Mercurial > repos > iuc > deg_annotate

annotate deg_annotate.xml @ 1:e98d4ab5b5bc draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit 44d3dae188cabf4a64dee7c1ebe41c855d95d1b0
author iuc
date Wed, 23 Jan 2019 07:47:22 -0500
parents b42373cddb77
children
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1
e98d4ab5b5bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate commit 44d3dae188cabf4a64dee7c1ebe41c855d95d1b0
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1 <tool id="deg_annotate" name="Annotate DESeq2/DEXSeq output tables" version="1.1.0">
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2 <description>Append annotation from GTF to differential expression tool outputs</description>
0
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3 <requirements>
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4 <requirement type="package" version="2.27.0">bedtools</requirement>
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5 <requirement type="package" version="0.6.4">bcbiogff</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 python '$__tool_directory__/deg_annotate.py' -in '$input_table'
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10 -m '$mode'
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11 -g '$annotation'
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12 -t '$advanced_parameters.gff_feature_type'
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13 -i '$advanced_parameters.gff_feature_attribute'
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14 -x '$advanced_parameters.gff_transcript_attribute'
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15 -a '$advanced_parameters.gff_attributes'
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16 -o '$output'
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="input_table"
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21 type="data"
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22 format="tabular"
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23 argument="-in"
1
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24 label="Tabular output of DESeq2/edgeR/limma/DEXSeq"/>
0
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25
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26 <param name="mode" type="select" argument="-m" label="Input file type">
1
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27 <option value="degseq">DESeq2/edgeR/limma</option>
0
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28 <option value="dexseq">DEXseq</option>
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29 </param>
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30
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31 <param name="annotation"
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32 type="data"
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33 format="gff,gtf,gff3"
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34 argument="-g"
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35 label="Reference annotation in GFF/GTF format" />
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36
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37 <section name="advanced_parameters" title="Advanced options">
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38 <param name="gff_feature_type"
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39 type="text"
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40 value="exon"
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41 argument="-t"
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42 label="GFF feature type"
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43 help="This is the 3rd column in GFF file. Only rows which have the matched feature type in the GTF annotation file will be included. `exon' by default." />
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44
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45 <param name="gff_feature_attribute"
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46 type="text"
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47 value="gene_id"
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48 argument="-i"
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49 label="GFF feature identifier"
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50 help="GFF attribute to be used as feature identifier. The value of this attribute should match the first column of DESeq2 output (default: gene_id)" />
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51
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52 <param name="gff_transcript_attribute"
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53 type="text"
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54 value="transcript_id"
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55 argument="-x"
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56 label="GFF transcript identifier"
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57 help="GFF attribute to be used as transcript identifier. This options is only used for DEXSeq output annotation. Exon numbers are counted for each transcript separately (default: transcript_id)" />
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58
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59 <param name="gff_attributes"
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60 type="text"
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61 value="gene_biotype, gene_name"
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62 argument="-a"
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63 label="GFF attributes to include"
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64 help="Comma separated list of attributes from GFF file to include in output. These attributes should associate with your chosen GFF feature type." />
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65 </section>
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66 </inputs>
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67 <outputs>
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68 <data name="output" format="tabular" label="${tool.name} on ${on_string}"/>
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69 </outputs>
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70 <tests>
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71 <test expect_num_outputs="1">
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72 <param name="input_table"
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73 value="deseq2_output.tabular"/>
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74 <param name="annotation"
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75 value="annotation.gtf"/>
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76 <output name="output">
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77 <assert_contents>
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78 <has_text_matching expression="FBgn0025111\t2192.32236942864\t2.69993841720991\t0.0979447231457099\t27.565940568266\t2.8504782974107e-167\t6.1121380892229e-164\tchrX\t10778953\t10786907\t-\tprotein_coding\tAnt2"/>
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79 </assert_contents>
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80 </output>
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81 </test>
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82 <test expect_num_outputs="1">
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83 <param name="input_table"
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84 value="dexseq_output.tabular"/>
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85 <param name="annotation"
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86 value="annotation.gtf"/>
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87 <param name="mode"
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88 value="dexseq"/>
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89 <output name="output">
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90 <assert_contents>
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91 <has_text_matching expression="FBgn0025111\+FBgn0003360:E005\tFBgn0025111\+FBgn0003360\tE005\t0.273966640920426\t6.62572321505791\t0.774068626605711\t0.378961325638675\tNA\t0.41523701984849\t1.17020080867011\t2.99101950917789\tchrX\t10780596\t10780661\t66\t-\t10\t0\t0\t0\t0\t0\t2\tFBtr0073425, FBtr0333963\tprotein_coding\+protein_coding\tAnt2\+sesB\tFBtr0073425:1,FBtr0333963:1"/>
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92 </assert_contents>
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93 </output>
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94 </test>
1
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95 <test expect_num_outputs="1">
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96 <param name="input_table"
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97 value="edger_output.tabular"/>
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98 <param name="annotation"
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99 value="annotation.gtf"/>
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100 <param name="mode"
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101 value="degseq"/>
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102 <output name="output">
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103 <assert_contents>
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104 <has_text_matching expression="FBgn0039155\t-4.40480020002641\t5.8344799947229\t573.433304439283\t1.62187751744916e-36\t2.54342832286378e-32\tchr3R\t24141394\t24147490\t\+\tprotein_coding\tKal1"/>
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105 </assert_contents>
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106 </output>
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107 </test>
0
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108 </tests>
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109
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110 <help>
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111 <![CDATA[
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112
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113 **What it does**
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114
1
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115 This tool appends the output table of DESeq2/edgeR/limma/DEXSeq with gene symbols, biotypes, positions etc. The information
0
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116 you want to add is configurable. This information should present in the input GTF/GFF file as attributes of feature
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117 you choose.
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118 DEXSeq-Count tool is used to prepare the DEXSeq compatible annotation (flattened GTF file) from input GTF/GFF. In
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119 this process, the exons that appear multiple times, once for each transcript are collapsed to so called
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120 *exon counting bins*. Counting bins for parts of exons arise when an exonic region appears with different
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121 boundaries in different transcripts. The resulting flattened GTF file contains pseudo exon ids per gene instead
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122 of per transcript. This tool maps the DEXSeq couting bins back to the original exon ids. This mapping is only
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123 possible if the input GTF/GFF file contains transcript identifier attribute for the chosen features type.
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124
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125 **Inputs**
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126
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127 **Differential gene expression tables**
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128 At the moment, this tool supports DESeq2 and DEXSeq tool outputs.
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129
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130 **Annotation**
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131 Annotation file ne GTF or GFF3 format that was used for counting.
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132
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133 **Outputs**
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134 Input tabular file and with chosen attributes appended as additional columns.
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135
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136 ]]>
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137 </help>
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138 </tool>