Mercurial > repos > iuc > crossmap_vcf
changeset 4:9d61d74f03a4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
| author | iuc |
|---|---|
| date | Wed, 11 Sep 2019 19:29:21 -0400 |
| parents | 9db73ff23c9f |
| children | 97979c3d179f |
| files | crossmap_vcf.xml macros.xml test-data/test_bigwig_01_output_a.bw test-data/test_vcf_01_output.vcf.unmap test-data/test_wig_01_output_a.bw |
| diffstat | 5 files changed, 5 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/crossmap_vcf.xml Thu May 24 19:09:50 2018 -0400 +++ b/crossmap_vcf.xml Wed Sep 11 19:29:21 2019 -0400 @@ -7,7 +7,7 @@ <expand macro="stdio"/> <expand macro="version_command"/> - <command><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ #set $input_file = str($seq_source.input) CrossMap.py vcf @@ -77,7 +77,6 @@ <has_text text="#CHROM"/> <has_text_matching expression="2.*?rs11449.*?PASS"/> <has_text_matching expression="2.*?rs84825.*?PASS"/> - <has_text_matching expression="2.*?rs84823.*?PASS"/> </assert_contents> </output> <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/>
--- a/macros.xml Thu May 24 19:09:50 2018 -0400 +++ b/macros.xml Wed Sep 11 19:29:21 2019 -0400 @@ -2,11 +2,12 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.2.7">crossmap</requirement> + <requirement type="package" version="@TOOL_VERSION@">crossmap</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">0.2.7</token> + <token name="@TOOL_VERSION@">0.3.7</token> + <token name="@WRAPPER_VERSION@">@TOOL_VERSION@</token> <xml name="stdio"> <stdio> <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
--- a/test-data/test_vcf_01_output.vcf.unmap Thu May 24 19:09:50 2018 -0400 +++ b/test-data/test_vcf_01_output.vcf.unmap Wed Sep 11 19:29:21 2019 -0400 @@ -3,3 +3,4 @@ ##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Probabilities"> ##FORMAT=<ID=PL,Number=G,Type=Float,Description="Phred-scaled Genotype Likelihoods"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMP001 SAMP002 +1 200 rs84823 T G . PASS . GT:PL ./.:. 1/1:10,5,0 Fail(REF==ALT)