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1 <tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.1">
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2 <description>Alignment coverage information</description>
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3 <command interpreter="python">
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4 maf_stats.py
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5 #if $maf_source_type.maf_source == "user":
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6 $maf_source_type.maf_source $input2 $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary
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7 #else:
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8 $maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary
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9 #end if
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10 ${GALAXY_DATA_INDEX_DIR}
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11 #if $maf_source_type.maf_source == "user":
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12 $input2.metadata.maf_index
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13 #end if
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14 </command>
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15 <inputs>
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16 <param format="interval" name="input1" label="Interval File" type="data">
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17 <validator type="unspecified_build" />
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18 </param>
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19 <conditional name="maf_source_type">
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20 <param name="maf_source" type="select" label="MAF Source">
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21 <option value="cached" selected="true">Locally Cached Alignments</option>
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22 <option value="user">Alignments in Your History</option>
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23 </param>
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24 <when value="user">
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25 <param format="maf" name="input2" label="MAF File" type="data">
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26 <options>
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27 <filter type="data_meta" ref="input1" key="dbkey" />
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28 </options>
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29 <validator type="dataset_ok_validator" />
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30 </param>
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31 </when>
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32 <when value="cached">
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33 <param name="mafType" type="select" label="MAF Type">
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34 <options from_file="maf_index.loc">
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35 <column name="name" index="0"/>
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36 <column name="value" index="1"/>
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37 <column name="dbkey" index="2"/>
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38 <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/>
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39 <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>
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40 </options>
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41 </param>
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42 </when>
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43 </conditional>
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44 <param name="summary" type="select" label="Type of Output">
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45 <option value="false" selected="true">Coverage by Region</option>
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46 <option value="true">Summarize Coverage</option>
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47 </param>
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48 </inputs>
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49 <outputs>
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50 <data format="interval" name="out_file1" metadata_source="input1">
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51 <change_format>
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52 <when input="summary" value="true" format="tabular" />
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53 </change_format>
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54 </data>
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55 </outputs>
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56 <requirements>
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57 <requirement type="python-module">numpy</requirement>
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58 </requirements>
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59 <tests>
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60 <test>
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61 <param name="input1" value="1.bed" dbkey="hg17" format="bed"/>
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62 <param name="maf_source" value="cached"/>
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63 <param name="mafType" value="8_WAY_MULTIZ_hg17"/>
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64 <output name="out_file1" file="maf_stats_interval_out.dat"/>
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65 <param name="summary" value="false"/>
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66 </test>
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67 <test>
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68 <param name="input1" value="1.bed" dbkey="hg17" format="bed"/>
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69 <param name="maf_source" value="cached"/>
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70 <param name="mafType" value="8_WAY_MULTIZ_hg17"/>
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71 <output name="out_file1" file="maf_stats_summary_out.dat"/>
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72 <param name="summary" value="true"/>
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73 </test>
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74 </tests>
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75 <help>
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76
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77 **What it does**
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78
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79 This tool takes a MAF file and an interval file and relates coverage information by interval for each species.
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80 If a column does not exist in the reference genome, it is not included in the output.
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81
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82 Consider the interval: "chrX 1000 1100 myInterval"
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83 Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this:
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84
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85 chrX 1000 1100 myInterval H XXX YYY
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86
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87 chrX 1000 1100 myInterval M XXX YYY
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88
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89 chrX 1000 1100 myInterval R XXX YYY
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90
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91
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92 where XXX and YYY are:
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93
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94 XXX = number of nucleotides
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95
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96 YYY = number of gaps
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97
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98 ----
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99
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100 Alternatively, you can request only summary information for a set of intervals:
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101
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102 ======== =========== ========
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103 #species nucleotides coverage
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104 ======== =========== ========
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105 hg18 30639 0.2372
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106 rheMac2 7524 0.0582
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107 panTro2 30390 0.2353
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108 ======== =========== ========
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109
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110 where **coverage** is the number of nucleotides divided by the total length of the provided intervals.
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111
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112 ------
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113
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114 **Citation**
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115
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116 If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_
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117
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118
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119 </help>
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120 </tool>
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