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comparison edger.xml @ 6:555659de7321 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629
author iuc
date Sat, 09 Feb 2019 07:20:20 -0500
parents fb9b9f0f2f06
children 334ce9b1bac5
comparison
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5:fb9b9f0f2f06 6:555659de7321
111 <option value="matrix">Single Count Matrix</option> 111 <option value="matrix">Single Count Matrix</option>
112 </param> 112 </param>
113 113
114 <when value="files"> 114 <when value="files">
115 <repeat name="rep_factor" title="Factor" min="1"> 115 <repeat name="rep_factor" title="Factor" min="1">
116 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Optional additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section for more information. NOTE: Please only use letters, numbers or underscores."> 116 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Optional additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section for more information. NOTE: Please only use letters, numbers or underscores, and the first character of each factor must be a letter">
117 <sanitizer> 117 <sanitizer>
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 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), and the first character of each group must be a letter">
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 files"/> 128 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
133 <when value="matrix"> 133 <when value="matrix">
134 <param name="counts" type="data" format="tabular" label="Count Matrix"/> 134 <param name="counts" type="data" format="tabular" label="Count Matrix"/>
135 135
136 <conditional name="fact"> 136 <conditional name="fact">
137 <param name="ffile" type="select" label="Input factor information from file?" 137 <param name="ffile" type="select" label="Input factor information from file?"
138 help="You can choose to input the factor and group information for the samples from a file or manually enter below."> 138 help="You can choose to input the factor and group information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), and the first character of each sample, factor and group must be a letter">
139 <option value="no">No</option> 139 <option value="no">No</option>
140 <option value="yes">Yes</option> 140 <option value="yes">Yes</option>
141 </param> 141 </param>
142 <when value="yes"> 142 <when value="yes">
143 <param name="finfo" type="data" format="tabular" label="Factor File"/> 143 <param name="finfo" type="data" format="tabular" label="Factor File"/>
144 </when> 144 </when>
145 <when value="no" > 145 <when value="no" >
146 <repeat name="rep_factor" title="Factor" min="1"> 146 <repeat name="rep_factor" title="Factor" min="1">
147 <param name="factorName" type="text" label="Factor Name" 147 <param name="factorName" type="text" label="Factor Name"
148 help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section below. NOTE: Please only use letters, numbers or underscores."> 148 help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section below. NOTE: Please only use letters, numbers or underscores, and the first character of each factor must be a letter">
149 <validator type="empty_field" /> 149 <validator type="empty_field" />
150 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator> 150 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
151 </param> 151 </param>
152 <param name="groupNames" type="text" label="Groups" 152 <param name="groupNames" type="text" label="Groups"
153 help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive)."> 153 help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive), and the first character of each group must be a letter">
154 <validator type="empty_field" /> 154 <validator type="empty_field" />
155 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator> 155 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
156 </param> 156 </param>
157 </repeat> 157 </repeat>
158 </when> 158 </when>
633 633
634 **Inputs** 634 **Inputs**
635 635
636 **Counts Data:** 636 **Counts Data:**
637 637
638 The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels and the first column containing the row/gene labels. Gene identifiers can be of any type but must be unique and not repeated within a counts file. 638 The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels and the first column containing the row/gene labels. The sample labels must start with a letter. Gene identifiers can be of any type but must be unique and not repeated within a counts file.
639 639
640 Example - **Separate Count Files**: 640 Example - **Separate Count Files**:
641 641
642 ========== ======= 642 ========== =======
643 **GeneID** **WT1** 643 **GeneID** **WT1**
696 Mut1 Mut b1 696 Mut1 Mut b1
697 Mut2 Mut b2 697 Mut2 Mut b2
698 Mut3 Mut b3 698 Mut3 Mut b3
699 ========== ============ ========= 699 ========== ============ =========
700 700
701 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, an additive linear model will be used. 701 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered, the name should start with a letter and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, an additive linear model will be used.
702 702
703 *Groups:* The names of the groups for the factor. These must be entered in the same order as the samples (to which the groups correspond) are listed in the columns of the counts matrix. Spaces must not be used and if entered into the tool form above, the values should be separated by commas. 703 *Groups:* The names of the groups for the factor. The names should start with a letter, and only contain letters, numbers and underscores, other characters such as spaces and hyphens must not be used. If entered into the tool form above, the order must be the same as the samples (to which the groups correspond) are listed in the columns of the counts matrix, with the values separated by commas.
704
705 704
706 **Contrasts of Interest:** 705 **Contrasts of Interest:**
707 The contrasts you wish to make between levels. 706 The contrasts you wish to make between levels.
708 A common contrast would be a simple difference between two levels: "Mut-WT" 707 A common contrast would be a simple difference between two levels: "Mut-WT"
709 represents the difference between the mutant and wild type genotypes. 708 represents the difference between the mutant and wild type genotypes.