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comparison deseq2.xml @ 6:982bd8bfa44c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
author iuc
date Sat, 05 Sep 2015 04:37:45 -0400
parents 4ba2afa87fce
children 681fd2c5f47a
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5:4ba2afa87fce 6:982bd8bfa44c
4 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> 4 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
5 <requirement type="package" version="3.2.1">R</requirement> 5 <requirement type="package" version="3.2.1">R</requirement>
6 <requirement type="package" version="3.10.2">atlas</requirement> 6 <requirement type="package" version="3.10.2">atlas</requirement>
7 <requirement type="package" version="1.8.1">deseq2</requirement> 7 <requirement type="package" version="1.8.1">deseq2</requirement>
8 </requirements> 8 </requirements>
9 <stdio>
10 <regex match="Execution halted"
11 source="both"
12 level="fatal"
13 description="Execution halted." />
14 <regex match="Error in"
15 source="both"
16 level="fatal"
17 description="An undefined error occured, please check your intput carefully and contact your administrator." />
18 <regex match="Fatal error"
19 source="both"
20 level="fatal"
21 description="An undefined error occured, please check your intput carefully and contact your administrator." />
22 </stdio>
9 <version_command> 23 <version_command>
10 <![CDATA[ 24 <![CDATA[
11 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2) ; 25 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
12 cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
13 ]]> 26 ]]>
14 </version_command> 27 </version_command>
15 <command interpreter="Rscript"> 28 <command interpreter="Rscript">
16 <![CDATA[ 29 <![CDATA[
17 #import json 30 #import json
18 \$DESEQ2_ROOT_PATH/inst/script/deseq2.R 31 \$DESEQ2_ROOT_PATH/script/deseq2.R
19 -o "$deseq_out" 32 -o "$deseq_out"
20 #if $pdf: 33 #if $pdf:
21 -p "$plots" 34 -p "$plots"
22 #end if 35 #end if
23 #set $temp_factor_names = list() 36 #set $temp_factor_names = list()
43 #if $many_contrasts: 56 #if $many_contrasts:
44 -m 57 -m
45 #end if 58 #end if
46 ]]> 59 ]]>
47 </command> 60 </command>
48 <stdio>
49 <regex match="Execution halted"
50 source="both"
51 level="fatal"
52 description="Execution halted." />
53 <regex match="Error in"
54 source="both"
55 level="fatal"
56 description="An undefined error occured, please check your intput carefully and contact your administrator." />
57 </stdio>
58 <inputs> 61 <inputs>
59 <repeat name="rep_factorName" title="Factor" min="1"> 62 <repeat name="rep_factorName" title="Factor" min="1">
60 <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 63 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
61 help="Only letters, numbers and underscores will be retained in this field"> 64 help="Only letters, numbers and underscores will be retained in this field">
62 <sanitizer> 65 <sanitizer>
68 help="Only letters, numbers and underscores will be retained in this field"> 71 help="Only letters, numbers and underscores will be retained in this field">
69 <sanitizer> 72 <sanitizer>
70 <valid initial="string.letters,string.digits"><add value="_" /></valid> 73 <valid initial="string.letters,string.digits"><add value="_" /></valid>
71 </sanitizer> 74 </sanitizer>
72 </param> 75 </param>
73 <param name="countsFile" type="data" multiple="true" label="Counts file(s)"/> 76 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
74 </repeat> 77 </repeat>
75 </repeat> 78 </repeat>
76 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true" 79 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
77 label="Visualising the analysis results" 80 label="Visualising the analysis results"
78 help="output an additional PDF files" /> 81 help="output an additional PDF files" />