Mercurial > repos > iuc > crossmap_bam

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