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comparison metaquantome_sample.xml @ 8:a1df90e6e7d4 draft default tip

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planemo upload
author galaxyp
date Fri, 08 Feb 2019 10:36:53 -0500
parents 5bc492a15b8b
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7:23540bdd354c 8:a1df90e6e7d4
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool id="sample" name="metaQuantome: create samples file" version="@VERSION@.3"> 2 <tool id="sample" name="metaQuantome: create samples file" version="@VERSION@.3">
3 <description></description> 3 <description> by specifying the experiment's groups and associated column names</description>
4 <macros> 4 <macros>
5 <token name="@VERSION@">1.1.2</token> 5 <token name="@VERSION@">1.1.2</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@VERSION@">megahit</requirement> 8 <requirement type="package" version="@VERSION@">megahit</requirement>
75 <output name="samples_file" file="samples.tab" ftype="tabular" /> 75 <output name="samples_file" file="samples.tab" ftype="tabular" />
76 </test> 76 </test>
77 </tests> 77 </tests>
78 <help><![CDATA[ 78 <help><![CDATA[
79 metaQuantome: create samples file 79 metaQuantome: create samples file
80 =================== 80 =================================
81 81
82 The *create samples file* module is used to generate the *samples file* input file for the metaQuantome workflow. This input file is used to specify which column names are affilated with which experimental groups. 82 The *create samples file* module is used to generate the *samples file* input file for the metaQuantome workflow. This input file is used to specify the column names used for each experimental group. These column names are referenced when handling the input data and performing statistical analysis. An example file is shown below.
83 83
84 *Create samples file* 84 *Create samples file*
85
86 ===== ==================== 85 ===== ====================
87 group colnames 86 group colnames
88 ===== ==================== 87 ===== ====================
89 NS X737NS,X852NS,X867NS 88 NS X737NS,X852NS,X867NS
90 WS X737WS,X852WS,X867WS 89 WS X737WS,X852WS,X867WS
93 92
94 There are two methods for generating this input file: 93 There are two methods for generating this input file:
95 94
96 1. **Specify Samples** You may specify the samples by providing the group names (ex: NS *no sucrose* and WS *with sucrose*) and each of their affilated column names (ex: X737WS, X737NS, etc...) from the input files (e.g., peptide intensity *int.tab*). 95 1. **Specify Samples** You may specify the samples by providing the group names (ex: NS *no sucrose* and WS *with sucrose*) and each of their affilated column names (ex: X737WS, X737NS, etc...) from the input files (e.g., peptide intensity *int.tab*).
97 96
98 2. **Select samples from existing file's header** Alternatively, you can indicate the column indices of the selected headers for each experimental group (ex: columns 1, 3, and 5 for NS; columns 2, 4, and 6 for WS). You need to specify which file from the history you are referencing. An example is shown below.
99 97
100 *Example int.tab file* 98 2. **Select samples from existing file's header** Alternatively, you can indicate the column indices of the selected headers for each experimental group (ex: columns 3, 5, and 7 for NS; columns 2, 4, and 6 for WS). You need to specify which file from the history you are referencing. An example is shown below.
101 ============ ====== ====== ====== ====== ====== ====== 99
102 peptide X737WS X737NS X852WS X852NS X867WS X867NS 100 *int.tab file*
103 ============ ====== ====== ====== ====== ====== ====== 101 ============ ====== ====== ====== ====== ====== ======
104 LPGQQHGTPSAK 1 2 3 4 5 6 102 peptide X737WS X737NS X852WS X852NS X867WS X867NS
105 ELPGLAALTDK 7 8 9 10 11 12 103 ============ ====== ====== ====== ====== ====== ======
106 ============ ====== ====== ====== ====== ====== ====== 104 LPGQQHGTPSAK 1 2 3 4 5 6
105 ELPGLAALTDK 7 8 9 10 11 12
106 ============ ====== ====== ====== ====== ====== ======
107 107
108 108
109 Questions, Comments, Problems, Kudos 109 Questions, Comments, Problems, Kudos
110 ------------------------------------ 110 ------------------------------------
111 111