Mercurial > repos > iuc > crossmap_bam
diff crossmap_bam.xml @ 4:5051467dc96a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
author | iuc |
---|---|
date | Wed, 11 Sep 2019 19:29:38 -0400 |
parents | cb3557cabc7b |
children | e5340c09200a |
line wrap: on
line diff
--- a/crossmap_bam.xml Thu May 24 19:10:46 2018 -0400 +++ b/crossmap_bam.xml Wed Sep 11 19:29:38 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>