Mercurial > repos > iuc > multiqc
comparison multiqc.xml @ 12:1c2db0054039 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984
author | iuc |
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date | Wed, 08 Aug 2018 08:49:39 -0400 |
parents | f0ec41881020 |
children | 161f4383df15 |
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11:f0ec41881020 | 12:1c2db0054039 |
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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"/> |