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annotate translate_bed.xml @ 0:038ecf54cbec draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed commit 383bb485120a193bcc14f88364e51356d6ede219
author galaxyp
date Mon, 22 Jan 2018 13:59:27 -0500
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0
038ecf54cbec planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed commit 383bb485120a193bcc14f88364e51356d6ede219
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1 <tool id="translate_bed" name="Translate BED transcripts" version="0.1.0">
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2 <description>cDNA in 3frames or CDS</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 <expand macro="twobit_requirements" />
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10 </requirements>
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11 <stdio>
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12 <exit_code range="1:" />
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13 </stdio>
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14 <command detect_errors="aggressive"><![CDATA[
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15 python '$__tool_directory__/translate_bed.py'
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16 #if $ref.ref_source == 'cached':
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17 --twobit='$ref.ref_loc.fields.path'
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18 #elif $ref.ref_source == 'history':
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19 --twobit='$ref.ref_file'
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20 #elif $ref.ref_source == 'last_column':
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21 --column '-1'
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22 #elif $ref.ref_source == 'select_column':
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23 --column ${int(str($ref.seq_column)) - 1}
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24 #elif $ref.ref_source == 'ensembl_rest':
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25 --ensembl
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26 #end if
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27 #if $translations.translate == 'CDS':
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28 --cds
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29 #elif $translations.translate == 'cDNA':
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30 --all
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31 #end if
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32 $translations.start_codon
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33 #if $bed_filters.biotypes:
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34 --biotypes '$bed_filters.biotypes'
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35 --ensembl
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36 #end if
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37 #if $bed_filters.regions:
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38 --regions '$bed_filters.regions'
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39 #end if
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40 --min_length $translations.min_length
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41 #if $translations.enzyme:
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42 --enzyme '$translations.enzyme'
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43 #end if
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44 #if $fa_id.fa_db:
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45 --fa_db='$fa_id.fa_db'
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46 #end if
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47 #if $fa_id.fa_sep:
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48 --fa_sep='$fa_id.fa_sep'
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49 #end if
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50 #if $fa_id.reference:
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51 --reference $fa_id.reference
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52 #else:
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53 --reference ${input.metadata.dbkey}
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54 #end if
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55 #if $fa_id.id_prefix:
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56 --id_prefix '$fa_id.id_prefix'
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57 #end if
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58 --bed '$translation_bed'
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59 --fasta '$translation_fasta'
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60 -v
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61 $input
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62 ]]></command>
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63 <inputs>
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64 <param name="input" type="data" format="bed" label="A BED file with 12 columns"
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65 help="thickStart and thickEnd define protein coding region, blocks define exon regions"/>
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66 <conditional name="ref">
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67 <param name="ref_source" type="select" label="Source for Genomic Sequence Data">
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68 <option value="cached">Locally cached twobit</option>
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69 <option value="history">History dataset twobit</option>
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70 <option value="last_column">Last Column in the BED file</option>
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71 <option value="select_column">Select Column in the BED file</option>
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72 <option value="ensembl_rest">Retrieve sequences from Ensembl (Slow and only for Ensembl Transcripts)</option>
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73 </param>
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74 <when value="cached">
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75 <param name="ref_loc" type="select" label="Select reference 2bit file">
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76 <options from_data_table="twobit" />
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77 </param>
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78 </when>
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79 <when value="history">
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80 <param name="ref_file" type="data" format="twobit" label="reference 2bit file" />
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81 </when>
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82 <when value="last_column"/>
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83 <when value="select_column">
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84 <param name="seq_column" type="data_column" data_ref="input" label="BED column conatining the genomic sequence"
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85 help="unspliced genomic sequence from chromStart to chromEnd (Extract Genomic DNA)"/>
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86 </when>
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87 <when value="ensembl_rest"/>
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88 </conditional>
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89 <section name="bed_filters" expanded="false" title="BED Filtering Options">
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90 <param name="regions" type="text" value="" optional="true" label="Restrict to features overlapping a comma-separated list of regions" >
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91 <help>Each region is specifed as: chr or chr:pos or chr:from-to</help>
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92 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
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93 </param>
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94 <param name="biotypes" type="text" value="" optional="true" label="Restrict Feature translation to these biotypes"
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95 help="For 20 column BED from Ensembl REST server">
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96 <expand macro="biotypes_help" />
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97 </param>
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98 </section>
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99 <section name="translations" expanded="false" title="Translation Options">
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100 <param name="translate" type="select" label="Feature translation">
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101 <option value="cDNA_minus_CDS">cDNA in 3 frames excluding known CDS</option>
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102 <option value="cDNA">cDNA in 3 frames</option>
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103 <option value="CDS">CDS proteins</option>
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104 </param>
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105 <param name="min_length" type="integer" value="10" min="1" label="Minimum length of protein translation to report"/>
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106 <param name="start_codon" type="boolean" truevalue="--start_codon" falsevalue="" checked="false"
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107 label="Require translations to start with Methionine, trim other leading Amino Acids"/>
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108 <param name="enzyme" type="select" optional="true" label="Digest enzyme"
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109 help="Split the protein into peptides according to enzyme digestion">
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110 <option value="trypsin">trypsin: ([KR](?=[^P]))|((?&lt;=W)K(?=P))|((?&lt;=M)R(?=P))</option>
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111 </param>
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112 </section>
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113 <section name="fa_id" expanded="false" title="Fasta ID Options">
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114 <param name="reference" type="text" value="" optional="true" label="Genome reference name"
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115 help="By default, the input bed dataset metadata will be used."/>
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116 <param name="fa_db" type="text" value="" optional="true" label="fasta ID source, e.g. generic"
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117 help="Any Compomics application such as PeptideShaker, requires a source for non reference proteins of 'generic' e.g.: generic|pep1|peptide description">
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118 </param>
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119 <param name="fa_sep" type="text" value="" optional="true" label="fasta ID line separator character"
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120 help="defaults to the pipe character, Ensembl FASTA files usually use a space character">
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121 </param>
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122 <param name="id_prefix" type="text" value="" optional="true" label="ID prefix for generated IDs"
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123 help="Can be used to distinguish samples">
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124 <validator type="regex" message="Allowed chars:a-z A-Z 0-9 _ - |">^[a-zA-Z0-9_-|]*$</validator>
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125 </param>
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126 </section>
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127 </inputs>
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128 <outputs>
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129 <!-- update translation_bed format to "probed" when datatype is available -->
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130 <data name="translation_bed" format="bed" label="Translate ${translations.translate} on ${on_string} ${input.name}.proBed">
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131 <actions>
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132 <action name="column_names" type="metadata"
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133 default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts,proteinAccession,peptideSequence,uniqueness,genomeReferenceVersion,psmScore,fdr,modifications,charge,expMassToCharge,calcMassToCharge,psmRank,datasetID,uri"/>
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134 </actions>
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135 </data>
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136 <data name="translation_fasta" format="fasta" label="Translate ${translations.translate} on ${on_string} ${input.name}.fasta"/>
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137 </outputs>
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138 <tests>
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139 <test>
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140 <param name="input" value="human_transcripts.bed" ftype="bed12"/>
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141 <param name="ref_source" value="ensembl_rest"/>
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142 <param name="translate" value="cDNA_minus_CDS"/>
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143 <output name="translation_bed">
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144 <assert_contents>
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145 <has_text text="ENST00000641515" />
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146 </assert_contents>
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147 </output>
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148 <output name="translation_fasta">
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149 <assert_contents>
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150 <has_text text=">ENST00000641515" />
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151 </assert_contents>
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152 </output>
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153 </test>
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154 <test>
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155 <param name="input" value="human_transcripts_seq.bed" ftype="bed12"/>
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156 <param name="ref_source" value="last_column"/>
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157 <param name="translate" value="cDNA_minus_CDS"/>
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158 <output name="translation_bed">
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159 <assert_contents>
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160 <has_text text="ENST00000488147" />
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161 <has_text text="FLLSSLLIGVPFCTSPHSCFSMFFGRSKAALTAKLTLMRV" />
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162 </assert_contents>
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163 </output>
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164 <output name="translation_fasta">
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165 <assert_contents>
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166 <has_text text="ENST00000488147" />
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167 <has_text text="FLLSSLLIGVPFCTSPHSCFSMFFGRSKAALTAKLTLMRV" />
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168 </assert_contents>
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169 </output>
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170 </test>
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171 <test>
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172 <param name="input" value="human_transcripts_seq.bed" ftype="bed12"/>
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173 <param name="ref_source" value="last_column"/>
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174 <param name="translate" value="CDS"/>
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175 <output name="translation_bed">
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176 <assert_contents>
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177 <has_text text="ENST00000641515" />
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178 <has_text text="MVTEFIFLGLSDSQELQTFLFMLFFVFY" />
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179 </assert_contents>
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180 </output>
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181 <output name="translation_fasta">
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182 <assert_contents>
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183 <has_text text="ENST00000641515" />
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184 <has_text text="MVTEFIFLGLSDSQELQTFLFMLFFVFY" />
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185 </assert_contents>
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186 </output>
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187 </test>
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188 <test>
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189 <param name="input" value="human_transcripts_seq.bed" ftype="bed12"/>
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190 <param name="ref_source" value="last_column"/>
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191 <param name="translate" value="cDNA_minus_CDS"/>
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192 <param name="biotypes" value="protein_coding"/>
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193 <param name="start_codon" value="False"/>
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194 <param name="fa_db" value="generic"/>
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195 <param name="id_prefix" value="test_"/>
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196 <output name="translation_bed">
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197 <assert_contents>
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198 <has_text text="test_ENST00000641515" />
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199 <has_text text="ELPHTLPQFIFQQLVCYILEYRYKVIMLSKYSFANS" />
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200 </assert_contents>
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201 </output>
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202 <output name="translation_fasta">
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203 <assert_contents>
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204 <has_text text="generic|test_ENST00000641515" />
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205 <has_text text="ELPHTLPQFIFQQLVCYILEYRYKVIMLSKYSFANS" />
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206 </assert_contents>
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207 </output>
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208 </test>
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209 <test>
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210 <param name="input" value="human_transcripts_seq.bed" ftype="bed12"/>
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211 <param name="ref_source" value="last_column"/>
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212 <param name="translate" value="cDNA_minus_CDS"/>
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213 <param name="biotypes" value="protein_coding"/>
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214 <param name="start_codon" value="True"/>
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215 <param name="fa_db" value="generic"/>
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216 <param name="id_prefix" value="test_"/>
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217 <output name="translation_bed">
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218 <assert_contents>
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219 <has_text text="test_ENST00000641515" />
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220 <has_text text="MLSKYSFANS" />
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221 <not_has_text text="ELPHTLPQFIFQQLVCYILEYRYKVIMLSKYSFANS" />
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222 </assert_contents>
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223 </output>
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224 <output name="translation_fasta">
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225 <assert_contents>
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226 <has_text text="generic|test_ENST00000641515" />
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227 <has_text text="MLSKYSFANS" />
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228 <not_has_text text="ELPHTLPQFIFQQLVCYILEYRYKVIMLSKYSFANS" />
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229 </assert_contents>
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230 </output>
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231 </test>
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232 <test>
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233 <param name="input" value="human_transcripts.bed" ftype="bed12"/>
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234 <param name="ref_source" value="history"/>
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235 <param name="ref_file" value="GRCh38.1.2bit" ftype="twobit"/>
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236 <param name="translate" value="cDNA_minus_CDS"/>
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237 <param name="regions" value="1:0-30000"/>
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238 <param name="start_codon" value="True"/>
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239 <param name="fa_db" value="generic"/>
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240 <param name="id_prefix" value="test_"/>
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241 <output name="translation_bed">
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242 <assert_contents>
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243 <has_text text="test_ENST00000488147" />
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244 <has_text text="MAPSSRAPRTLACRDAPATGSRASTAPWTSGPCRRS" />
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245 <not_has_text text="ENST00000335137" />
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246 </assert_contents>
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247 </output>
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248 <output name="translation_fasta">
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249 <assert_contents>
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250 <has_text text="generic|test_ENST00000488147" />
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251 <has_text text="MAPSSRAPRTLACRDAPATGSRASTAPWTSGPCRRS" />
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252 <not_has_text text="ENST00000335137" />
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253 </assert_contents>
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254 </output>
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255 </test>
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256 </tests>
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257 <help><![CDATA[
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258 Translate transcripts from the input BED file into protein sequences.
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259
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260 The genomic sequence:
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261
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262 - may be supplied in an extra column in the BED input file
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263 - retrieved from a twobit genomic reference file
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264 - retrieved from the Ensembl REST API for Ensembl transcripts
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galaxyp
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265
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266
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267 **INPUTS**
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268
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269 - BED file with at least the standard 12 columns
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270 - Genome reference in twobit format (optional)
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271
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272
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273 **OUTPUTS**
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274
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275 - FASTA of transcript translations
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276 - BED with the genomic location of the translated protein. The added 13th column contains the protein sequence.
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277
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278
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279 **OPTIONS**
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280
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281 - Feature translation
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282
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283 - cDNA - three frame translations of the cDNA sequences with an output for each sequence between STOP codons
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284 - CDS - three frame translations of CDS (coding sequence defined by thickStart and thickEnd in the BED file)
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285
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286 - Translation filtering
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287
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288 - can be trimmed to a Methionine start codon
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289 - can be split into peptides by an enzyme digestion
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290 - must exceed specified minimum length
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291
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292
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293 - BED Filtering
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294
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295 - genomic regions
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296 - ensembl biotype if the BED contains the 20 columns as retrieved from the Ensembl REST API
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297
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298
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299 ]]></help>
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300 <citations>
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301 <citation type="doi">10.1093/bioinformatics/btu613</citation>
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302 <citation type="doi">10.1093/nar/gku1010</citation>
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303 </citations>
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304 </tool>