| Previous changeset 12:1c2db0054039 (2018-08-08) Next changeset 14:b2f1f75d49c4 (2019-04-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b |
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modified:
multiqc.xml test-data/pre_alignment_soft_stats.tabular |
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added:
test-data/slamdunk_readrates_plus.tabular test-data/slamdunk_reads1_overallrates.csv test-data/slamdunk_reads2_overallrates.csv test-data/slamdunk_summary.txt |
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| diff -r 1c2db0054039 -r 161f4383df15 multiqc.xml --- a/multiqc.xml Wed Aug 08 08:49:39 2018 -0400 +++ b/multiqc.xml Sun Jan 20 05:20:30 2019 -0500 |
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| @@ -1,7 +1,7 @@ <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@"> <description>aggregate results from bioinformatics analyses into a single report</description> <macros> - <token name="@WRAPPER_VERSION@">1.6</token> + <token name="@WRAPPER_VERSION@">1.7</token> <token name="@ESCAPE_IDENTIFIER@"> <![CDATA[ #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) @@ -372,6 +372,9 @@ @LN_3_FILES@ #end if #end for + #elif str($repeat.software_cond.software) == "slamdunk" + #set $pattern = "# slamdunk" + @LN_FILES@ #elif str($repeat.software_cond.software) == "snpeff" #set $pattern = "SnpEff_version" @LN_FILES@ @@ -539,7 +542,7 @@ <option value="samtools">Samtools</option> <!--<option value="sargasso">Sargasso</option>--> <!--<option value="skewer">Skewer</option>--> - <!--<option value="slamdunk">Slamdunk</option>--> + <option value="slamdunk">Slamdunk</option> <option value="snpeff">SnpEff</option> <option value="sortmerna">SortMeRNA</option> <option value="star">STAR</option> @@ -732,12 +735,15 @@ </conditional> </repeat> </when> - <when value="sortmerna"> - <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/> + <when value="slamdunk"> + <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of Slamdunk Alleyoop" help="It should contain '# slamdunk'"/> </when> <when value="snpeff"> <param name="input" type="data" format="csv" multiple="true" label="Output of SnpEff"/> </when> + <when value="sortmerna"> + <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/> + </when> <when value="star"> <repeat name="output" title="STAR output" min="1"> <conditional name="type"> @@ -846,6 +852,12 @@ </repeat> <repeat name="results"> <conditional name="software_cond"> + <param name="software" value="slamdunk" /> + <param name="input" value="slamdunk_summary.txt,slamdunk_reads1_overallrates.csv,slamdunk_reads2_overallrates.csv" /> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> <param name="software" value="sortmerna" /> <param name="input" value="sortmerna.txt" /> </conditional> @@ -867,6 +879,7 @@ <has_text text="An ultra-fast all-in-one FASTQ preprocessor" /> <has_text text="fastqc_seq_heatmap_key_t" /> <has_text text="flexbar_plot" /> + <has_text text="a tool to analyze SLAMSeq data" /> <has_text text="sortmerna-detailed-plot" /> <has_text text="trimmomatic_plot" /> </assert_contents> @@ -878,6 +891,7 @@ <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/> <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/> <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/> + <element name="slamdunk_readrates_plus" file="slamdunk_readrates_plus.tabular" compare="sim_size" delta="10"/> <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/> <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/> </output_collection> |
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| diff -r 1c2db0054039 -r 161f4383df15 test-data/pre_alignment_soft_stats.tabular --- a/test-data/pre_alignment_soft_stats.tabular Wed Aug 08 08:49:39 2018 -0400 +++ b/test-data/pre_alignment_soft_stats.tabular Sun Jan 20 05:20:30 2019 -0500 |
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| @@ -1,9 +1,11 @@ -Sample SortMeRNA_mqc-generalstats-sortmerna-rRNA_pct Trimmomatic_mqc-generalstats-trimmomatic-dropped_pct fastp_mqc-generalstats-fastp-pct_duplication fastp_mqc-generalstats-fastp-after_filtering_q30_rate fastp_mqc-generalstats-fastp-after_filtering_q30_bases fastp_mqc-generalstats-fastp-after_filtering_gc_content fastp_mqc-generalstats-fastp-pct_surviving fastp_mqc-generalstats-fastp-pct_adapter Cutadapt_mqc-generalstats-cutadapt-percent_trimmed FastQC_mqc-generalstats-fastqc-percent_duplicates FastQC_mqc-generalstats-fastqc-percent_gc FastQC_mqc-generalstats-fastqc-avg_sequence_length FastQC_mqc-generalstats-fastqc-percent_fails FastQC_mqc-generalstats-fastqc-total_sequences Flexbar_mqc-generalstats-flexbar-removed_bases_pct -25839_merged 1.099299750020029 -C2 17.98 -R1_fq 0.0 0.79021 226.0 0.367133 100.0 -bwa-mem-fastq1_fq 0.0 0.907789 41653.0 0.479928 97.97979797979798 33.33333333333333 -dataset_33 10.776820436239396 -poulet5_1 36.30591159931017 48.0 101.0 8.333333333333332 267849.0 -poulet5_2 36.173388748054116 48.0 101.0 8.333333333333332 267849.0 -result_right 45.26066350710901 +Sample SortMeRNA_mqc-generalstats-sortmerna-rRNA_pct Trimmomatic_mqc-generalstats-trimmomatic-dropped_pct fastp_mqc-generalstats-fastp-pct_duplication fastp_mqc-generalstats-fastp-after_filtering_q30_rate fastp_mqc-generalstats-fastp-after_filtering_q30_bases fastp_mqc-generalstats-fastp-after_filtering_gc_content fastp_mqc-generalstats-fastp-pct_surviving fastp_mqc-generalstats-fastp-pct_adapter Cutadapt_mqc-generalstats-cutadapt-percent_trimmed FastQC_mqc-generalstats-fastqc-percent_duplicates FastQC_mqc-generalstats-fastqc-percent_gc FastQC_mqc-generalstats-fastqc-avg_sequence_length FastQC_mqc-generalstats-fastqc-percent_fails FastQC_mqc-generalstats-fastqc-total_sequences Slamdunk_mqc-generalstats-slamdunk-counted Slamdunk_mqc-generalstats-slamdunk-retained Slamdunk_mqc-generalstats-slamdunk-mapped Slamdunk_mqc-generalstats-slamdunk-sequenced Flexbar_mqc-generalstats-flexbar-removed_bases_pct +25839_merged 1.099299750020029 +C2 17.98 +R1_fq 0.0 0.79021 226.0 0.367133 100.0 +bwa-mem-fastq1_fq 0.0 0.907789 41653.0 0.479928 97.97979797979798 33.33333333333333 +dataset_33 10.776820436239396 +poulet5_1 36.30591159931017 48.0 101.0 8.333333333333332 267849.0 +poulet5_2 36.173388748054116 48.0 101.0 8.333333333333332 267849.0 +reads1 16 12 12 12 +reads2 12 6 6 6 +result_right 45.26066350710901 |
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| diff -r 1c2db0054039 -r 161f4383df15 test-data/slamdunk_readrates_plus.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/slamdunk_readrates_plus.tabular Sun Jan 20 05:20:30 2019 -0500 |
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| @@ -0,0 +1,3 @@ +Sample A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C T>G +slamdunk_reads1_overallrates_csv 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.7735849056603774 0.0 +slamdunk_reads2_overallrates_csv 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.260869565217391 0.0 |
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| diff -r 1c2db0054039 -r 161f4383df15 test-data/slamdunk_reads1_overallrates.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/slamdunk_reads1_overallrates.csv Sun Jan 20 05:20:30 2019 -0500 |
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| @@ -0,0 +1,7 @@ +# slamdunk rates v0.3.3 + A a C c G g T t N n +A 93 20 0 0 0 1 0 0 0 0 +C 0 0 106 12 0 0 0 0 0 0 +G 0 0 0 0 82 33 0 0 0 0 +T 0 0 4 1 0 0 102 47 0 0 +N 0 0 0 0 0 0 0 0 0 0 |
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| diff -r 1c2db0054039 -r 161f4383df15 test-data/slamdunk_reads2_overallrates.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/slamdunk_reads2_overallrates.csv Sun Jan 20 05:20:30 2019 -0500 |
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| @@ -0,0 +1,7 @@ +# slamdunk rates v0.3.3 + A a C c G g T t N n +A 42 0 0 0 0 0 0 0 0 0 +C 0 0 25 0 0 0 0 0 0 0 +G 0 0 0 0 61 0 0 0 0 0 +T 0 0 3 0 0 0 89 0 0 0 +N 0 0 0 0 0 0 0 0 0 0 |
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| diff -r 1c2db0054039 -r 161f4383df15 test-data/slamdunk_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/slamdunk_summary.txt Sun Jan 20 05:20:30 2019 -0500 |
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| @@ -0,0 +1,4 @@ +# slamdunk summary v0.3.3 +FileName SampleName SampleType SampleTime Sequenced Mapped Deduplicated MQ-Filtered Identity-Filtered NM-Filtered Multimap-Filtered Retained Counted Annotation +./filter/reads1.bam sample_1 NA -1 12 12 0 0 0 0 0 12 16 +./filter/reads2.bam sample_2 NA -1 6 6 0 0 0 0 0 6 12 |