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comparison multiqc.xml @ 18:c19b16e5729c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
author iuc
date Thu, 19 Nov 2020 21:54:37 +0000
parents 5e33b465d8d5
children f7985e0479b9
comparison
equal deleted inserted replaced
17:5e33b465d8d5 18:c19b16e5729c
1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy1"> 1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy2">
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@">1.8</token> 4 <token name="@WRAPPER_VERSION@">1.8</token>
5 <token name="@ESCAPE_IDENTIFIER@"> 5 <token name="@ESCAPE_IDENTIFIER@">
6 <![CDATA[ 6 <![CDATA[
840 </when> 840 </when>
841 </conditional> 841 </conditional>
842 </repeat> 842 </repeat>
843 <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"/> 843 <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"/>
844 <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"/> 844 <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"/>
845 <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="False" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/> 845 <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="false" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/>
846 <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"/> 846 <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"/>
847 </inputs> 847 </inputs>
848 <outputs> 848 <outputs>
849 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" /> 849 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" />
850 <data name="log" format="txt" from_work_dir="report_data/multiqc.log" label="${tool.name} on ${on_string}: Log"> 850 <data name="log" format="txt" from_work_dir="report_data/multiqc.log" label="${tool.name} on ${on_string}: Log">
851 <filter>saveLog</filter> 851 <filter>saveLog</filter>
852 </data> 852 </data>
853 <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats"> 853 <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats">
854 <discover_datasets pattern="multiqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" /> 854 <discover_datasets pattern="multiqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" />
855 </collection> 855 </collection>
856 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots"> 856 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
857 <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+_plot_.+)\.txt" format="tabular" directory="report_data" /> 857 <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" />
858 <filter>flat</filter>
858 </collection> 859 </collection>
859 </outputs> 860 </outputs>
860 <tests> 861 <tests>
861 <test> 862 <test expect_num_outputs="4">
862 <repeat name="results"> 863 <repeat name="results">
863 <conditional name="software_cond"> 864 <conditional name="software_cond">
864 <param name="software" value="cutadapt" /> 865 <param name="software" value="cutadapt" />
865 <param name="input" value="cutadapt.txt" /> 866 <param name="input" value="cutadapt.txt" />
866 </conditional> 867 </conditional>
904 <param name="input" value="trimmomatic.txt" /> 905 <param name="input" value="trimmomatic.txt" />
905 </conditional> 906 </conditional>
906 </repeat> 907 </repeat>
907 <param name="title" value="Title of the report"/> 908 <param name="title" value="Title of the report"/>
908 <param name="comment" value="Commment for the report"/> 909 <param name="comment" value="Commment for the report"/>
909 <param name="saveLog" value="True"/> 910 <param name="flat" value="true"/>
911 <param name="saveLog" value="true"/>
910 <output name="html_report"> 912 <output name="html_report">
911 <assert_contents> 913 <assert_contents>
912 <has_text text="Title of the report" /> 914 <has_text text="Title of the report" />
913 <has_text text="Commment for the report" /> 915 <has_text text="Commment for the report" />
914 <has_text text="cutadapt_plot" /> 916 <has_text text="cutadapt_plot" />
918 <has_text text="a tool to analyze SLAMSeq data" /> 920 <has_text text="a tool to analyze SLAMSeq data" />
919 <has_text text="sortmerna-detailed-plot" /> 921 <has_text text="sortmerna-detailed-plot" />
920 <has_text text="trimmomatic_plot" /> 922 <has_text text="trimmomatic_plot" />
921 </assert_contents> 923 </assert_contents>
922 </output> 924 </output>
923 <output name="log" file="pre_alignment_soft_log.txt" compare="sim_size"/> 925 <output name="log">
924 <output_collection name="stats" type="list"> 926 <assert_contents>
927 <has_text_matching expression="\[INFO \] MultiQC complete$"/>
928 </assert_contents>
929 </output>
930 <output_collection name="stats" type="list" count="11">
925 <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/> 931 <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/>
926 <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/> 932 <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/>
927 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/> 933 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>
928 <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/> 934 <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/>
929 <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/> 935 <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/>
930 <element name="slamdunk_readrates_plus" file="slamdunk_readrates_plus.tabular" compare="sim_size" delta="10"/> 936 <element name="slamdunk_readrates_plus" file="slamdunk_readrates_plus.tabular" compare="sim_size" delta="10"/>
931 <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/> 937 <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/>
932 <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/> 938 <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/>
933 </output_collection> 939 </output_collection>
940 <output_collection name="plots" type="list" count="29"/>
934 </test> 941 </test>
935 <test> 942 <test expect_num_outputs="2">
936 <repeat name="results"> 943 <repeat name="results">
937 <conditional name="software_cond"> 944 <conditional name="software_cond">
938 <param name="software" value="bismark" /> 945 <param name="software" value="bismark" />
939 <repeat name="output"> 946 <repeat name="output">
940 <param name="type" value="align"/> 947 <param name="type" value="align"/>
993 <conditional name="software_cond"> 1000 <conditional name="software_cond">
994 <param name="software" value="tophat" /> 1001 <param name="software" value="tophat" />
995 <param name="input" value="tophat.txt" /> 1002 <param name="input" value="tophat.txt" />
996 </conditional> 1003 </conditional>
997 </repeat> 1004 </repeat>
998 <param name="saveLog" value="False"/> 1005 <param name="saveLog" value="false"/>
999 <output name="html_report"> 1006 <output name="html_report">
1000 <assert_contents> 1007 <assert_contents>
1001 <has_text text="bismark-alignment" /> 1008 <has_text text="bismark-alignment" />
1002 <has_text text="bowtie2_se_plot" /> 1009 <has_text text="bowtie2_se_plot" />
1003 <has_text text="hisat2_se_plot" /> 1010 <has_text text="hisat2_se_plot" />
1007 <has_text text="tophat_alignment" /> 1014 <has_text text="tophat_alignment" />
1008 <has_text text="hicexplorer" /> 1015 <has_text text="hicexplorer" />
1009 <has_text text="hicexplorer1_log_1" /> 1016 <has_text text="hicexplorer1_log_1" />
1010 </assert_contents> 1017 </assert_contents>
1011 </output> 1018 </output>
1012 <output_collection name="stats" type="list"> 1019 <output_collection name="stats" type="list" count="8">
1013 <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/> 1020 <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/>
1014 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/> 1021 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/>
1015 <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/> 1022 <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/>
1016 <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="20"/> 1023 <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="20"/>
1017 <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> --> 1024 <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> -->
1019 <element name="macs" file="macs_stats.tabular" compare="sim_size" delta="10"/> 1026 <element name="macs" file="macs_stats.tabular" compare="sim_size" delta="10"/>
1020 <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/> 1027 <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/>
1021 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/> 1028 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/>
1022 </output_collection> 1029 </output_collection>
1023 </test> 1030 </test>
1024 <test> 1031 <test expect_num_outputs="2">
1025 <repeat name="results"> 1032 <repeat name="results">
1026 <conditional name="software_cond"> 1033 <conditional name="software_cond">
1027 <param name="software" value="bamtools" /> 1034 <param name="software" value="bamtools" />
1028 <param name="input" value="bamtools.txt" /> 1035 <param name="input" value="bamtools.txt" />
1029 </conditional> 1036 </conditional>
1219 <has_text text="quast-stats" /> 1226 <has_text text="quast-stats" />
1220 <has_text text="samtools-flagstat-dp" /> 1227 <has_text text="samtools-flagstat-dp" />
1221 <has_text text="snpeff" /> 1228 <has_text text="snpeff" />
1222 </assert_contents> 1229 </assert_contents>
1223 </output> 1230 </output>
1224 <output_collection name="stats" type="list"> 1231 <output_collection name="stats" type="list" count="19">
1225 <element name="bamtools_stats" file="bamtools_stats.tabular" compare="sim_size" delta="10"/> 1232 <element name="bamtools_stats" file="bamtools_stats.tabular" compare="sim_size" delta="10"/>
1226 <element name="bcftools_stats" file="bcftools_stats.tabular" compare="sim_size" delta="0"/> 1233 <element name="bcftools_stats" file="bcftools_stats.tabular" compare="sim_size" delta="0"/>
1227 <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="10"/> 1234 <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="10"/>
1228 <element name="featureCounts" file="featureCounts_stats.tabular" compare="sim_size" delta="25"/> 1235 <element name="featureCounts" file="featureCounts_stats.tabular" compare="sim_size" delta="25"/>
1229 <element name="gatk_varianteval" file="gatk_varianteval_stats.tabular" compare="sim_size" delta="20"/> 1236 <element name="gatk_varianteval" file="gatk_varianteval_stats.tabular" compare="sim_size" delta="20"/>
1247 </element> 1254 </element>
1248 <element name="samtools_stats" file="samtools_stats_stats.tabular" compare="sim_size" delta="15"/> 1255 <element name="samtools_stats" file="samtools_stats_stats.tabular" compare="sim_size" delta="15"/>
1249 <element name="snpeff" file="snpeff_stats.tabular" compare="sim_size" delta="10"/> 1256 <element name="snpeff" file="snpeff_stats.tabular" compare="sim_size" delta="10"/>
1250 </output_collection> 1257 </output_collection>
1251 </test> 1258 </test>
1252 <test> 1259 <test expect_num_outputs="2">
1253 <repeat name="results"> 1260 <repeat name="results">
1254 <conditional name="software_cond"> 1261 <conditional name="software_cond">
1255 <param name="software" value="custom_content" /> 1262 <param name="software" value="custom_content" />
1256 <param name="cc_select" value="manual" /> 1263 <param name="cc_select" value="manual" />
1257 <param name="plot_type" value="linegraph" /> 1264 <param name="plot_type" value="linegraph" />
1262 <param name="ylab" value="Base Peak Intensity" /> 1269 <param name="ylab" value="Base Peak Intensity" />
1263 <param name="input" value="cc_ko15.bpc.tab,cc_wt15.bpc.tab" /> 1270 <param name="input" value="cc_ko15.bpc.tab,cc_wt15.bpc.tab" />
1264 </conditional> 1271 </conditional>
1265 </repeat> 1272 </repeat>
1266 <output name="html_report" file="report_manual_custom_content.html" compare="sim_size"/> 1273 <output name="html_report" file="report_manual_custom_content.html" compare="sim_size"/>
1274 <output_collection name="stats" type="list" count="1"/>
1267 </test> 1275 </test>
1268 <test> 1276 <test expect_num_outputs="3">
1269 <repeat name="results"> 1277 <repeat name="results">
1270 <conditional name="software_cond"> 1278 <conditional name="software_cond">
1271 <param name="software" value="fastqc" /> 1279 <param name="software" value="fastqc" />
1272 <repeat name="output"> 1280 <repeat name="output">
1273 <param name="type" value="data"/> 1281 <param name="type" value="data"/>
1275 </repeat> 1283 </repeat>
1276 </conditional> 1284 </conditional>
1277 </repeat> 1285 </repeat>
1278 <param name="title" value="Title of the report"/> 1286 <param name="title" value="Title of the report"/>
1279 <param name="comment" value="Commment for the report"/> 1287 <param name="comment" value="Commment for the report"/>
1280 <param name="flat" value="True"/> 1288 <param name="flat" value="true"/>
1281 <output name="html_report"> 1289 <output name="html_report">
1282 <assert_contents> 1290 <assert_contents>
1283 <has_text text="Title of the report" /> 1291 <has_text text="Title of the report" />
1284 <has_text text="Commment for the report" /> 1292 <has_text text="Commment for the report" />
1285 <has_text text="fastqc_seq_heatmap_key_t" /> 1293 <has_text text="fastqc_seq_heatmap_key_t" />
1286 </assert_contents> 1294 </assert_contents>
1287 </output> 1295 </output>
1288 <output_collection name="plots" type="list"> 1296 <output_collection name="stats" type="list" count="1"/>
1297 <output_collection name="plots" type="list" count="1">
1289 <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/> 1298 <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/>
1290 </output_collection> 1299 </output_collection>
1291 </test> 1300 </test>
1292 </tests> 1301 </tests>
1293 <help><![CDATA[ 1302 <help><![CDATA[