Mercurial > repos > galaxyp > retrieve_ensembl_bed

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
author galaxyp
date Mon, 07 Oct 2019 16:14:39 -0400
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da1b538b87e5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
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1 <tool id="retrieve_ensembl_bed" name="Retrieve Ensembl features in BED format" version="0.1.0">
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2 <description>using Ensembl REST API</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 <requirements>
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7 <expand macro="ensembl_requirements" />
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8 <expand macro="bedutil_requirements" />
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 python '$__tool_directory__/retrieve_ensembl_bed.py'
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12 --species '$species'
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13 #if $extended_bed:
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14 --extended_bed
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15 #end if
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16 $ucsc_chrom_names
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17 #if $biotypes:
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18 --biotypes '$biotypes'
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19 #end if
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20 #if $regions:
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21 --regions '$regions'
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22 #end if
1
9c4a48f5d4e7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 6babd357845126292cb202aaea0f70ff68819525"
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23 #if $interval_file:
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24 #if $interval_file.ext.find('bed') > -1
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25 --interval_format bed
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26 #elif $interval_file.ext in ['gff','gtf','gff3']
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27 --interval_format gff
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28 #else
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29 --interval_format interval
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30 #end if
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31 --interval_file '$interval_file'
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32 #end if
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33 '$transcript_bed'
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34 ]]></command>
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35 <inputs>
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36 <param name="species" type="text" value="" label="Ensembl species" >
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37 <help>
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38 </help>
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39 <expand macro="species_options" />
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40 <validator type="regex" message="Enter an Ensembl organism">^\w+.*$</validator>
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41 </param>
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42 <param name="extended_bed" type="boolean" truevalue=",second_name,cds_start_status,cds_end_status,exon_frames,type,gene_name,second_gene_name,gene_type" falsevalue="" checked="true"
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43 label="Keep extra columns from ensembl BED"/>
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44 <param name="ucsc_chrom_names" type="boolean" truevalue="--ucsc_chrom_names" falsevalue="" checked="false"
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45 label="Use the UCSC names for Chromosomes"/>
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46 <param name="biotypes" type="text" value="" optional="true" label="Restrict Feature retrieval to these biotypes" >
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47 <expand macro="biotypes_help" />
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48 </param>
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49 <param name="regions" type="text" value="" optional="true" label="Restrict Feature retrieval to comma-separated list of regions" >
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50 <help>Each region is specifed as: chr or chr:pos or chr:from-to</help>
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51 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
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52 </param>
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53 <param name="interval_file" type="data" format="bed,gff,interval" label="Retrieve the intervals from this file" optional="true"/>
0
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54 </inputs>
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55 <outputs>
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56 <data name="transcript_bed" format="bed" label="Ensembl ${species} transcripts.bed">
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57 <actions>
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58 <action name="column_names" type="metadata"
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59 default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts${extended_bed}"/>
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60 </actions>
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61 </data>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="species" value="human"/>
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66 <param name="biotypes" value="protein_coding"/>
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67 <param name="regions" value="1:51194990-51275150"/>
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68 <output name="transcript_bed">
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69 <assert_contents>
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70 <has_text_matching expression="(chr)?1\t\d+\t\d+\tENST" />
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71 </assert_contents>
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72 </output>
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73 </test>
1
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74 <test>
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75 <param name="species" value="mouse"/>
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76 <param name="biotypes" value="protein_coding"/>
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77 <param name="interval_file" ftype="bed" value="test.bed"/>
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78 <output name="transcript_bed">
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79 <assert_contents>
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80 <has_text_matching expression="(chr)?1\t\d+\t\d+\tENSMUST" />
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81 </assert_contents>
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82 </output>
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83 </test>
0
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84 </tests>
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85 <help><![CDATA[
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86 Retrieve Ensembl cDNAs in BED format
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87
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88 usage: retrieve_ensembl_bed.py [-h] [-s SPECIES] [-R REGIONS] [-B BIOTYPES]
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89 [-X] [-U] [-t] [-v] [-d]
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90 output
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91
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92 positional arguments:
1
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93 output Output BED filepath, or for stdout: "-"
0
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94
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95 optional arguments:
1
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96 -h, --help show this help message and exit
0
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97 -s SPECIES, --species SPECIES
1
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98 Ensembl Species to retrieve
0
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99 -R REGIONS, --regions REGIONS
1
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100 Restrict Ensembl retrieval to regions e.g.
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101 X,2:20000-25000,3:100-500+
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102 -i INTERVAL_FILE, --interval_file INTERVAL_FILE
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103 Regions from a bed, gff, or interval file
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104
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105 -f {bed,gff,interval}, --interval_format {bed,gff,interval}
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106 Interval format has TAB-separated
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107 columns: Seq, Start, End, Strand
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108
0
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109 -B BIOTYPES, --biotypes BIOTYPES
1
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110 Restrict Ensembl biotypes to retrieve
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111 -X, --extended_bed Include the extended columns returned from Ensembl
0
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112 -U, --ucsc_chrom_names
1
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113 Use the UCSC names for Chromosomes
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114 -t, --toplevel Print Ensembl toplevel for species
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115 -v, --verbose Verbose
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116 -d, --debug Debug
0
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117
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118
1
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119 **Output**
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120
0
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121 Ensembl REST API returns an extended BED format with these additional columns::
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122
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123 second_name, cds_start_status, cds_end_status, exon_frames, type, gene_name, second_gene_name, gene_type
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124
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125 ]]></help>
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126 <citations>
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127 <citation type="doi">10.1093/bioinformatics/btu613</citation>
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128 <citation type="doi">10.1093/nar/gku1010</citation>
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129 </citations>
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130 </tool>