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comparison crossmap_bam.xml @ 11:8f5580caf79b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
author iuc
date Mon, 02 Sep 2024 11:59:42 +0000
parents c413cbb69f3c
children
comparison
equal deleted inserted replaced
10:5e3b182af35c 11:8f5580caf79b
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 10
11 ln -s '${input}' ./input.bam && 11 ln -s '${input}' ./input.bam &&
12 12
13 CrossMap.py bam 13 CrossMap bam
14 '${chain_source.input_chain}' 14 '${chain_source.input_chain}'
15 $optional_tags 15 $optional_tags
16 16
17 -m $insert_size 17 -m $insert_size
18 -s $insert_size_stdev 18 -s $insert_size_stdev
21 ./input.bam 21 ./input.bam
22 output 22 output
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <param name="input" type="data" format="bam" label="BAM file"/> 25 <param name="input" type="data" format="bam" label="BAM file"/>
26 26 <expand macro="chain"/>
27 <expand macro="chain" />
28
29 <param name="optional_tags" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM Headers"/> 27 <param name="optional_tags" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM Headers"/>
30
31 <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/> 28 <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/>
32 <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/> 29 <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/>
33 <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" 30 <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/>
34 help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/>
35 </inputs> 31 </inputs>
36
37 <outputs> 32 <outputs>
38 <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam" /> 33 <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam"/>
39 <!-- CrossMap 0.2.5 does not produce output_unmapped --> 34 <!-- CrossMap 0.2.5 does not produce output_unmapped -->
40 </outputs> 35 </outputs>
41
42 <tests> 36 <tests>
43 <test> 37 <test>
44 <param name="index_source" value="history"/> 38 <param name="index_source" value="history"/>
45 <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/> 39 <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/>
46 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> 40 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
47 <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="4" /> 41 <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="6"/>
48 </test> 42 </test>
49 <test> 43 <test>
50 <param name="index_source" value="cached"/> 44 <param name="index_source" value="cached"/>
51 <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/> 45 <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/>
52 <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="4" /> 46 <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="6"/>
53 </test> 47 </test>
54 </tests> 48 </tests>
55 <help><![CDATA[ 49 <help><![CDATA[
56 @HELP_GENERAL@ 50 @HELP_GENERAL@
57 51
110 SM 104 SM
111 multiple mapped 105 multiple mapped
112 SU 106 SU
113 uniquely mapped 107 uniquely mapped
114 ]]></help> 108 ]]></help>
115
116 <citations> 109 <citations>
117 <citation type="doi">10.1093/bioinformatics/btt730</citation> 110 <citation type="doi">10.1093/bioinformatics/btt730</citation>
118 </citations> 111 </citations>
119 </tool> 112 </tool>