Mercurial > repos > iuc > multiqc
changeset 19:f7985e0479b9 draft
"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 |
| files | multiqc.xml |
| diffstat | 1 files changed, 9 insertions(+), 5 deletions(-) [+] |
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--- a/multiqc.xml Thu Nov 19 21:54:37 2020 +0000 +++ b/multiqc.xml Sat Nov 21 12:54:24 2020 +0000 @@ -1,7 +1,7 @@ -<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy2"> +<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@"> <description>aggregate results from bioinformatics analyses into a single report</description> <macros> - <token name="@WRAPPER_VERSION@">1.8</token> + <token name="@WRAPPER_VERSION@">1.9</token> <token name="@ESCAPE_IDENTIFIER@"> <![CDATA[ #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) @@ -479,6 +479,7 @@ #end if $flat +$export #if $configfile == "T" --config '$multiqc_config' @@ -843,6 +844,7 @@ <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"/> <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"/> <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."/> + <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"/> <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"/> </inputs> <outputs> @@ -855,7 +857,7 @@ </collection> <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots"> <discover_datasets pattern="mqc_(?P<designation>.+)\.txt" format="tabular" directory="report_data" /> - <filter>flat</filter> + <filter>export</filter> </collection> </outputs> <tests> @@ -908,12 +910,13 @@ <param name="title" value="Title of the report"/> <param name="comment" value="Commment for the report"/> <param name="flat" value="true"/> + <param name="export" value="true"/> <param name="saveLog" value="true"/> <output name="html_report"> <assert_contents> <has_text text="Title of the report" /> <has_text text="Commment for the report" /> - <has_text text="cutadapt_plot" /> + <has_text text="cutadapt_trimmed_sequences_plot" /> <has_text text="An ultra-fast all-in-one FASTQ preprocessor" /> <has_text text="fastqc_seq_heatmap_key_t" /> <has_text text="flexbar_plot" /> @@ -927,7 +930,7 @@ <has_text_matching expression="\[INFO \] MultiQC complete$"/> </assert_contents> </output> - <output_collection name="stats" type="list" count="11"> + <output_collection name="stats" type="list" count="10"> <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/> <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/> <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/> @@ -1286,6 +1289,7 @@ <param name="title" value="Title of the report"/> <param name="comment" value="Commment for the report"/> <param name="flat" value="true"/> + <param name="export" value="true"/> <output name="html_report"> <assert_contents> <has_text text="Title of the report" />