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comparison crossmap_bam.xml @ 2:6463cf32d733 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
author iuc
date Thu, 19 Oct 2017 12:36:24 -0400
parents 9bcfe0aabf5d
children d2c1f9f2cd0e
comparison
equal deleted inserted replaced
1:b340f0750aa5 2:6463cf32d733
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 #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}' '${input_file}'
16 #end if
17 10
18 CrossMap.py 11 CrossMap.py bam
19 bam 12 '${chain_source.input_chain}'
13 $optional_tags
20 14
21 "$chain_source.input_chain" 15 -m $insert_size
22 $optional_tags 16 -s $insert_size_stdev
17 -t $insert_size_fold
23 18
24 -m $insert_size 19 '${input}'
25 -s $insert_size_stdev 20 '${output}'
26 -t $insert_size_fold
27 21
28 '${input_file}' 22 && mv '${output}.sorted.bam' '${output}'
29 '${output}' 23 ]]></command>
24 <inputs>
25 <param name="input" type="data" format="bam" label="BAM file"/>
30 26
31 && samtools sort "${output}.sam" > '${output}' 27 <expand macro="chain" />
32 && samtools sort "${output}.unmap.sam" > '${output_unmapped}'
33 ]]></command>
34 28
35 <inputs> 29 <param name="optional_tags" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM Headers"/>
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 30
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]"/> 31 <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/>
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]"/> 32 <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/>
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]"/> 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"/>
65 </inputs> 34 </inputs>
66 35
67 <outputs> 36 <outputs>
68 <data format="bam" name="output" label="${tool.name} on ${on_string}" /> 37 <data name="output" format="bam" label="${tool.name} on ${on_string}" />
69 <data format="bam" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}" /> 38 <!-- CrossMap 0.2.5 does not produce output_unmapped -->
70 </outputs> 39 </outputs>
71 40
72 <tests> 41 <tests>
73 <!-- BAM/SAM -->
74 <test> 42 <test>
75 <param name="index_source" value="history"/> 43 <param name="index_source" value="history"/>
76 <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/> 44 <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/>
77 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> 45 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
78 <param name="include_fails" value="False"/> 46 <param name="include_fails" value="False"/>
79 47
80 <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/> 48 <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"/> 49 </test>
50 <test>
51 <param name="index_source" value="cached"/>
52
53 <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/>
54 <param name="include_fails" value="False"/>
55
56 <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/>
82 </test> 57 </test>
83 </tests> 58 </tests>
84 <help><![CDATA[ 59 <help><![CDATA[
85 @HELP_GENERAL@ 60 @HELP_GENERAL@
86 61
87 SAM / BAM 62 BAM
88 --------- 63 ---------
89 64
90 CrossMap updates chromosomes, genome coordinates, header sections, and all 65 CrossMap updates chromosomes, genome coordinates, header sections, and all
91 SAM flags accordingly. The program version (of CrossMap) is inserted into the 66 BAM 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 67 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. 68 file. For pair-end sequencing, insert size is also recalculated.
94 69
95 70
96 **Optional tags** 71 **Optional tags**
97 72
98 Q 73 Q
99 QC. QC failed. 74 QC. QC failed.
100 75
101 N 76 N
102 Unmapped. Originally unmapped or originally mapped but failed to liftover to new assembly. 77 Unmapped. Originally unmapped or originally mapped but failed to liftover to new assembly.
103 78
104 M 79 M
105 Multiple mapped. Alignment can be liftover to multiple places. 80 Multiple mapped. Alignment can be liftover to multiple places.
106 81
107 U 82 U
108 Unique mapped. Alignment can be liftover to only 1 place. 83 Unique mapped. Alignment can be liftover to only 1 place.
109 84
110 **Tags for pair-end sequencing include:** 85 **Tags for pair-end sequencing include:**
111 86
112 QF = QC failed 87 QF
113 NN = both read1 and read2 unmapped 88 QC failed
114 NU = read1 unmapped, read2 unique mapped 89 NN
115 NM = read1 unmapped, multiple mapped 90 both read1 and read2 unmapped
116 UN = read1 uniquely mapped, read2 unmap 91 NU
117 UU = both read1 and read2 uniquely mapped 92 read1 unmapped, read2 unique mapped
118 UM = read1 uniquely mapped, read2 multiple mapped 93 NM
119 MN = read1 multiple mapped, read2 unmapped 94 read1 unmapped, multiple mapped
120 MU = read1 multiple mapped, read2 unique mapped 95 UN
121 MM = both read1 and read2 multiple mapped 96 read1 uniquely mapped, read2 unmap
97 UU
98 both read1 and read2 uniquely mapped
99 UM
100 read1 uniquely mapped, read2 multiple mapped
101 MN
102 read1 multiple mapped, read2 unmapped
103 MU
104 read1 multiple mapped, read2 unique mapped
105 MM
106 both read1 and read2 multiple mapped
122 107
123 **Tags for single-end sequencing include** 108 **Tags for single-end sequencing include**
124 109
125 QF = QC failed 110 QF
126 SN = unmaped 111 QC failed
127 SM = multiple mapped 112 SN
128 SU = uniquely mapped 113 unmaped
114 SM
115 multiple mapped
116 SU
117 uniquely mapped
129 118
130 See `the manual <http://crossmap.sourceforge.net/#convert-bam-sam-format-files>`__ for more details 119 ]]></help>
131 ]]></help>
132 120
133 <citations> 121 <citations>
134 <citation type="doi">10.1093/bioinformatics/btt730</citation> 122 <citation type="doi">10.1093/bioinformatics/btt730</citation>
135 </citations> 123 </citations>
136 </tool> 124 </tool>