Mercurial > repos > yating-l > twobit_mask_340

annotate twobit_mask.xml @ 0:fb318f9a36f3 draft default tip

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planemo upload commit c1f0c5ceaac87b6b1db12160a8f5b287635db61b
author yating-l
date Thu, 01 Jun 2017 14:10:35 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 <?xml version="1.0"?>
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2 <tool id="twobit_mask" name="twoBitMask" version="1.0">
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3 <description>Apply repeat masking to a twoBit file</description>
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4
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5 <macros>
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6 <import>ucsc_macros.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements_twobit" />
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10
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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13 #if str($maskfile_type.maskfile_type_selector) == "out":
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14 ## twoBitMask expects the first column of the RepeatMasker header to
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15 ## contain only three leading spaces. RepeatMasker output with large
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16 ## SW scores could contain more leading spaces.
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17
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18 awk '{ sub(/^\s+SW/, " SW"); print }' "${out_maskfile}" |
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19 twoBitMask
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20 ${add_mask}
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21 -type=.out
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22 "${twobit_input}" stdin "${twobit_output}"
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23 #else:
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24 ## The BED Output from TRF is in bed4+ format, but twoBitMask
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25 ## only uses the first three fields of a BED file.
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26 ## The extra columns result in a warning from twoBitMask
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27
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28 awk 'BEGIN { OFS="\t" } { print $1, $2, $3 }' "${bed_maskfile}" |
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29 twoBitMask
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30 ${add_mask}
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31 -type=.bed
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32 "${twobit_input}" stdin "${twobit_output}"
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33 #end if
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34 ]]>
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35 </command>
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36 <inputs>
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37 <param name="twobit_input" type="data" format="twobit" label="twoBit input file" />
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38
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39 <param name="add_mask" type="boolean" checked="true"
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40 truevalue="-add" falsevalue=""
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41 label="Keep pre-existing masking"
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42 help="-add" />
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43
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44 <conditional name="maskfile_type">
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45 <param name="maskfile_type_selector" type="select"
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46 label="Choose the type of mask file"
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47 help="Mask file can be a RepeatMasker .out file or a BED file">
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48 <option value="out">RepeatMasker .out file</option>
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49 <option value="bed" selected="true">BED file</option>
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50 </param>
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51
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52 <when value="out">
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53 <param name="out_maskfile" type="data" format="txt"
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54 label="Mask file in RepeatMasker .out format" />
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55 </when>
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56
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57 <when value="bed">
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58 <param name="bed_maskfile" type="data" format="bed"
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59 label="Mask file in BED format" />
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60 </when>
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61 </conditional>
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62 </inputs>
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63 <outputs>
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64 <data name="twobit_output" format="twobit" />
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65 </outputs>
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66 <tests>
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67 <test>
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68 <!-- Test standard RepeatMasker .out file -->
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69 <param name="twobit_input" value="contig1.2bit" ftype="twobit" />
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70 <param name="maskfile_type_selector" value="out" />
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71 <param name="out_maskfile" value="contig1.fasta.out" />
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72 <output name="twobit_output" file="contig1.out.2bit" />
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73 </test>
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74 <test>
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75 <!-- Test RepeatMasker .out file with extra space in header -->
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76 <param name="twobit_input" value="contig1.2bit" ftype="twobit" />
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77 <param name="maskfile_type_selector" value="out" />
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78 <param name="out_maskfile" value="contig1.fasta.extraspace.out" />
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79 <output name="twobit_output" file="contig1.out.2bit" />
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80 </test>
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81 <test>
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82 <!-- Test TRF .bed output -->
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83 <param name="twobit_input" value="contig1.2bit" ftype="twobit" />
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84 <param name="maskfile_type_selector" value="bed" />
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85 <param name="bed_maskfile" value="contig1.fasta.bed" ftype="bed" />
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86 <output name="twobit_output" file="contig1.bed.2bit" />
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87 </test>
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88 <test>
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89 <!-- Test keep pre-existing masking -->
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90 <param name="twobit_input" value="contig1.bed.2bit" ftype="twobit" />
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91 <param name="maskfile_type_selector" value="out" />
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92 <param name="out_maskfile" value="contig1.fasta.out" />
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93 <output name="twobit_output" file="contig1.both.2bit" />
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94 </test>
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95 <test>
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96 <!-- Test ignore pre-existing masking -->
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97 <param name="twobit_input" value="contig1.bed.2bit" ftype="twobit" />
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98 <param name="maskfile_type_selector" value="out" />
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99 <param name="out_maskfile" value="contig1.fasta.out" />
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100 <param name="add_mask" value="" />
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101 <output name="twobit_output" file="contig1.out.2bit" />
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102 </test>
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103 </tests>
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104 <help>
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105 <![CDATA[
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106 **What it does**
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107
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108 twoBitMask applies a mask to a twoBit file based on repeat information
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109 from a `RepeatMasker <http://www.repeatmasker.org/>`_ .out file or
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110 a BED file (e.g., from
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111 `Tandem Repeats Finder <https://tandem.bu.edu/trf/trf.html>`_).
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112
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113 ]]></help>
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114
fb318f9a36f3 planemo upload commit c1f0c5ceaac87b6b1db12160a8f5b287635db61b
yating-l
parents:
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115 <expand macro="citations" />
fb318f9a36f3 planemo upload commit c1f0c5ceaac87b6b1db12160a8f5b287635db61b
yating-l
parents:
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116 </tool>