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comparison deg_annotate.xml @ 1:1d7756a90af9 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 07:46:46 -0500
parents c88e2de781b3
children
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0:c88e2de781b3 1:1d7756a90af9
1 <tool id="deg_annotate" name="Annotate DESeq2/DEXSeq output tables" version="1.0"> 1 <tool id="deg_annotate" name="Annotate DESeq2/DEXSeq output tables" version="1.1.0">
2 <description>Append useful information from annotation files to DESeq2/DEXSeq outputs</description> 2 <description>Append annotation from GTF to differential expression tool outputs</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.27.0">bedtools</requirement> 4 <requirement type="package" version="2.27.0">bedtools</requirement>
5 <requirement type="package" version="0.6.4">bcbiogff</requirement> 5 <requirement type="package" version="0.6.4">bcbiogff</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command>
19 <inputs> 19 <inputs>
20 <param name="input_table" 20 <param name="input_table"
21 type="data" 21 type="data"
22 format="tabular" 22 format="tabular"
23 argument="-in" 23 argument="-in"
24 label="Tabular output of DESeq2 or DEXSeq"/> 24 label="Tabular output of DESeq2/edgeR/limma/DEXSeq"/>
25 25
26 <param name="mode" type="select" argument="-m" label="Input file type"> 26 <param name="mode" type="select" argument="-m" label="Input file type">
27 <option value="deseq2">DESeq2</option> 27 <option value="degseq">DESeq2/edgeR/limma</option>
28 <option value="dexseq">DEXseq</option> 28 <option value="dexseq">DEXseq</option>
29 </param> 29 </param>
30 30
31 <param name="annotation" 31 <param name="annotation"
32 type="data" 32 type="data"
90 <assert_contents> 90 <assert_contents>
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"/> 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"/>
92 </assert_contents> 92 </assert_contents>
93 </output> 93 </output>
94 </test> 94 </test>
95 <test expect_num_outputs="1">
96 <param name="input_table"
97 value="edger_output.tabular"/>
98 <param name="annotation"
99 value="annotation.gtf"/>
100 <param name="mode"
101 value="degseq"/>
102 <output name="output">
103 <assert_contents>
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"/>
105 </assert_contents>
106 </output>
107 </test>
95 </tests> 108 </tests>
96 109
97 <help> 110 <help>
98 <![CDATA[ 111 <![CDATA[
99 112
100 **What it does** 113 **What it does**
101 114
102 This tool appends the output table of DESeq2 or DEXSeq with gene symbols, biotypes, positions etc. The information 115 This tool appends the output table of DESeq2/edgeR/limma/DEXSeq with gene symbols, biotypes, positions etc. The information
103 you want to add is configurable. This information should present in the input GTF/GFF file as attributes of feature 116 you want to add is configurable. This information should present in the input GTF/GFF file as attributes of feature
104 you choose. 117 you choose.
105 DEXSeq-Count tool is used to prepare the DEXSeq compatible annotation (flattened GTF file) from input GTF/GFF. In 118 DEXSeq-Count tool is used to prepare the DEXSeq compatible annotation (flattened GTF file) from input GTF/GFF. In
106 this process, the exons that appear multiple times, once for each transcript are collapsed to so called 119 this process, the exons that appear multiple times, once for each transcript are collapsed to so called
107 *exon counting bins*. Counting bins for parts of exons arise when an exonic region appears with different 120 *exon counting bins*. Counting bins for parts of exons arise when an exonic region appears with different