Mercurial > repos > iuc > gtftobed12

annotate gtfToBed12.xml @ 2:b026dae67fba draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 commit 2f9e5a51a632217e4966aa3b8e9d2b88a09a36e3"
author iuc
date Thu, 20 Feb 2020 13:45:34 -0500
parents 57d45064f114
children
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75a14cc16d4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 commit adc4f5c431fca0bcdf93188b7065bdc4c9c424c6
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1 <tool id="gtftobed12" name="Convert GTF to BED12" version="357">
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2 <requirements>
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3 <requirement type="package" version="357">ucsc-gtftogenepred</requirement>
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4 <requirement type="package" version="357">ucsc-genepredtobed</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive"><![CDATA[
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7 gtfToGenePred
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8 #if $advanced_options.advanced_options_selector == "advanced":
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9 $advanced_options.ignoreGroupsWithoutExons
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10 $advanced_options.simple
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11 $advanced_options.allErrors
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12 $advanced_options.impliedStopAfterCds
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13 $advanced_options.includeVersion
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14 #if $advanced_options.infoOut:
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15 -infoOut='${transcript_info_file}'
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16 #end if
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17 #for $prefix in $advanced_options.sourcePrefixes
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18 -sourcePrefix='${prefix.sourcePrefix}'
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19 #end for
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20 #end if
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21 '${gtf_file}'
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22 'temp.genePred' &&
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23 genePredToBed 'temp.genePred' '${bed_file}'
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24 ]]>
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25 </command>
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26 <inputs>
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27 <param name="gtf_file" type="data" format="gtf" label="GTF File to convert" />
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28 <conditional name="advanced_options">
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29 <param name="advanced_options_selector" type="select" label="Advanced options"
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30 help="Advanced options for gtfToGenePred.">
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31 <option value="default" selected="true">Use default options</option>
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32 <option value="advanced">Set advanced options</option>
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33 </param>
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34 <when value="default" />
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35 <when value="advanced">
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36 <repeat name="sourcePrefixes" title="Source Prefixes"
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37 help="Only process entries where the source name has the specified prefixes">
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38 <param argument="-sourcePrefix" label="Source prefix"
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39 type="text" />
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40 </repeat>
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41 <param argument="-ignoreGroupsWithoutExons" label="Ignore groups without exons"
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42 help="Ignore groups that do not have exons, otherwise they will cause an error."
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43 type="boolean" truevalue="-ignoreGroupsWithoutExons" falsevalue="" checked="false" />
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44 <param argument="-simple" label="Skip hierarchy check"
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45 help="Only check column validity, not heirarchy, may result in invalid output."
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46 type="boolean" truevalue="-simple" falsevalue="" checked="false" />
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47 <param argument="-allErrors" label="Skip all errors"
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48 help="Skip groups with errors rather than aborting. Useful for getting information
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49 about as many errors as possible."
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50 type="boolean" truevalue="-allErrors" falsevalue="" checked="false" />
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51 <param argument="-impliedStopAfterCds" label="Implied stop codon in after CDS"
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52 help="Assume there is an implied stop codon after CDS."
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53 type="boolean" truevalue="-impliedStopAfterCds" falsevalue="" checked="false" />
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54 <param argument="-includeVersion" label="Include gene and transcript version"
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55 help="If gene_version and/or transcript_version attributes exist, include the version
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56 in the corresponding identifiers."
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57 type="boolean" truevalue="-includeVersion" falsevalue="" checked="false" />
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58 <param argument="-infoOut" label="Output transcript information file"
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59 help="Outputs a file with information about each transcript."
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60 type="boolean" checked="false" />
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61 </when>
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62 </conditional>
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63 </inputs>
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64 <outputs>
1
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65 <data name="bed_file" format="bed12" metadata_source="gtf_file" label="${tool.name} on ${on_string}: BED12"/>
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66 <data name="transcript_info_file" format="tabular" metadata_source="gtf_file" label="${tool.name} on ${on_string}: Table">
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67 <filter>(advanced_options['advanced_options_selector'] == 'advanced') and (advanced_options['infoOut'])</filter>
0
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68 </data>
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69 </outputs>
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70 <tests>
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71 <test expect_num_outputs="1" >
0
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72 <param name="gtf_file" value="gtf2bed_test.gtf"/>
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73 <output name="bed_file" file="gtf2bed_test.bed" ftype="bed12"/>
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74 </test>
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75 <test expect_num_outputs="1" >
0
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76 <param name="gtf_file" value="gtf2bed_test_missing_exon.gtf"/>
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77 <param name="advanced_options_selector" value="advanced" />
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78 <param name="ignoreGroupsWithoutExons" value="true" />
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79 <output name="bed_file" file="gtf2bed_test_missing_exon.bed" ftype="bed12"/>
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80 </test>
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81 <test expect_num_outputs="1" >
0
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82 <param name="gtf_file" value="gtf2bed_test.gtf"/>
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83 <param name="advanced_options_selector" value="advanced" />
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84 <param name="includeVersion" value="true" />
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85 <output name="bed_file" file="gtf2bed_test_include_version.bed" ftype="bed12"/>
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86 </test>
2
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87 <test expect_num_outputs="2" >
0
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88 <param name="gtf_file" value="gtf2bed_test.gtf"/>
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89 <param name="advanced_options_selector" value="advanced" />
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90 <param name="infoOut" value="true" />
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91 <output name="bed_file" file="gtf2bed_test.bed" ftype="bed12"/>
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92 <output name="transcript_info_file" file="gtf2bed_test_transcript_info.txt" ftype="tabular"/>
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93 </test>
2
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94 <test expect_num_outputs="1" >
0
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95 <param name="gtf_file" value="gtf2bed_test.gtf"/>
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96 <param name="advanced_options_selector" value="advanced" />
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97 <repeat name="sourcePrefixes">
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98 <param name="sourcePrefix" value="hav" />
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99 </repeat>
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100 <output name="bed_file" file="gtf2bed_test_havana.bed" ftype="bed12"/>
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101 </test>
2
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102 <test expect_num_outputs="1" >
0
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103 <param name="gtf_file" value="gtf2bed_test.gtf"/>
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104 <param name="advanced_options_selector" value="advanced" />
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105 <repeat name="sourcePrefixes">
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106 <param name="sourcePrefix" value="hav" />
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107 </repeat>
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108 <repeat name="sourcePrefixes">
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109 <param name="sourcePrefix" value="ens" />
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110 </repeat>
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111 <output name="bed_file" file="gtf2bed_test.bed" ftype="bed12"/>
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112 </test>
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113 </tests>
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114 <help><![CDATA[
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115 Converts a GTF_ file to a BED12_ formatted file using UCSC tools from Jim Kent.
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116
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117 ``gtfToGenePred``, followed by ``genePredToBed``
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118
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119 .. _GTF: https://genome.ucsc.edu/FAQ/FAQformat.html#format4
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120 .. _BED12: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
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121 ]]>
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122 </help>
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123
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124 <citations>
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125 <citation type="doi">10.1101/gr.229102</citation>
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126 </citations>
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127 </tool>