Mercurial > repos > iuc > multiqc
changeset 21:75c93c70d094 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
| author | iuc |
|---|---|
| date | Tue, 02 Mar 2021 21:08:49 +0000 |
| parents | c1a4b5f3b432 |
| children | 9a913cdee30e |
| files | multiqc.xml test-data/pycoqc.json |
| diffstat | 2 files changed, 1291 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- 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**
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