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comparison edger.xml @ 3:d79ed3ec25fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
author iuc
date Sun, 06 May 2018 13:38:41 -0400
parents a1634a9c2ee1
children 4730985c816f
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2:a1634a9c2ee1 3:d79ed3ec25fe
1 <tool id="edger" name="edgeR" version="3.20.7.1"> 1 <tool id="edger" name="edgeR" version="3.20.7.2">
2 <description> 2 <description>
3 Perform differential expression of count data 3 Perform differential expression of count data
4 </description> 4 </description>
5 5
6 <requirements> 6 <requirements>
118 <valid initial="string.letters,string.digits"><add value="_" /></valid> 118 <valid initial="string.letters,string.digits"><add value="_" /></valid>
119 </sanitizer> 119 </sanitizer>
120 </param> 120 </param>
121 <repeat name="rep_group" title="Group" min="2" default="2"> 121 <repeat name="rep_group" title="Group" min="2" default="2">
122 <param name="groupName" type="text" label="Name" 122 <param name="groupName" type="text" label="Name"
123 help="Name of group that the counts files(s) belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive)."> 123 help="Name of group that the counts files belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive).">
124 <sanitizer> 124 <sanitizer>
125 <valid initial="string.letters,string.digits"><add value="_" /></valid> 125 <valid initial="string.letters,string.digits"><add value="_" /></valid>
126 </sanitizer> 126 </sanitizer>
127 </param> 127 </param>
128 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> 128 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
129 </repeat> 129 </repeat>
130 </repeat> 130 </repeat>
131 </when> 131 </when>
132 132
133 <when value="matrix"> 133 <when value="matrix">
681 681
682 682
683 **Gene Annotations:** 683 **Gene Annotations:**
684 Optional input for gene annotations, this can contain more 684 Optional input for gene annotations, this can contain more
685 information about the genes than just an ID number. The annotations will 685 information about the genes than just an ID number. The annotations will
686 be available in the differential expression results table and the optional normalised counts table. 686 be available in the differential expression results table and the optional normalised counts table. The file must contain a header row and have the gene IDs in the first column. The number of rows should match that of the counts files, add NA for any gene IDs with no annotation. The Galaxy tool **annotateMyIDs** can be used to obtain annotations for human, mouse, fly and zebrafish.
687 687
688 Example: 688 Example:
689 689
690 ========== ========== =================================================== 690 ========== ========== ===================================================
691 **GeneID** **Symbol** **GeneName** 691 **GeneID** **Symbol** **GeneName**
692 ---------- ---------- --------------------------------------------------- 692 ---------- ---------- ---------------------------------------------------
693 1287 Pzp pregnancy zone protein 693 11287 Pzp pregnancy zone protein
694 1298 Aanat arylalkylamine N-acetyltransferase 694 11298 Aanat arylalkylamine N-acetyltransferase
695 1302 Aatk apoptosis-associated tyrosine kinase 695 11302 Aatk apoptosis-associated tyrosine kinase
696 1303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1 696 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
697 1304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4 697 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
698 1305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2 698 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
699 ========== ========== =================================================== 699 ========== ========== ===================================================
700 700
701 **Contrasts of Interest:** 701 **Contrasts of Interest:**
702 The contrasts you wish to make between levels. 702 The contrasts you wish to make between levels.
703 A common contrast would be a simple difference between two levels: "Mut-WT" 703 A common contrast would be a simple difference between two levels: "Mut-WT"