| Previous changeset 20:c1a4b5f3b432 (2021-03-02) Next changeset 22:9a913cdee30e (2021-11-03) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985" |
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modified:
multiqc.xml |
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added:
test-data/pycoqc.json |
| b |
| diff -r c1a4b5f3b432 -r 75c93c70d094 multiqc.xml --- a/multiqc.xml Tue Mar 02 08:02:36 2021 +0000 +++ b/multiqc.xml Tue Mar 02 21:08:49 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@"> +<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy1"> <description>aggregate results from bioinformatics analyses into a single report</description> <macros> <token name="@WRAPPER_VERSION@">1.9</token> @@ -12,7 +12,7 @@ #set $file_path += '_' + str($file_paths.count($file_path)) #end if #set $file_paths += [$file_path] -grep -q "$pattern" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" && +grep -q '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" && ln -s '$file' '$file_path' && ]]></token> <token name="@CREATE_REPEAT_DIR_1@"> @@ -282,6 +282,9 @@ #elif str($repeat.software_cond.software) == "prokka" #set $pattern = "contigs:" @LN_FILES@ + #elif str($repeat.software_cond.software) == "pycoqc" + #set $pattern = "\"pycoqc\":" + @LN_FILES@ #elif str($repeat.software_cond.software) == "qualimap" #for $file in $repeat.software_cond.input #if re.search("genome_results", str($file.element_identifier)) @@ -570,6 +573,7 @@ <option value="picard">Picard</option> <!--<option value="preseq">Preseq</option>--> <option value="prokka">Prokka</option> + <option value="pycoqc">PycoQC</option> <!--<option value="qorts">QoRTs</option>--> <option value="qualimap">Qualimap (BamQC or RNASeq output)</option> <option value="quast">QUAST</option> @@ -702,6 +706,9 @@ <when value="prokka"> <param name="input" type="data" format="txt" multiple="true" label="Output of Prokka" help="It should contain 'contigs:'"/> </when> + <when value="pycoqc"> + <param name="input" type="data" format="txt,json" multiple="true" label="Output of PycoQC"/> + </when> <when value="qualimap"> <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report" /> </when> @@ -1320,6 +1327,28 @@ <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> + <test expect_num_outputs="2"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="pycoqc" /> + <param name="input" value="pycoqc.json"/> + </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="General Statistics" /> + <has_text text="pycoqc_count_plot" /> + <has_text text="pycoqc_read_len_plot" /> + <has_text text="pycoqc_read_qual_plot" /> + </assert_contents> + </output> + <output_collection name="stats" type="list" count="2"/> + </test> </tests> <help><![CDATA[ **What it does** |
| b |
| diff -r c1a4b5f3b432 -r 75c93c70d094 test-data/pycoqc.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pycoqc.json Tue Mar 02 21:08:49 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1260 @@\n+{\n+ "pycoqc": {\n+ "version": "2.5.2",\n+ "date": "02/03/21"\n+ },\n+ "All Reads": {\n+ "run": {\n+ "run_duration": 0.07199815538194444,\n+ "active_channels": 375,\n+ "runid_number": 1,\n+ "barcodes_number": 0\n+ },\n+ "basecall": {\n+ "reads_number": 1000,\n+ "bases_number": 3233722,\n+ "N50": 7421,\n+ "len_percentiles": [\n+ 5.0,\n+ 196.89,\n+ 225.82000000000002,\n+ 239.97,\n+ 257.96000000000004,\n+ 273.0,\n+ 281.94,\n+ 297.86,\n+ 305.0,\n+ 317.82,\n+ 327.9,\n+ 336.0,\n+ 342.88,\n+ 350.87,\n+ 362.86,\n+ 370.84999999999997,\n+ 379.68,\n+ 385.0,\n+ 395.0,\n+ 406.81,\n+ 422.40000000000003,\n+ 435.58,\n+ 447.0,\n+ 459.31000000000006,\n+ 475.0,\n+ 491.5,\n+ 509.74,\n+ 520.6500000000001,\n+ 541.0,\n+ 557.0,\n+ 582.7,\n+ 603.8299999999999,\n+ 625.72,\n+ 661.3600000000001,\n+ 688.6600000000001,\n+ 703.6500000000001,\n+ 727.0,\n+ 759.52,\n+ 789.86,\n+ 843.83,\n+ 870.8000000000001,\n+ 906.1300000000002,\n+ 939.3199999999999,\n+ 974.71,\n+ 1019.56,\n+ 1050.3,\n+ 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