Mercurial > repos > rnateam > ribotaper

annotate ribotaper_part1_create_annotation_files.xml @ 5:9bc0a9b45b8b draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/ commit 6ede79703d2f4ed200c5e1d273cad674be486900"
author rnateam
date Wed, 08 Jun 2022 15:05:03 +0000
parents 74b0ca4446af
children
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1 <tool id="ribotaper_create_annotation" name="ribotaper part 1: creation of annotation files" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile='20.01'>
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <expand macro='bio_tools'/>
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6 <expand macro='requirements'/>
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7 <stdio>
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8 <exit_code range="1:"/>
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9 </stdio>
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10 <command><![CDATA[
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11 #if $reference_genome.source == 'history':
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12 #set $ref_genome = 'reference.fasta'
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13 ln -s -f '${reference_genome.history_item}' $ref_genome &&
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14 samtools faidx $ref_genome &&
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15 #else:
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16 #set $ref_genome = $reference_genome.index.fields.path
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17 #end if
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18 create_annotations_files.bash
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19 '${gtf}'
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20 '${ref_genome}'
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21 $ccdsid
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22 $appris
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23 './annotation_path'
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24 &&
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25 tar czvf '${output2}' './annotation_path'
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27 ]]></command>
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28 <inputs>
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29 <param name="gtf" type="data" format="GTF" label="Annotation file"
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30 help="The GTF file should contain: 1) coding and non-coding genes, 2) a 'transcript_id' and a 'gene_id' field for each 'exon' and 'CDS' row."/>
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31 <conditional name="reference_genome">
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32 <param name="source" type="select" label="Source for the genome" help="Built-in references were created using default options.">
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33 <option value="indexed" selected="true">Use a built-in genome</option>
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34 <option value="history">Use a genome from history</option>
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35 </param>
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36 <when value="indexed">
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37 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team.">
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38 <options from_data_table="fasta_indexes">
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39 <filter type="sort_by" column="2" />
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40 <validator type="no_options" message="No genomes are available for the selected input dataset" />
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41 </options>
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42 </param>
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43 </when>
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44 <when value="history">
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45 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
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46 </when>
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47 </conditional>
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48 <param name="ccdsid" type="boolean" falsevalue="false" truevalue="true" checked="true"
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49 label="Use CCDS annotation (valid for Human Gencode 19 and Mouse Gencode M3)"
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50 help="If yes, only exons/transcripts with the CCDS tag will be used as CCDS exons/transcripts, otherwise all exons/transcripts with a CDS region are going to be annotated as CCDS."/>
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51 <param name="appris" type="boolean" falsevalue="false" truevalue="true" checked="true" label="Use Appris annotation (valid for Human Gencode 19 and Mouse Gencode M3)"
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52 help=" If yes, only exons/transcripts with the appris tag will be used, using only 1 transcript per appris gene (the appris_principal transcript or other appris transcript).
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53 If a gene does not have appris transcript, all the annotated transcript structures are used."/>
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54 </inputs>
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55 <outputs>
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56 <data name="output1" format="bed" from_work_dir="annotation_path/start_stops_FAR.bed" label="${tool.name} on ${on_string}: start_stops FAR"/>
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57 <data name="output2" format="tgz" label="${tool.name} on ${on_string}: Annotation path"/>
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58 </outputs>
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59 <tests>
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60 <test expect_num_outputs="2">
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61 <param name="gtf" value="test.gtf"/>
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62 <conditional name="reference_genome">
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63 <param name="source" value="history"/>
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64 <param name="history_item" value="test.fa"/>
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65 </conditional>
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66 <param name="ccdsid" value="true"/>
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67 <param name="appris" value="true"/>
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68 <output name="output1" file="annotation_path/start_stops_FAR.bed"/>
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69 </test>
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70 <test expect_num_outputs="2">
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71 <param name="gtf" value="test.gtf"/>
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72 <conditional name="reference_genome">
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73 <param name="source" value="indexed"/>
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74 <param name="index" value="phix174"/>
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75 </conditional>
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76 <param name="ccdsid" value="true"/>
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77 <param name="appris" value="true"/>
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78 <output name="output1" file="annotation_path/start_stops_FAR_indexed.bed"/>
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82 Overview
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83 --------
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84
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85 RiboTaper is an analysis pipeline for Ribosome Profiling
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86 (Ribo-seq) experiments,
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87 which exploits the triplet periodicity of
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88 ribosomal footprints to call translated regions.
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89 See
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90 https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/ for details.
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91
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92
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93 The Ribotaper Galaxy tool set consists of three tools:
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94
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95 - ``ribotaper part 1``: creation of annotation files
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96 - ``ribotaper part 2``: metagene analysis for P-sites definition
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97 - ``ribotaper part 3``: ribosome profiling
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98
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99 The order of execution should follow:
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100 ``ribotaper part 1, part 2 and part 3``.
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101
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102 The current tool is ``ribotaper part 1``,
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103 creation of annotation files.
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104
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105 Output
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106 ------
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107
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108 ``Ribotaper part 1`` builds a list of exon coordinates,
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109 exon sequences and transcript structures.
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110
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111 ``Ribotaper part 1`` generates two files:
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112
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113 - **start_stops_FAR** in BED format
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114 - **annotation_path** in format of tar
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115
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116 *Start_stops_FAR*
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117 is used as an input for ``ribotaper part 2``.
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118 *Annotation_path*
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119 is used as an input for ``ribotaper part 3``.
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120
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121
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122 ]]></help>
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123 <expand macro="citations"/>
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124 </tool>