Mercurial > repos > iuc > crossmap_bam
changeset 5:c76b5389bb34 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
| author | iuc |
|---|---|
| date | Wed, 11 Sep 2019 19:26:44 -0400 |
| parents | dde84a63f767 |
| children | 8c275847f3fa |
| files | crossmap_bam.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, 10 insertions(+), 4 deletions(-) [+] |
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--- a/crossmap_bam.xml Thu May 24 19:09:17 2018 -0400 +++ b/crossmap_bam.xml Wed Sep 11 19:26:44 2019 -0400 @@ -7,6 +7,9 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ + +ln -s '${input}' ./input.bam && + CrossMap.py bam '${chain_source.input_chain}' $optional_tags @@ -15,7 +18,7 @@ -s $insert_size_stdev -t $insert_size_fold -'${input}' +./input.bam output ]]></command> <inputs> @@ -27,7 +30,8 @@ <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/> <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/> - <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/> + <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" + help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/> </inputs> <outputs>
--- a/macros.xml Thu May 24 19:09:17 2018 -0400 +++ b/macros.xml Wed Sep 11 19:26:44 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 19:09:17 2018 -0400 +++ b/test-data/test_vcf_01_output.vcf.unmap Wed Sep 11 19:26:44 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)