Mercurial > repos > greg > vsnp_statistics
changeset 28:e219f5c06dc0 draft default tip
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit fd6150d1cb5a9e50aa10694b9ac85cb575ed7525"
| author | greg |
|---|---|
| date | Mon, 15 Nov 2021 23:24:03 +0000 |
| parents | c9208cc0f5dd |
| children | |
| files | test-data/vsnp_statistics1.tabular test-data/vsnp_statistics2.tabular test-data/vsnp_statistics4.tabular vsnp_statistics.xml |
| diffstat | 4 files changed, 15 insertions(+), 9 deletions(-) [+] |
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--- a/test-data/vsnp_statistics1.tabular Mon Nov 15 23:15:14 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -FASTQ File Size Mean Read Length Mean Read Quality Reads Passing Q30 Total Reads All Mapped Reads Unmapped Reads Unmapped Reads Percentage of Total Reference with Coverage Average Depth of Coverage Good SNP Count Reference -Mcap_Deer_DE_SRR650221_fastq_gz 1.6 MB
--- a/test-data/vsnp_statistics2.tabular Mon Nov 15 23:15:14 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Read1 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Read2 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Total Reads All Mapped Reads Unmapped Reads Unmapped Reads Percentage of Total Reference with Coverage Average Depth of Coverage Good SNP Count Reference -13-1941-6_S4_L001_R1_600000_fastq_gz 8.7 KB 100
--- a/test-data/vsnp_statistics4.tabular Mon Nov 15 23:15:14 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Read1 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Read2 FASTQ File Size Reads Mean Read Length Mean Read Quality Reads Passing Q30 Total Reads All Mapped Reads Unmapped Reads Unmapped Reads Percentage of Total Reference with Coverage Average Depth of Coverage Good SNP Count Reference -Unnamed Collection_R1 8.7 KB 100
--- a/vsnp_statistics.xml Mon Nov 15 23:15:14 2021 +0000 +++ b/vsnp_statistics.xml Mon Nov 15 23:24:03 2021 +0000 @@ -76,7 +76,11 @@ <param name="read1" value="Mcap_Deer_DE_SRR650221.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> <param name="samtools_idxstats" value="samtools_idxstats1.tabular" ftype="tabular" dbkey="89"/> <param name="vsnp_azc_metrics" value="add_zc_metrics1.tabular" ftype="tabular" dbkey="89"/> - <output name="output" file="vsnp_statistics1.tabular" ftype="tabular" compare="contains"/> + <output name="output" ftype="tabular"> + <assert_contents> + <has_size value="332"/> + </assert_contents> + </output> </test> <!-- A set of paired fastq files --> <test expect_num_outputs="1"> @@ -85,7 +89,11 @@ <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> <param name="samtools_idxstats" value="samtools_idxstats2.tabular" ftype="tabular" dbkey="89"/> <param name="vsnp_azc_metrics" value="add_zc_metrics2.tabular" ftype="tabular" dbkey="89"/> - <output name="output" file="vsnp_statistics2.tabular" ftype="tabular" compare="contains"/> + <output name="output" ftype="tabular"> + <assert_contents> + <has_size value="500"/> + </assert_contents> + </output> </test> <!-- A collection of paired fastq files --> <test expect_num_outputs="1"> @@ -98,7 +106,11 @@ </param> <param name="samtools_idxstats" value="samtools_idxstats5.tabular" ftype="tabular" dbkey="89"/> <param name="vsnp_azc_metrics" value="add_zc_metrics5.tabular" ftype="tabular" dbkey="89"/> - <output name="output" file="vsnp_statistics4.tabular" ftype="tabular" compare="contains"/> + <output name="output" ftype="tabular"> + <assert_contents> + <has_size value="466"/> + </assert_contents> + </output> </test> </tests> <help>