| Previous changeset 14:b2f1f75d49c4 (2019-04-13) Next changeset 16:bf675f34b056 (2020-05-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8d98220b36762b2fe7401423d3081242839519b6" |
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modified:
multiqc.xml |
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added:
test-data/mqc_fastqc_per_base_sequence_quality_plot_1.txt |
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| diff -r b2f1f75d49c4 -r 3d93dd18d9f8 multiqc.xml --- a/multiqc.xml Sat Apr 13 08:30:21 2019 -0400 +++ b/multiqc.xml Sat Jan 18 03:08:54 2020 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@"> +<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1"> <description>aggregate results from bioinformatics analyses into a single report</description> <macros> <token name="@WRAPPER_VERSION@">1.7</token> @@ -456,6 +456,8 @@ --comment "$comment" #end if +$flat + #if $configfile == "T" --config '$multiqc_config' #end if @@ -809,7 +811,7 @@ </repeat> <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 name="saveLog" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/> + <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 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> @@ -820,6 +822,9 @@ <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats"> <discover_datasets pattern="multiqc_(?P<designation>.+)\.txt" format="tabular" directory="report_data" /> </collection> + <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots"> + <discover_datasets pattern="mqc_(?P<designation>.+_plot_.+)\.txt" format="tabular" directory="report_data" /> + </collection> </outputs> <tests> <test> @@ -1221,6 +1226,30 @@ </repeat> <output name="html_report" file="report_manual_custom_content.html" compare="sim_size"/> </test> + <test> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="fastqc" /> + <repeat name="output"> + <param name="type" value="data"/> + <param name="input" value="fastqc_1.txt,fastqc_2.txt"/> + </repeat> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" 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="fastqc_seq_heatmap_key_t" /> + </assert_contents> + </output> + <output_collection name="plots" type="list"> + <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/> + </output_collection> + </test> </tests> <help><![CDATA[ **What it does** |
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| diff -r b2f1f75d49c4 -r 3d93dd18d9f8 test-data/mqc_fastqc_per_base_sequence_quality_plot_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mqc_fastqc_per_base_sequence_quality_plot_1.txt Sat Jan 18 03:08:54 2020 -0500 |
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| @@ -0,0 +1,3 @@ +Sample 1 2 3 4 5 6 7 8 9 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 +poulet5_1 20.91988023102569 20.71684045861661 20.351574954545285 22.531542025544244 24.673566076408722 25.813099918237516 27.587864804423386 27.598941941168345 27.07115949658203 27.129873548155864 27.009298149330405 27.123565889736383 27.086309823818645 27.07924614241606 27.082520375286073 27.054301117420636 27.06350966402712 27.082996389756914 27.065495857740743 27.09608772106672 27.087097581099798 27.098251253504774 27.05184077595959 27.06521958267531 27.072148859992012 27.065725464720796 27.07168031241483 27.048083061725073 27.04642354460909 27.062865644448927 27.01859629866081 26.994157155710866 27.110127347871376 26.995846540401494 27.00461640700544 26.981614641085088 26.98900313236189 27.001189102815392 26.917739099268616 26.98481793846533 26.89518908041471 26.93677034448514 26.87640237596556 26.906094478605482 26.80463992772047 26.717012197170796 26.46960974280285 26.442842795754324 26.34282375517549 26.03493946215965 25.833215729758187 25.503102494315826 24.52807178671565 23.202399486277717 23.72906749698524 +poulet5_2 20.590586487162543 20.458478471078855 20.178608096352797 22.495204387546714 24.59397272343746 25.77560491172265 26.651378201897337 27.54968284369178 27.089005372429988 27.058984726469017 26.954911162632676 27.066410552214123 27.04552938409328 27.025118630273028 27.019042445557012 27.010315513591614 27.03931879529138 26.978450544896567 27.003714779595967 27.025971722873706 27.017791740868923 27.00628899118533 27.00906294218011 27.034922661648913 27.005346295860726 27.000909094303132 27.004913216028434 26.979999925331065 26.941037674211962 26.99995146519121 26.95084543903468 26.97609847339359 26.99262270906369 26.942271578389317 26.88024222603034 26.866450873439888 26.947610407356386 26.975012040366025 26.966286975124042 26.917634562757375 26.885127441207544 26.846286527110426 26.769134848366058 26.709703975000842 26.551336760637525 26.42626069165836 26.309463541024982 26.127226534353312 25.91885539987082 25.674260497519125 25.371903572535274 24.758753999454918 23.84710415196622 22.40618968149965 23.009550156991438 |