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 (2021-11-15)
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(-) [+]
line wrap: on
line diff
--- 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>