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comparison multiqc.xml @ 13:161f4383df15 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b
author iuc
date Sun, 20 Jan 2019 05:20:30 -0500
parents 1c2db0054039
children 3d93dd18d9f8
comparison
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12:1c2db0054039 13:161f4383df15
1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@"> 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@">1.6</token> 4 <token name="@WRAPPER_VERSION@">1.7</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@">
370 #elif str($repeat2.type.type) == "rmdup" 370 #elif str($repeat2.type.type) == "rmdup"
371 #set $pattern = "[bam_rmdup" 371 #set $pattern = "[bam_rmdup"
372 @LN_3_FILES@ 372 @LN_3_FILES@
373 #end if 373 #end if
374 #end for 374 #end for
375 #elif str($repeat.software_cond.software) == "slamdunk"
376 #set $pattern = "# slamdunk"
377 @LN_FILES@
375 #elif str($repeat.software_cond.software) == "snpeff" 378 #elif str($repeat.software_cond.software) == "snpeff"
376 #set $pattern = "SnpEff_version" 379 #set $pattern = "SnpEff_version"
377 @LN_FILES@ 380 @LN_FILES@
378 #elif str($repeat.software_cond.software) == "sortmerna" 381 #elif str($repeat.software_cond.software) == "sortmerna"
379 #set $pattern = "Minimal SW score based on E-value" 382 #set $pattern = "Minimal SW score based on E-value"
537 <!--<option value="salmon">Salmon</option>--> 540 <!--<option value="salmon">Salmon</option>-->
538 <option value="samblaster">Samblaster</option> 541 <option value="samblaster">Samblaster</option>
539 <option value="samtools">Samtools</option> 542 <option value="samtools">Samtools</option>
540 <!--<option value="sargasso">Sargasso</option>--> 543 <!--<option value="sargasso">Sargasso</option>-->
541 <!--<option value="skewer">Skewer</option>--> 544 <!--<option value="skewer">Skewer</option>-->
542 <!--<option value="slamdunk">Slamdunk</option>--> 545 <option value="slamdunk">Slamdunk</option>
543 <option value="snpeff">SnpEff</option> 546 <option value="snpeff">SnpEff</option>
544 <option value="sortmerna">SortMeRNA</option> 547 <option value="sortmerna">SortMeRNA</option>
545 <option value="star">STAR</option> 548 <option value="star">STAR</option>
546 <!--<option value="supernova">Supernova</option>--> 549 <!--<option value="supernova">Supernova</option>-->
547 <!--<option value="theta2">THeTA2</option>--> 550 <!--<option value="theta2">THeTA2</option>-->
730 <param name="input" type="data" format="txt" multiple="true" label="Samtools rmdup output" help="It should contain '[bam_rmdup'"/> 733 <param name="input" type="data" format="txt" multiple="true" label="Samtools rmdup output" help="It should contain '[bam_rmdup'"/>
731 </when> 734 </when>
732 </conditional> 735 </conditional>
733 </repeat> 736 </repeat>
734 </when> 737 </when>
738 <when value="slamdunk">
739 <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of Slamdunk Alleyoop" help="It should contain '# slamdunk'"/>
740 </when>
741 <when value="snpeff">
742 <param name="input" type="data" format="csv" multiple="true" label="Output of SnpEff"/>
743 </when>
735 <when value="sortmerna"> 744 <when value="sortmerna">
736 <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'"/> 745 <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'"/>
737 </when>
738 <when value="snpeff">
739 <param name="input" type="data" format="csv" multiple="true" label="Output of SnpEff"/>
740 </when> 746 </when>
741 <when value="star"> 747 <when value="star">
742 <repeat name="output" title="STAR output" min="1"> 748 <repeat name="output" title="STAR output" min="1">
743 <conditional name="type"> 749 <conditional name="type">
744 <param name="type" type="select" label="Type of STAR output?"> 750 <param name="type" type="select" label="Type of STAR output?">
844 <param name="input" value="flexbar.txt" /> 850 <param name="input" value="flexbar.txt" />
845 </conditional> 851 </conditional>
846 </repeat> 852 </repeat>
847 <repeat name="results"> 853 <repeat name="results">
848 <conditional name="software_cond"> 854 <conditional name="software_cond">
855 <param name="software" value="slamdunk" />
856 <param name="input" value="slamdunk_summary.txt,slamdunk_reads1_overallrates.csv,slamdunk_reads2_overallrates.csv" />
857 </conditional>
858 </repeat>
859 <repeat name="results">
860 <conditional name="software_cond">
849 <param name="software" value="sortmerna" /> 861 <param name="software" value="sortmerna" />
850 <param name="input" value="sortmerna.txt" /> 862 <param name="input" value="sortmerna.txt" />
851 </conditional> 863 </conditional>
852 </repeat> 864 </repeat>
853 <repeat name="results"> 865 <repeat name="results">
865 <has_text text="Commment for the report" /> 877 <has_text text="Commment for the report" />
866 <has_text text="cutadapt_plot" /> 878 <has_text text="cutadapt_plot" />
867 <has_text text="An ultra-fast all-in-one FASTQ preprocessor" /> 879 <has_text text="An ultra-fast all-in-one FASTQ preprocessor" />
868 <has_text text="fastqc_seq_heatmap_key_t" /> 880 <has_text text="fastqc_seq_heatmap_key_t" />
869 <has_text text="flexbar_plot" /> 881 <has_text text="flexbar_plot" />
882 <has_text text="a tool to analyze SLAMSeq data" />
870 <has_text text="sortmerna-detailed-plot" /> 883 <has_text text="sortmerna-detailed-plot" />
871 <has_text text="trimmomatic_plot" /> 884 <has_text text="trimmomatic_plot" />
872 </assert_contents> 885 </assert_contents>
873 </output> 886 </output>
874 <output name="log" file="pre_alignment_soft_log.txt" compare="sim_size"/> 887 <output name="log" file="pre_alignment_soft_log.txt" compare="sim_size"/>
876 <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/> 889 <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/>
877 <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/> 890 <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/>
878 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/> 891 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>
879 <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/> 892 <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/>
880 <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/> 893 <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/>
894 <element name="slamdunk_readrates_plus" file="slamdunk_readrates_plus.tabular" compare="sim_size" delta="10"/>
881 <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/> 895 <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/>
882 <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/> 896 <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/>
883 </output_collection> 897 </output_collection>
884 </test> 898 </test>
885 <test> 899 <test>