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comparison crossmap_bam.xml @ 4:dde84a63f767 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
author iuc
date Thu, 24 May 2018 19:09:17 -0400
parents d2c1f9f2cd0e
children c76b5389bb34
comparison
equal deleted inserted replaced
3:d2c1f9f2cd0e 4:dde84a63f767
1 <tool id="crossmap_bam" name="CrossMap BAM" version="@WRAPPER_VERSION@-0"> 1 <tool id="crossmap_bam" name="CrossMap BAM" version="@WRAPPER_VERSION@">
2 <description>Convert genome coordinates or annotation files between genome assemblies</description> 2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
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 CrossMap.py bam 10 CrossMap.py bam
12 '${chain_source.input_chain}' 11 '${chain_source.input_chain}'
13 $optional_tags 12 $optional_tags
14 13
15 -m $insert_size 14 -m $insert_size
16 -s $insert_size_stdev 15 -s $insert_size_stdev
17 -t $insert_size_fold 16 -t $insert_size_fold
18 17
19 '${input}' 18 '${input}'
20 '${output}' 19 output
21
22 && mv '${output}.sorted.bam' '${output}'
23 ]]></command> 20 ]]></command>
24 <inputs> 21 <inputs>
25 <param name="input" type="data" format="bam" label="BAM file"/> 22 <param name="input" type="data" format="bam" label="BAM file"/>
26 23
27 <expand macro="chain" /> 24 <expand macro="chain" />
32 <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/> 29 <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/>
33 <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"/> 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"/>
34 </inputs> 31 </inputs>
35 32
36 <outputs> 33 <outputs>
37 <data name="output" format="bam" label="${tool.name} on ${on_string}" /> 34 <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam" />
38 <!-- CrossMap 0.2.5 does not produce output_unmapped --> 35 <!-- CrossMap 0.2.5 does not produce output_unmapped -->
39 </outputs> 36 </outputs>
40 37
41 <tests> 38 <tests>
42 <test> 39 <test>
43 <param name="index_source" value="history"/> 40 <param name="index_source" value="history"/>
44 <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/> 41 <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/>
45 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> 42 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
46 <param name="include_fails" value="False"/> 43 <param name="include_fails" value="False"/>
47 44
48 <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/> 45 <output name="output" file="test_bam_01_output_a.bam" ftype="bam" />
49 </test> 46 </test>
50 <test> 47 <test>
51 <param name="index_source" value="cached"/> 48 <param name="index_source" value="cached"/>
52 49
53 <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/> 50 <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/>
54 <param name="include_fails" value="False"/> 51 <param name="include_fails" value="False"/>
55 52
56 <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/> 53 <output name="output" file="test_bam_01_output_a.bam" ftype="bam" />
57 </test> 54 </test>
58 </tests> 55 </tests>
59 <help><![CDATA[ 56 <help><![CDATA[
60 @HELP_GENERAL@ 57 @HELP_GENERAL@
61 58
113 unmaped 110 unmaped
114 SM 111 SM
115 multiple mapped 112 multiple mapped
116 SU 113 SU
117 uniquely mapped 114 uniquely mapped
118
119 ]]></help> 115 ]]></help>
120 116
121 <citations> 117 <citations>
122 <citation type="doi">10.1093/bioinformatics/btt730</citation> 118 <citation type="doi">10.1093/bioinformatics/btt730</citation>
123 </citations> 119 </citations>