Mercurial > repos > iuc > crossmap_bam

comparison crossmap_bam.xml @ 5:c76b5389bb34 draft

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"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 acd53aae2d46
comparison
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4:dde84a63f767 5:c76b5389bb34
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10
11 ln -s '${input}' ./input.bam &&
12
10 CrossMap.py bam 13 CrossMap.py bam
11 '${chain_source.input_chain}' 14 '${chain_source.input_chain}'
12 $optional_tags 15 $optional_tags
13 16
14 -m $insert_size 17 -m $insert_size
15 -s $insert_size_stdev 18 -s $insert_size_stdev
16 -t $insert_size_fold 19 -t $insert_size_fold
17 20
18 '${input}' 21 ./input.bam
19 output 22 output
20 ]]></command> 23 ]]></command>
21 <inputs> 24 <inputs>
22 <param name="input" type="data" format="bam" label="BAM file"/> 25 <param name="input" type="data" format="bam" label="BAM file"/>
23 26
25 28
26 <param name="optional_tags" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM Headers"/> 29 <param name="optional_tags" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM Headers"/>
27 30
28 <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/> 31 <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/>
29 <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/> 32 <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/>
30 <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"/> 33 <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange"
34 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"/>
31 </inputs> 35 </inputs>
32 36
33 <outputs> 37 <outputs>
34 <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam" /> 38 <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam" />
35 <!-- CrossMap 0.2.5 does not produce output_unmapped --> 39 <!-- CrossMap 0.2.5 does not produce output_unmapped -->