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comparison crossmap_bam.xml @ 0:d04d5afec2e0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
author iuc
date Tue, 26 Sep 2017 05:44:53 -0400
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children 8e5feca6a518
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-1:000000000000 0:d04d5afec2e0
1 <tool id="crossmap_bam" name="CrossMap BAM" version="@WRAPPER_VERSION@-0">
2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 #if $input_file.extension == "bam":
11 #set $input_file = "input.sam"
12 samtools view -h '${seq_source.input}' > '${input_file}' &&
13 #else:
14 #set $input_file = "input.bam"
15 ln -s '${seq_source.input}' '${input_file}'
16 #end if
17
18 CrossMap.py
19 bam
20
21 "$chain_source.input_chain"
22 $optional_tags
23
24 -m $insert_size
25 -s $insert_size_stdev
26 -t $insert_size_fold
27
28 '${input_file}'
29 '${output}'
30
31 && samtools sort "${output}.sam" > '${output}'
32 && samtools sort "${output}.unmap.sam" > '${output_unmapped}'
33 ]]></command>
34
35 <inputs>
36 <conditional name="seq_source">
37 <expand macro="source" />
38 <when value="cached">
39 <param type="data" format="bam" name="input" label="BAM file">
40 <validator type="unspecified_build"/>
41 <!-- Gives error in tests
42 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
43 -->
44 </param>
45 <param name="input_chain" type="select" label="Lift Over To">
46 <options from_file="liftOver.loc">
47 <column name="name" index="1"/>
48 <column name="value" index="2"/>
49 <column name="dbkey" index="0"/>
50 <filter type="data_meta" ref="input" key="dbkey" column="0"/>
51 </options>
52 </param>
53 </when>
54 <when value="history">
55 <param type="data" format="bam" name="input" label="BAM/SAM file"/>
56 <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/>
57 </when>
58 </conditional>
59 <expand macro="chain" />
60 <param name="optional_tags" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM/SAM Headers" argument="-a"/>
61
62 <param name="insert_size" type="float" value="200.0" label="Insert size" argument="-m" help="Average insert size of pair-end sequencing (bp) [default=200.0]"/>
63 <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev" argument="-s" help="Stanadard deviation of insert size. [default=30.0]"/>
64 <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange" argument="-t" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]"/>
65 </inputs>
66
67 <outputs>
68 <data format="bam" name="output" label="${tool.name} on ${on_string}" />
69 <data format="bam" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}" />
70 </outputs>
71
72 <tests>
73 <!-- BAM/SAM -->
74 <test>
75 <param name="index_source" value="history"/>
76 <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/>
77 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
78 <param name="include_fails" value="False"/>
79
80 <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/>
81 <output name="output_unmapped" file="test_bam_01_output_a.unmap.bam" compare="diff" lines_diff="8"/>
82 </test>
83 </tests>
84 <help><![CDATA[
85 @HELP_GENERAL@
86
87 SAM / BAM
88 ---------
89
90 CrossMap updates chromosomes, genome coordinates, header sections, and all
91 SAM flags accordingly. The program version (of CrossMap) is inserted into the
92 header section, along with the names of the original BAM file and the chain
93 file. For pair-end sequencing, insert size is also recalculated.
94
95
96 **Optional tags**
97
98 Q
99 QC. QC failed.
100
101 N
102 Unmapped. Originally unmapped or originally mapped but failed to liftover to new assembly.
103
104 M
105 Multiple mapped. Alignment can be liftover to multiple places.
106
107 U
108 Unique mapped. Alignment can be liftover to only 1 place.
109
110 **Tags for pair-end sequencing include:**
111
112 QF = QC failed
113 NN = both read1 and read2 unmapped
114 NU = read1 unmapped, read2 unique mapped
115 NM = read1 unmapped, multiple mapped
116 UN = read1 uniquely mapped, read2 unmap
117 UU = both read1 and read2 uniquely mapped
118 UM = read1 uniquely mapped, read2 multiple mapped
119 MN = read1 multiple mapped, read2 unmapped
120 MU = read1 multiple mapped, read2 unique mapped
121 MM = both read1 and read2 multiple mapped
122
123 **Tags for single-end sequencing include**
124
125 QF = QC failed
126 SN = unmaped
127 SM = multiple mapped
128 SU = uniquely mapped
129
130 See `the manual <http://crossmap.sourceforge.net/#convert-bam-sam-format-files>`__ for more details
131 ]]></help>
132
133 <citations>
134 <citation type="doi">10.1093/bioinformatics/btt730</citation>
135 </citations>
136 </tool>