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comparison deseq2.xml @ 3:248e9c78346e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit f33b04533bca91242b8a0a4077e1d593f5a874e0
author iuc
date Tue, 19 Apr 2016 18:10:31 -0400
parents afe2a77c5900
children 8702e49e68b6
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2:afe2a77c5900 3:248e9c78346e
57 #end if 57 #end if
58 ]]> 58 ]]>
59 </command> 59 </command>
60 <inputs> 60 <inputs>
61 <repeat name="rep_factorName" title="Factor" min="1"> 61 <repeat name="rep_factorName" title="Factor" min="1">
62 <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 62 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
63 help="Only letters, numbers and underscores will be retained in this field"> 63 help="Only letters, numbers and underscores will be retained in this field">
64 <sanitizer> 64 <sanitizer>
65 <valid initial="string.letters,string.digits"><add value="_" /></valid> 65 <valid initial="string.letters,string.digits"><add value="_" /></valid>
66 </sanitizer> 66 </sanitizer>
67 </param> 67 </param>
103 <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}"> 103 <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}">
104 <filter>many_contrasts is False</filter> 104 <filter>many_contrasts is False</filter>
105 </data> 105 </data>
106 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}"> 106 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
107 <filter>many_contrasts is True</filter> 107 <filter>many_contrasts is True</filter>
108 <discover_datasets pattern="vs" visible="true"/> 108 <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
109 </collection> 109 </collection>
110 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}"> 110 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
111 <filter>pdf == True</filter> 111 <filter>pdf == True</filter>
112 </data> 112 </data>
113 </outputs> 113 </outputs>
131 </tests> 131 </tests>
132 <help> 132 <help>
133 <![CDATA[ 133 <![CDATA[
134 .. class:: infomark 134 .. class:: infomark
135 135
136 **What it does** 136 **What it does**
137 137
138 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution 138 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution
139 139
140 140
141 **Inputs** 141 **Inputs**
143 DESeq2_ takes count tables that generated from the htseq-count as input. Count tables must be generated for each sample individually. DESeq2 is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. You also input several secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level. 143 DESeq2_ takes count tables that generated from the htseq-count as input. Count tables must be generated for each sample individually. DESeq2 is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. You also input several secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.
144 144
145 The following table gives some examples of factors and their levels: 145 The following table gives some examples of factors and their levels:
146 146
147 ========= ============== =============== 147 ========= ============== ===============
148 Factor Factor level 1 Factor level 2 148 Factor Factor level 1 Factor level 2
149 --------- -------------- --------------- 149 --------- -------------- ---------------
150 Treatment Treated Untreated 150 Treatment Treated Untreated
151 --------- -------------- --------------- 151 --------- -------------- ---------------
152 Condition Knockdown Wildtype 152 Condition Knockdown Wildtype
153 --------- -------------- --------------- 153 --------- -------------- ---------------