparison
equal deleted inserted replaced
19:f7985e0479b9 20:c1a4b5f3b432
51 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) 51 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
52 #set file_path = os.path.join($repeat_dir, str($identifier)) 52 #set file_path = os.path.join($repeat_dir, str($identifier))
53 @CHECK_LN_FILE@ 53 @CHECK_LN_FILE@
54 #end for 54 #end for
55 ]]></token> 55 ]]></token>
56 <xml name="element_assert" token_name="" token_lines="" token_columns="" token_text="">
57 <element name="@NAME@">
58 <assert_contents>
59 <has_n_columns n="@COLUMNS@"/>
60 <has_n_lines n="@LINES@"/>
61 <has_text text="@TEXT@"/>
62 <yield/>
63 </assert_contents>
64 </element>
65 </xml>
56 </macros> 66 </macros>
57 <requirements> 67 <requirements>
58 <requirement type="package" version="@WRAPPER_VERSION@">multiqc</requirement> 68 <requirement type="package" version="@WRAPPER_VERSION@">multiqc</requirement>
59 </requirements> 69 </requirements>
60 <version_command>multiqc --version</version_command> 70 <version_command>multiqc --version</version_command>
337 #elif str($repeat2.type.type) == "read_distribution" 347 #elif str($repeat2.type.type) == "read_distribution"
338 #set $pattern = "Group Total_bases Tag_count Tags/Kb" 348 #set $pattern = "Group Total_bases Tag_count Tags/Kb"
339 @LN_3_FILES@ 349 @LN_3_FILES@
340 #elif str($repeat2.type.type) == "read_duplication_pos" 350 #elif str($repeat2.type.type) == "read_duplication_pos"
341 #for $k, $file in enumerate($repeat2.type.input) 351 #for $k, $file in enumerate($repeat2.type.input)
342 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls') 352 #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls')
343 ln -s '$file' '$file_path' && 353 ln -s '$file' '$file_path' &&
344 #end for 354 #end for
345 #elif str($repeat2.type.type) == "infer_experiment" 355 #elif str($repeat2.type.type) == "infer_experiment"
346 #set $pattern = "Fraction of reads explained by" 356 #set $pattern = "Fraction of reads explained by"
347 #for $file in $repeat2.type.input 357 #for $file in $repeat2.type.input
929 <assert_contents> 939 <assert_contents>
930 <has_text_matching expression="\[INFO \] MultiQC complete$"/> 940 <has_text_matching expression="\[INFO \] MultiQC complete$"/>
931 </assert_contents> 941 </assert_contents>
932 </output> 942 </output>
933 <output_collection name="stats" type="list" count="10"> 943 <output_collection name="stats" type="list" count="10">
934 <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/> 944 <expand macro="element_assert" name="cutadapt" columns="8" lines="2" text="dataset_33"/>
935 <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/> 945 <expand macro="element_assert" name="fastp" columns="2" lines="3" text="R1_fq"/>
936 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/> 946 <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_1"/>
937 <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/> 947 <expand macro="element_assert" name="flexbar" columns="11" lines="2" text="result_right"/>
938 <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/> 948 <expand macro="element_assert" name="general_stats" columns="20" lines="11" text="bwa-mem-fastq1_fq"/>
939 <element name="slamdunk_readrates_plus" file="slamdunk_readrates_plus.tabular" compare="sim_size" delta="10"/> 949 <expand macro="element_assert" name="slamdunk_readrates_plus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/>
940 <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/> 950 <expand macro="element_assert" name="slamdunk_readrates_minus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/>
941 <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/> 951 <expand macro="element_assert" name="sortmerna" columns="22" lines="2" text="25839_merged"/>
952 <expand macro="element_assert" name="sources" columns="4" lines="7" text="Module"/>
953 <expand macro="element_assert" name="trimmomatic" columns="6" lines="2" text="C2"/>
942 </output_collection> 954 </output_collection>
943 <output_collection name="plots" type="list" count="29"/> 955 <output_collection name="plots" type="list" count="29"/>
944 </test> 956 </test>
945 <test expect_num_outputs="2"> 957 <test expect_num_outputs="2">
946 <repeat name="results"> 958 <repeat name="results">
1017 <has_text text="tophat_alignment" /> 1029 <has_text text="tophat_alignment" />
1018 <has_text text="hicexplorer" /> 1030 <has_text text="hicexplorer" />
1019 <has_text text="hicexplorer1_log_1" /> 1031 <has_text text="hicexplorer1_log_1" />
1020 </assert_contents> 1032 </assert_contents>
1021 </output> 1033 </output>
1022 <output_collection name="stats" type="list" count="8"> 1034 <output_collection name="stats" type="list" count="11">
1023 <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/> 1035 <expand macro="element_assert" name="bismark_alignment" columns="21" lines="2" text="bismark_txt_SE_report"/>
1024 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/> 1036 <expand macro="element_assert" name="bowtie2" columns="7" lines="3" text="bowtie2_1_txt"/>
1025 <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/> 1037 <expand macro="element_assert" name="cutadapt" columns="8" lines="5" text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2"/>
1026 <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="20"/> 1038 <expand macro="element_assert" name="general_stats" columns="21" lines="19" text="treat2"/>
1027 <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> --> 1039 <expand macro="element_assert" name="hicexplorer" columns="41" lines="4" text="hicexplorer_3_hicexplorer2_log_small_test_rf"/>
1028 <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/> 1040 <expand macro="element_assert" name="hisat2" columns="6" lines="3" text="hisat2_2_txt"/>
1029 <element name="macs" file="macs_stats.tabular" compare="sim_size" delta="10"/> 1041 <expand macro="element_assert" name="kallisto" columns="6" lines="3" text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1"/>
1030 <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/> 1042 <expand macro="element_assert" name="macs" columns="11" lines="3" text="treat2"/>
1031 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/> 1043 <expand macro="element_assert" name="sources" columns="4" lines="18" text="Cutadapt"/>
1044 <expand macro="element_assert" name="star" columns="27" lines="2" text="star_log_txt"/>
1045 <expand macro="element_assert" name="tophat.txt" columns="9" lines="2" text="tophat_txtalign"/>
1032 </output_collection> 1046 </output_collection>
1033 </test> 1047 </test>
1034 <test expect_num_outputs="2"> 1048 <test expect_num_outputs="2">
1035 <repeat name="results"> 1049 <repeat name="results">
1036 <conditional name="software_cond"> 1050 <conditional name="software_cond">
1229 <has_text text="quast-stats" /> 1243 <has_text text="quast-stats" />
1230 <has_text text="samtools-flagstat-dp" /> 1244 <has_text text="samtools-flagstat-dp" />
1231 <has_text text="snpeff" /> 1245 <has_text text="snpeff" />
1232 </assert_contents> 1246 </assert_contents>
1233 </output> 1247 </output>
1234 <output_collection name="stats" type="list" count="19"> 1248 <output_collection name="stats" type="list" count="21">
1235 <element name="bamtools_stats" file="bamtools_stats.tabular" compare="sim_size" delta="10"/> 1249 <expand macro="element_assert" name="bamtools_stats" columns="20" lines="2" text="bamtools_txt"/>
1236 <element name="bcftools_stats" file="bcftools_stats.tabular" compare="sim_size" delta="0"/> 1250 <expand macro="element_assert" name="bcftools_stats" columns="28" lines="2" text="Test1"/>
1237 <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="10"/> 1251 <expand macro="element_assert" name="busco" columns="8" lines="2" text="busco_txt"/>
1238 <element name="featureCounts" file="featureCounts_stats.tabular" compare="sim_size" delta="25"/> 1252 <expand macro="element_assert" name="featureCounts" columns="14" lines="7" text="5: TopHat on data 1, data 14, and data 13"/>
1239 <element name="gatk_varianteval" file="gatk_varianteval_stats.tabular" compare="sim_size" delta="20"/> 1253 <expand macro="element_assert" name="gatk_varianteval" columns="12" lines="2" text="gatk_varianteval_txt"/>
1240 <element name="general_stats" file="post_aligner_soft_stats.tabular" compare="sim_size" delta="25"/> 1254 <expand macro="element_assert" name="general_stats" columns="44" lines="23" text="x_bam"/>
1241 <element name="htseq" file="htseq_stats.tabular" compare="sim_size" delta="10"/> 1255 <expand macro="element_assert" name="htseq" columns="9" lines="2" text="htseq_txt"/>
1242 <element name="picard_AlignmentSummaryMetrics" file="picard_AlignmentSummaryMetrics_stats.tabular" compare="sim_size" delta="0"/> 1256 <expand macro="element_assert" name="picard_AlignmentSummaryMetrics" columns="26" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/>
1243 <element name="picard_RnaSeqMetrics" file="picard_RnaSeqMetrics_stats.tabular" compare="sim_size" delta="40"/> 1257 <expand macro="element_assert" name="picard_RnaSeqMetrics" columns="27" lines="2" text="picard_CollectRnaSeqMetrics_bam"/>
1244 <element name="picard_baseContent" file="picard_baseContent_stats.tabular" compare="sim_size" delta="50"/> 1258 <expand macro="element_assert" name="picard_baseContent" columns="11" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/>
1245 <element name="picard_dups" file="picard_dups_stats.tabular" compare="sim_size" delta="0"/> 1259 <expand macro="element_assert" name="picard_dups" columns="10" lines="2" text="dataset_114"/>
1246 <element name="picard_insertSize" file="picard_insertSize_stats.tabular" compare="sim_size" delta="0"/> 1260 <expand macro="element_assert" name="picard_insertSize" columns="23" lines="2" text="dataset_197_FR"/>
1247 <element name="prokka" file="prokka_stats.tabular" compare="sim_size" delta="0"/> 1261 <expand macro="element_assert" name="prokka" columns="11" lines="3" text="Sample2"/>
1248 <element name="qualimap_bamqc_genome_results" file="qualimap_bamqc_genome_results.tabular" compare="sim_size" delta="0"/> 1262 <expand macro="element_assert" name="qualimap_bamqc_genome_results" columns="12" lines="2" text="x_bam"/>
1249 <element name="quast" file="quast_stats.tabular" compare="sim_size" delta="0"/> 1263 <expand macro="element_assert" name="quast" columns="50" lines="2" text="14892_1#15"/>
1250 <element name="samblaster" file="samblaster_stats.tabular" compare="sim_size" delta="0"/> 1264 <expand macro="element_assert" name="samblaster" columns="5" lines="2" text="virtual-normal"/>
1251 <element name="samtools_flagstat"> 1265 <expand macro="element_assert" name="samtools_flagstat" columns="34" lines="2" text="samtools_flagstat_txt">
1252 <assert_contents> 1266 <has_text text="samtools_flagstat" />
1253 <has_text text="samtools_flagstat" /> 1267 <has_text text="mapped_passed" />
1254 <has_text text="mapped_passed" /> 1268 <has_text text="20689039" />
1255 <has_text text="20689039" /> 1269 </expand>
1256 </assert_contents> 1270 <expand macro="element_assert" name="samtools_idxstats" columns="68" lines="2" text="samtools_idxstats_txt_idxstat"/>
1257 </element> 1271 <expand macro="element_assert" name="samtools_stats" columns="40" lines="2" text="samtools_stats_txt"/>
1258 <element name="samtools_stats" file="samtools_stats_stats.tabular" compare="sim_size" delta="15"/> 1272 <expand macro="element_assert" name="snpeff" columns="169" lines="2" text="snpeff_csv"/>
1259 <element name="snpeff" file="snpeff_stats.tabular" compare="sim_size" delta="10"/> 1273 <expand macro="element_assert" name="sources" columns="4" lines="33" text="Bamtools"/>
1260 </output_collection> 1274 </output_collection>
1261 </test> 1275 </test>
1262 <test expect_num_outputs="2"> 1276 <test expect_num_outputs="2">
1263 <repeat name="results"> 1277 <repeat name="results">
1264 <conditional name="software_cond"> 1278 <conditional name="software_cond">
1295 <has_text text="Title of the report" /> 1309 <has_text text="Title of the report" />
1296 <has_text text="Commment for the report" /> 1310 <has_text text="Commment for the report" />
1297 <has_text text="fastqc_seq_heatmap_key_t" /> 1311 <has_text text="fastqc_seq_heatmap_key_t" />
1298 </assert_contents> 1312 </assert_contents>
1299 </output> 1313 </output>
1300 <output_collection name="stats" type="list" count="1"/> 1314 <output_collection name="stats" type="list" count="3">
1301 <output_collection name="plots" type="list" count="1"> 1315 <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_2"/>
1316 <expand macro="element_assert" name="general_stats" columns="6" lines="3" text="poulet5_2"/>
1317 <expand macro="element_assert" name="sources" columns="4" lines="3" text="FastQC"/>
1318 </output_collection>
1319 <output_collection name="plots" type="list" count="7">
1302 <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/> 1320 <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/>
1303 </output_collection> 1321 </output_collection>
1304 </test> 1322 </test>
1305 </tests> 1323 </tests>
1306 <help><![CDATA[ 1324 <help><![CDATA[