Repository 'slamdunk'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/slamdunk

Changeset 5:8b62f89924a7 (2020-01-18)
Previous changeset 4:fe3fe68b09a7 (2019-05-24) Next changeset 6:141f65f7c7c8 (2021-07-13)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 64bbe6ec9a3f3cd6241fa4cf0e0548e0e67629a0"
modified:
macros.xml
slamdunk.xml
test-data/reads1_overallrates.csv
test-data/reads_slamdunk_mapped_filtered_tcount.tsv
test-data/summary.txt
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diff -r fe3fe68b09a7 -r 8b62f89924a7 macros.xml
--- a/macros.xml Fri May 24 13:30:30 2019 -0400
+++ b/macros.xml Sat Jan 18 12:59:37 2020 -0500
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@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">0.3.3</token>
+    <token name="@TOOL_VERSION@">0.4.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">slamdunk</requirement>
@@ -29,7 +29,7 @@
     </xml>
     <xml name="citations">
         <citation type="doi">
- 10.1186/s12859-019-2849-7
+            10.1186/s12859-019-2849-7
         </citation>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
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diff -r fe3fe68b09a7 -r 8b62f89924a7 slamdunk.xml
--- a/slamdunk.xml Fri May 24 13:30:30 2019 -0400
+++ b/slamdunk.xml Sat Jan 18 12:59:37 2020 -0500
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@@ -125,7 +125,7 @@
             </output_collection>
             <output_collection name="outputTsv">
                 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
-                lines_diff="2"  />
+                compare="re_match"  />
             </output_collection>
             <output_collection name="outputVcf">
                 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" />
@@ -134,6 +134,7 @@
         <test>
             <!--Ensure built-in fasta works -->
             <param name="reference_source_selector" value="cached" />
+            <param name="ref_file" value="hg38full" />
             <param name="Reference" value="actb.bed" />
             <param name="reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" />
             <param name="readLength" value="100" />
@@ -148,7 +149,7 @@
             </output_collection>
             <output_collection name="outputTsv">
                 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
-                lines_diff="2"  />
+                compare="re_match"  />
             </output_collection>
             <output_collection name="outputVcf">
                 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" />
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diff -r fe3fe68b09a7 -r 8b62f89924a7 test-data/reads1_overallrates.csv
--- a/test-data/reads1_overallrates.csv Fri May 24 13:30:30 2019 -0400
+++ b/test-data/reads1_overallrates.csv Sat Jan 18 12:59:37 2020 -0500
b
@@ -1,4 +1,4 @@
-# slamdunk rates v0.3.3
+# slamdunk rates v0.4.1
  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
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diff -r fe3fe68b09a7 -r 8b62f89924a7 test-data/reads_slamdunk_mapped_filtered_tcount.tsv
--- a/test-data/reads_slamdunk_mapped_filtered_tcount.tsv Fri May 24 13:30:30 2019 -0400
+++ b/test-data/reads_slamdunk_mapped_filtered_tcount.tsv Sat Jan 18 12:59:37 2020 -0500
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@@ -1,2 +1,4 @@
+#slamdunk v0.4.1 3 sample info: sample_0 0 NA -1
+#annotation: dataset_.*.dat .*
 Chromosome Start End Name Length Strand ConversionRate ReadsCPM Tcontent CoverageOnTs ConversionsOnTs ReadCount TcReadCount multimapCount ConversionRateLower ConversionRateUpper
-chr5 120498 122492 Actb 1994 + 0.0222222222222 666666.666667 445 90 2 8 4 0 -1.0 -1.0
+chr5 120498 122492 Actb 1994 \+ 0.022\d* 666666.66\d* 445 90 2 8 4 0 -1\.0 -1\.0
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diff -r fe3fe68b09a7 -r 8b62f89924a7 test-data/summary.txt
--- a/test-data/summary.txt Fri May 24 13:30:30 2019 -0400
+++ b/test-data/summary.txt Sat Jan 18 12:59:37 2020 -0500
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@@ -1,4 +1,4 @@
-# slamdunk summary v0.3.3
+# slamdunk summary v0.4.1
 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