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comparison multiqc.xml @ 19:f7985e0479b9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 2b946616b7d12eed507d95ebbd8fd257ae37d83b"
author iuc
date Sat, 21 Nov 2020 12:54:24 +0000
parents c19b16e5729c
children c1a4b5f3b432
comparison
equal deleted inserted replaced
18:c19b16e5729c 19:f7985e0479b9
1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy2"> 1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@">
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@">1.9</token>
5 <token name="@ESCAPE_IDENTIFIER@"> 5 <token name="@ESCAPE_IDENTIFIER@">
6 <![CDATA[ 6 <![CDATA[
7 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) 7 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
8 ]]></token> 8 ]]></token>
9 <token name="@CHECK_LN_FILE@"> 9 <token name="@CHECK_LN_FILE@">
477 #if str($comment) 477 #if str($comment)
478 --comment "$comment" 478 --comment "$comment"
479 #end if 479 #end if
480 480
481 $flat 481 $flat
482 $export
482 483
483 #if $configfile == "T" 484 #if $configfile == "T"
484 --config '$multiqc_config' 485 --config '$multiqc_config'
485 #end if 486 #end if
486 ]]></command> 487 ]]></command>
841 </conditional> 842 </conditional>
842 </repeat> 843 </repeat>
843 <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"/> 844 <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"/>
844 <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"/> 845 <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"/>
845 <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="false" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/> 846 <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="false" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/>
847 <param argument="--export" type="boolean" truevalue="--export" falsevalue="" checked="false" label="Output the multiQC plots raw data?" help="This will output a file for each plot containing the raw data used to generate the plot"/>
846 <param name="saveLog" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/> 848 <param name="saveLog" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/>
847 </inputs> 849 </inputs>
848 <outputs> 850 <outputs>
849 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" /> 851 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" />
850 <data name="log" format="txt" from_work_dir="report_data/multiqc.log" label="${tool.name} on ${on_string}: Log"> 852 <data name="log" format="txt" from_work_dir="report_data/multiqc.log" label="${tool.name} on ${on_string}: Log">
853 <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats"> 855 <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats">
854 <discover_datasets pattern="multiqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" /> 856 <discover_datasets pattern="multiqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" />
855 </collection> 857 </collection>
856 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots"> 858 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
857 <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" /> 859 <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" />
858 <filter>flat</filter> 860 <filter>export</filter>
859 </collection> 861 </collection>
860 </outputs> 862 </outputs>
861 <tests> 863 <tests>
862 <test expect_num_outputs="4"> 864 <test expect_num_outputs="4">
863 <repeat name="results"> 865 <repeat name="results">
906 </conditional> 908 </conditional>
907 </repeat> 909 </repeat>
908 <param name="title" value="Title of the report"/> 910 <param name="title" value="Title of the report"/>
909 <param name="comment" value="Commment for the report"/> 911 <param name="comment" value="Commment for the report"/>
910 <param name="flat" value="true"/> 912 <param name="flat" value="true"/>
913 <param name="export" value="true"/>
911 <param name="saveLog" value="true"/> 914 <param name="saveLog" value="true"/>
912 <output name="html_report"> 915 <output name="html_report">
913 <assert_contents> 916 <assert_contents>
914 <has_text text="Title of the report" /> 917 <has_text text="Title of the report" />
915 <has_text text="Commment for the report" /> 918 <has_text text="Commment for the report" />
916 <has_text text="cutadapt_plot" /> 919 <has_text text="cutadapt_trimmed_sequences_plot" />
917 <has_text text="An ultra-fast all-in-one FASTQ preprocessor" /> 920 <has_text text="An ultra-fast all-in-one FASTQ preprocessor" />
918 <has_text text="fastqc_seq_heatmap_key_t" /> 921 <has_text text="fastqc_seq_heatmap_key_t" />
919 <has_text text="flexbar_plot" /> 922 <has_text text="flexbar_plot" />
920 <has_text text="a tool to analyze SLAMSeq data" /> 923 <has_text text="a tool to analyze SLAMSeq data" />
921 <has_text text="sortmerna-detailed-plot" /> 924 <has_text text="sortmerna-detailed-plot" />
925 <output name="log"> 928 <output name="log">
926 <assert_contents> 929 <assert_contents>
927 <has_text_matching expression="\[INFO \] MultiQC complete$"/> 930 <has_text_matching expression="\[INFO \] MultiQC complete$"/>
928 </assert_contents> 931 </assert_contents>
929 </output> 932 </output>
930 <output_collection name="stats" type="list" count="11"> 933 <output_collection name="stats" type="list" count="10">
931 <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/> 934 <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/>
932 <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/> 935 <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/>
933 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/> 936 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>
934 <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/> 937 <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/>
935 <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/> 938 <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/>
1284 </conditional> 1287 </conditional>
1285 </repeat> 1288 </repeat>
1286 <param name="title" value="Title of the report"/> 1289 <param name="title" value="Title of the report"/>
1287 <param name="comment" value="Commment for the report"/> 1290 <param name="comment" value="Commment for the report"/>
1288 <param name="flat" value="true"/> 1291 <param name="flat" value="true"/>
1292 <param name="export" value="true"/>
1289 <output name="html_report"> 1293 <output name="html_report">
1290 <assert_contents> 1294 <assert_contents>
1291 <has_text text="Title of the report" /> 1295 <has_text text="Title of the report" />
1292 <has_text text="Commment for the report" /> 1296 <has_text text="Commment for the report" />
1293 <has_text text="fastqc_seq_heatmap_key_t" /> 1297 <has_text text="fastqc_seq_heatmap_key_t" />