Mercurial > repos > iuc > crossmap_bam

annotate crossmap_bam.xml @ 7:e5340c09200a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
author iuc
date Thu, 15 Jul 2021 16:18:13 +0000
parents 5051467dc96a
children e13f565068d6
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1 <tool id="crossmap_bam" name="CrossMap BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
4
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11 ln -s '${input}' ./input.bam &&
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13 CrossMap.py bam
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14 '${chain_source.input_chain}'
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15 $optional_tags
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17 -m $insert_size
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18 -s $insert_size_stdev
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19 -t $insert_size_fold
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21 ./input.bam
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22 output
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23 ]]></command>
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24 <inputs>
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25 <param name="input" type="data" format="bam" label="BAM file"/>
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0
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27 <expand macro="chain" />
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29 <param name="optional_tags" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM Headers"/>
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1
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31 <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/>
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32 <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/>
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33 <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange"
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34 help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/>
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35 </inputs>
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37 <outputs>
3
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38 <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam" />
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39 <!-- CrossMap 0.2.5 does not produce output_unmapped -->
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40 </outputs>
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42 <tests>
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43 <test>
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44 <param name="index_source" value="history"/>
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45 <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/>
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46 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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47 <param name="include_fails" value="False"/>
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48
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49 <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="4" />
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50 </test>
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51 <test>
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52 <param name="index_source" value="cached"/>
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54 <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/>
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55 <param name="include_fails" value="False"/>
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57 <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="4" />
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 @HELP_GENERAL@
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62
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63 BAM
0
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64 ---------
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65
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66 CrossMap updates chromosomes, genome coordinates, header sections, and all
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67 BAM flags accordingly. The program version (of CrossMap) is inserted into the
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68 header section, along with the names of the original BAM file and the chain
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69 file. For pair-end sequencing, insert size is also recalculated.
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72 **Optional tags**
0
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74 Q
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75 QC. QC failed.
0
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1
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77 N
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78 Unmapped. Originally unmapped or originally mapped but failed to liftover to new assembly.
0
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1
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80 M
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81 Multiple mapped. Alignment can be liftover to multiple places.
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82
1
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83 U
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84 Unique mapped. Alignment can be liftover to only 1 place.
0
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85
1
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86 **Tags for pair-end sequencing include:**
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87
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88 QF
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89 QC failed
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90 NN
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iuc
parents: 0
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91 both read1 and read2 unmapped
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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92 NU
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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93 read1 unmapped, read2 unique mapped
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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94 NM
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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95 read1 unmapped, multiple mapped
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents: 0
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96 UN
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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97 read1 uniquely mapped, read2 unmap
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents: 0
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98 UU
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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99 both read1 and read2 uniquely mapped
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents: 0
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100 UM
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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101 read1 uniquely mapped, read2 multiple mapped
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents: 0
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102 MN
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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103 read1 multiple mapped, read2 unmapped
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents: 0
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104 MU
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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105 read1 multiple mapped, read2 unique mapped
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents: 0
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106 MM
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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107 both read1 and read2 multiple mapped
0
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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108
1
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109 **Tags for single-end sequencing include**
0
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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110
1
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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111 QF
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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112 QC failed
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents: 0
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113 SN
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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114 unmaped
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents: 0
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115 SM
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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116 multiple mapped
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents: 0
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117 SU
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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118 uniquely mapped
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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119 ]]></help>
0
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120
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121 <citations>
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122 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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123 </citations>
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124 </tool>