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comparison deseq2.xml @ 15:d856341e03c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit dd85747b08272b72c7161de9b18d19598bb49de1
author iuc
date Tue, 31 May 2016 06:24:39 -0400
parents 0fb62f07f8b7
children a7bf54ecfa9d
comparison
equal deleted inserted replaced
14:0fb62f07f8b7 15:d856341e03c8
50 -a 50 -a
51 #end if 51 #end if
52 #if $outlier_filter_off: 52 #if $outlier_filter_off:
53 -b 53 -b
54 #end if 54 #end if
55 #if $auto_mean_filter_off:
56 -c
57 #end if
55 #if $many_contrasts: 58 #if $many_contrasts:
56 -m 59 -m
57 #end if 60 #end if
58 ]]> 61 ]]>
59 </command> 62 </command>
60 <inputs> 63 <inputs>
61 <repeat name="rep_factorName" title="Factor" min="1"> 64 <repeat name="rep_factorName" title="Factor" min="1">
62 <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 65 <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"> 66 help="Only letters, numbers and underscores will be retained in this field">
64 <sanitizer> 67 <sanitizer>
65 <valid initial="string.letters,string.digits"><add value="_" /></valid> 68 <valid initial="string.letters,string.digits"><add value="_" /></valid>
66 </sanitizer> 69 </sanitizer>
67 </param> 70 </param>
103 <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}"> 106 <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}">
104 <filter>many_contrasts is False</filter> 107 <filter>many_contrasts is False</filter>
105 </data> 108 </data>
106 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}"> 109 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
107 <filter>many_contrasts is True</filter> 110 <filter>many_contrasts is True</filter>
108 <discover_datasets pattern="vs" visible="true"/> 111 <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
109 </collection> 112 </collection>
110 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}"> 113 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
111 <filter>pdf == True</filter> 114 <filter>pdf == True</filter>
112 </data> 115 </data>
113 </outputs> 116 </outputs>
131 </tests> 134 </tests>
132 <help> 135 <help>
133 <![CDATA[ 136 <![CDATA[
134 .. class:: infomark 137 .. class:: infomark
135 138
136 **What it does** 139 **What it does**
137 140
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 141 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
139 142
140 143
141 **Inputs** 144 **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. 146 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.
144 147
145 The following table gives some examples of factors and their levels: 148 The following table gives some examples of factors and their levels:
146 149
147 ========= ============== =============== 150 ========= ============== ===============
148 Factor Factor level 1 Factor level 2 151 Factor Factor level 1 Factor level 2
149 --------- -------------- --------------- 152 --------- -------------- ---------------
150 Treatment Treated Untreated 153 Treatment Treated Untreated
151 --------- -------------- --------------- 154 --------- -------------- ---------------
152 Condition Knockdown Wildtype 155 Condition Knockdown Wildtype
153 --------- -------------- --------------- 156 --------- -------------- ---------------