Mercurial > repos > iuc > crossmap_bam

annotate crossmap_bam.xml @ 2:083774cc8472 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 39a5f30a013c6d71ea84807b72511e3aa4bab147
author iuc
date Fri, 20 Oct 2017 11:33:02 -0400
parents 8e5feca6a518
children cb3557cabc7b
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1 <tool id="crossmap_bam" name="CrossMap BAM" version="@WRAPPER_VERSION@-0">
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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[
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11 CrossMap.py bam
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12 '${chain_source.input_chain}'
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13 $optional_tags
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15 -m $insert_size
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16 -s $insert_size_stdev
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17 -t $insert_size_fold
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19 '${input}'
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20 '${output}'
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22 && mv '${output}.sorted.bam' '${output}'
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23 ]]></command>
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24 <inputs>
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25 <param name="input" type="data" format="bam" label="BAM file"/>
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27 <expand macro="chain" />
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29 <param name="optional_tags" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM Headers"/>
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31 <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/>
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32 <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/>
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33 <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/>
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34 </inputs>
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36 <outputs>
1
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37 <data name="output" format="bam" label="${tool.name} on ${on_string}" />
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38 <!-- CrossMap 0.2.5 does not produce output_unmapped -->
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39 </outputs>
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41 <tests>
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42 <test>
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43 <param name="index_source" value="history"/>
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44 <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/>
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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45 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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46 <param name="include_fails" value="False"/>
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47
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48 <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/>
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49 </test>
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50 <test>
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51 <param name="index_source" value="cached"/>
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52
2
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53 <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/>
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54 <param name="include_fails" value="False"/>
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56 <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/>
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 @HELP_GENERAL@
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62 BAM
0
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63 ---------
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64
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65 CrossMap updates chromosomes, genome coordinates, header sections, and all
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66 BAM flags accordingly. The program version (of CrossMap) is inserted into the
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67 header section, along with the names of the original BAM file and the chain
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68 file. For pair-end sequencing, insert size is also recalculated.
0
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69
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1
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71 **Optional tags**
0
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72
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73 Q
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74 QC. QC failed.
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75
1
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76 N
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77 Unmapped. Originally unmapped or originally mapped but failed to liftover to new assembly.
0
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78
1
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79 M
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80 Multiple mapped. Alignment can be liftover to multiple places.
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81
1
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82 U
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83 Unique mapped. Alignment can be liftover to only 1 place.
0
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84
1
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85 **Tags for pair-end sequencing include:**
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86
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87 QF
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88 QC failed
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89 NN
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90 both read1 and read2 unmapped
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iuc
parents: 0
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91 NU
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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92 read1 unmapped, 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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93 NM
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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94 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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95 UN
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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96 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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97 UU
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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98 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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99 UM
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 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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101 MN
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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102 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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103 MU
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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104 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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105 MM
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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106 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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107
1
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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108 **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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109
1
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
parents: 0
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110 QF
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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111 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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112 SN
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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113 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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114 SM
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
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115 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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116 SU
8e5feca6a518 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
iuc
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117 uniquely mapped
0
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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118
1
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119 ]]></help>
0
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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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>
d04d5afec2e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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124 </tool>