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comparison multiqc.xml @ 12:a7e3e7e1019c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
author iuc
date Wed, 08 Aug 2018 08:49:10 -0400
parents 46d7ad9aa59f
children e89e08ca4d30
comparison
equal deleted inserted replaced
11:46d7ad9aa59f 12:a7e3e7e1019c
1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.2"> 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@">1.5</token> 4 <token name="@WRAPPER_VERSION@">1.6</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@">
154 #elif str($repeat2.type) == "plotFingerprintOutRawCounts" 154 #elif str($repeat2.type) == "plotFingerprintOutRawCounts"
155 #set $pattern = "#plotFingerprint --outRawCounts" 155 #set $pattern = "#plotFingerprint --outRawCounts"
156 @LN_2_FILES@ 156 @LN_2_FILES@
157 #end if 157 #end if
158 #end for 158 #end for
159 #elif str($repeat.software_cond.software) == "fastp"
160 #set $pattern = "report_title"
161 #for $file in $repeat.software_cond.input
162 @ESCAPE_IDENTIFIER@
163 #set file_path = os.path.join($software_dir, str($identifier) + 'fastp.json')
164 ln -s '$file' '$file_path' &&
165 grep -q "$pattern" '$file_path' || die "'$pattern' or 'report_title' not found in the file" &&
166 #end for
159 #elif str($repeat.software_cond.software) == "fastqc" 167 #elif str($repeat.software_cond.software) == "fastqc"
160 #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) 168 #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
161 @CREATE_REPEAT_DIR_1@ 169 @CREATE_REPEAT_DIR_1@
162 #if str($repeat2.type) == "data" 170 #if str($repeat2.type) == "data"
163 #for $k, $file in enumerate($repeat2.input) 171 #for $k, $file in enumerate($repeat2.input)
497 <!--<option value="conpair">Conpair</option>--> 505 <!--<option value="conpair">Conpair</option>-->
498 <!--<option value="dedup">DeDup</option>--> 506 <!--<option value="dedup">DeDup</option>-->
499 <option value="deeptools">deepTools</option> 507 <option value="deeptools">deepTools</option>
500 <!--<option value="disambiguate">Disambiguate</option>--> 508 <!--<option value="disambiguate">Disambiguate</option>-->
501 <!--<option value="fastq_screen">FastQ Screen</option>--> 509 <!--<option value="fastq_screen">FastQ Screen</option>-->
510 <option value="fastp">fastp</option>
502 <option value="fastqc">FastQC</option> 511 <option value="fastqc">FastQC</option>
503 <option value="featureCounts">featureCounts</option> 512 <option value="featureCounts">featureCounts</option>
504 <option value="flexbar">Flexbar</option> 513 <option value="flexbar">Flexbar</option>
505 <option value="gatk">GATK</option> 514 <option value="gatk">GATK</option>
506 <!--<option value="goleft_indexcov">goleft indexcov</option>--> 515 <!--<option value="goleft_indexcov">goleft indexcov</option>-->
582 <option value="plotFingerprintOutQualityMetrics">plotFingerprintOutQualityMetrics</option> 591 <option value="plotFingerprintOutQualityMetrics">plotFingerprintOutQualityMetrics</option>
583 </param> 592 </param>
584 <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/> 593 <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/>
585 </repeat> 594 </repeat>
586 </when> 595 </when>
596 <when value="fastp">
597 <param name="input" type="data" format="json" multiple="true" label="Output of fastp" help="It should be the json report from fastp containing 'report_title'"/>
598 </when>
587 <when value="fastqc"> 599 <when value="fastqc">
588 <repeat name="output" title="FastQC output" min="1"> 600 <repeat name="output" title="FastQC output" min="1">
589 <param name="type" type="select" label="Type of FastQC output?"> 601 <param name="type" type="select" label="Type of FastQC output?">
590 <option value="data">Raw data</option> 602 <option value="data">Raw data</option>
591 <option value="theoretical_gc">Theorectical GC</option> 603 <option value="theoretical_gc">Theorectical GC</option>
811 <param name="input" value="cutadapt.txt" /> 823 <param name="input" value="cutadapt.txt" />
812 </conditional> 824 </conditional>
813 </repeat> 825 </repeat>
814 <repeat name="results"> 826 <repeat name="results">
815 <conditional name="software_cond"> 827 <conditional name="software_cond">
828 <param name="software" value="fastp" />
829 <param name="input" value="fastp1.json.txt,fastp2.json.txt" />
830 </conditional>
831 </repeat>
832 <repeat name="results">
833 <conditional name="software_cond">
816 <param name="software" value="fastqc" /> 834 <param name="software" value="fastqc" />
817 <repeat name="output"> 835 <repeat name="output">
818 <param name="type" value="data"/> 836 <param name="type" value="data"/>
819 <param name="input" value="fastqc_1.txt,fastqc_2.txt"/> 837 <param name="input" value="fastqc_1.txt,fastqc_2.txt"/>
820 </repeat> 838 </repeat>
844 <output name="html_report"> 862 <output name="html_report">
845 <assert_contents> 863 <assert_contents>
846 <has_text text="Title of the report" /> 864 <has_text text="Title of the report" />
847 <has_text text="Commment for the report" /> 865 <has_text text="Commment for the report" />
848 <has_text text="cutadapt_plot" /> 866 <has_text text="cutadapt_plot" />
867 <has_text text="An ultra-fast all-in-one FASTQ preprocessor" />
849 <has_text text="fastqc_seq_heatmap_key_t" /> 868 <has_text text="fastqc_seq_heatmap_key_t" />
850 <has_text text="flexbar_plot" /> 869 <has_text text="flexbar_plot" />
851 <has_text text="sortmerna-detailed-plot" /> 870 <has_text text="sortmerna-detailed-plot" />
852 <has_text text="trimmomatic_plot" /> 871 <has_text text="trimmomatic_plot" />
853 </assert_contents> 872 </assert_contents>
854 </output> 873 </output>
855 <output name="log" file="pre_alignment_soft_log.txt" compare="sim_size"/> 874 <output name="log" file="pre_alignment_soft_log.txt" compare="sim_size"/>
856 <output_collection name="stats" type="list"> 875 <output_collection name="stats" type="list">
857 <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/> 876 <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"/>
858 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/> 878 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>
859 <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/> 879 <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/>
860 <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/> 880 <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/>
861 <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/> 881 <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/>
862 <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/> 882 <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/>