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comparison dexseq.xml @ 1:f1c406f9554c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 93f63600a8d492e6c9006c1426fbae84de5ca232
author iuc
date Sun, 29 Jan 2017 06:59:35 -0500
parents 4ca0e679f21e
children 6e8b61c54ff3
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0:4ca0e679f21e 1:f1c406f9554c
1 <tool id="dexseq" name="DEXSeq" version="1.0"> 1 <tool id="dexseq" name="DEXSeq" version="1.20.1">
2 <description>Determines differential exon usage from count tables</description> 2 <description>Determines differential exon usage from count tables</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.14">dexseq</requirement> 4 <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement>
5 <requirement type="package" version="1.20.0">r-getopt</requirement>
6 <requirement type="package" version="0.2.15">r-rjson</requirement>
5 </requirements> 7 </requirements>
6 <code file="dexseq_helper.py" /> 8 <code file="dexseq_helper.py" />
7 <stdio> 9 <stdio>
8 <regex match="Execution halted" 10 <regex match="Execution halted"
9 source="both" 11 source="both"
10 level="fatal" 12 level="fatal"
11 description="Execution halted." /> 13 description="Execution halted." />
12 <regex match="Input-Error 01" 14 <regex match="Input-Error 01"
13 source="both" 15 source="both"
14 level="fatal" 16 level="fatal"
15 description="Error in your input parameters: Make sure you only apply factors to selected samples." /> 17 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
16 <regex match="Error in" 18 <regex match="Error in"
17 source="both" 19 source="both"
18 level="fatal" 20 level="fatal"
19 description="An undefined error occured, please check your input carefully and contact your administrator." /> 21 description="An undefined error occured, please check your input carefully and contact your administrator." />
29 </version_command> 31 </version_command>
30 <command> 32 <command>
31 <![CDATA[ 33 <![CDATA[
32 mkdir ./html_out && 34 mkdir ./html_out &&
33 #import json 35 #import json
34 Rscript $__tool_directory__/dexseq.R 36 Rscript '$__tool_directory__/dexseq.R'
35 -o "$dexseq_out" 37 -o '$dexseq_out'
36 -p \${GALAXY_SLOTS:-4} 38 -p \${GALAXY_SLOTS:-4}
37 #set $temp_factor_names = list() 39 #set $temp_factor_names = list()
38 #for $factor in $rep_factorName: 40 #for $factor in $rep_factorName:
39 #set $temp_factor = list() 41 #set $temp_factor = list()
40 #set $count_files1 = list() 42 #set $count_files1 = list()
55 -c $fdr_cutoff 57 -c $fdr_cutoff
56 58
57 #if $report: 59 #if $report:
58 -r ./html_out 60 -r ./html_out
59 && 61 &&
60 mkdir $htmlreport.extra_files_path 62 mkdir '$htmlreport.extra_files_path'
61 && 63 &&
62 cp ./html_out/testForDEU.html $htmlreport 64 cp ./html_out/testForDEU.html $htmlreport
63 && 65 &&
64 cp -r ./html_out/* $htmlreport.extra_files_path 66 cp -r ./html_out/* '$htmlreport.extra_files_path'
65 #end if 67 #end if
66 68
67 ]]> 69 ]]>
68 </command> 70 </command>
69 <inputs> 71 <inputs>
70 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/> 72 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
71 <repeat name="rep_factorName" title="Factor" min="1"> 73 <repeat name="rep_factorName" title="Factor" min="1">
72 <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 74 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
73 help="Only letters, numbers and underscores will be retained in this field"> 75 help="Only letters, numbers and underscores will be retained in this field">
74 <sanitizer> 76 <sanitizer>
75 <valid initial="string.letters,string.digits"><add value="_" /></valid> 77 <valid initial="string.letters,string.digits"><add value="_" /></valid>
76 </sanitizer> 78 </sanitizer>
77 </param> 79 </param>
126 </tests> 128 </tests>
127 <help> 129 <help>
128 <![CDATA[ 130 <![CDATA[
129 .. class:: infomark 131 .. class:: infomark
130 132
131 **What it does** 133 **What it does**
132 134
133 Inference of differential exon usage in RNA-Seq. 135 Inference of differential exon usage in RNA-Seq.
134 136
135 137
136 **Inputs** 138 **Inputs**
142 You need to select appropriate count table from your history for each factor level. 144 You need to select appropriate count table from your history for each factor level.
143 145
144 The following table gives some examples of factors and their levels: 146 The following table gives some examples of factors and their levels:
145 147
146 ========= ============== =============== 148 ========= ============== ===============
147 Factor Factor level 1 Factor level 2 149 Factor Factor level 1 Factor level 2
148 --------- -------------- --------------- 150 --------- -------------- ---------------
149 condition Knockdown Wildtype 151 condition Knockdown Wildtype
150 --------- -------------- --------------- 152 --------- -------------- ---------------
151 treatment Treated Untreated 153 treatment Treated Untreated
152 --------- -------------- --------------- 154 --------- -------------- ---------------