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comparison dexseq.xml @ 3:a26a82bed63f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
author iuc
date Fri, 25 Sep 2015 16:26:39 -0400
parents b19cb9385f28
children 7069d55968fb
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2:b19cb9385f28 3:a26a82bed63f
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="1.14">dexseq</requirement>
5 </requirements> 5 </requirements>
6 <code file="dexseq_helper.py" /> 6 <code file="dexseq_helper.py" />
7 <stdio>
8 <regex match="Execution halted"
9 source="both"
10 level="fatal"
11 description="Execution halted." />
12 <regex match="Input-Error 01"
13 source="both"
14 level="fatal"
15 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
16 <regex match="Error in"
17 source="both"
18 level="fatal"
19 description="An undefined error occured, please check your intput carefully and contact your administrator." />
20 </stdio>
7 <command> 21 <command>
8 <![CDATA[ 22 <![CDATA[
9 mkdir ./html_out && 23 mkdir ./html_out &&
10 #import json 24 #import json
11 Rscript $__tool_directory__/dexseq.R 25 Rscript $__tool_directory__/dexseq.R
36 && 50 &&
37 cp -r ./html_out/* $htmlreport.extra_files_path 51 cp -r ./html_out/* $htmlreport.extra_files_path
38 && 52 &&
39 ]]> 53 ]]>
40 </command> 54 </command>
41 <stdio>
42 <regex match="Execution halted"
43 source="both"
44 level="fatal"
45 description="Execution halted." />
46 <regex match="Input-Error 01"
47 source="both"
48 level="fatal"
49 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
50 <regex match="Error in"
51 source="both"
52 level="fatal"
53 description="An undefined error occured, please check your intput carefully and contact your administrator." />
54 </stdio>
55 <inputs> 55 <inputs>
56 <param name="gtf" type="data" label="GTF file created from DEXSeq-Count tool"/> 56 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
57 <repeat name="rep_factorName" title="Factor" min="1"> 57 <repeat name="rep_factorName" title="Factor" min="1">
58 <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 58 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
59 help="Only letters, numbers and underscores will be retained in this field"> 59 help="Only letters, numbers and underscores will be retained in this field">
60 <sanitizer> 60 <sanitizer>
61 <valid initial="string.letters,string.digits"><add value="_" /></valid> 61 <valid initial="string.letters,string.digits"><add value="_" /></valid>
66 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">
67 <sanitizer> 67 <sanitizer>
68 <valid initial="string.letters,string.digits"><add value="_" /></valid> 68 <valid initial="string.letters,string.digits"><add value="_" /></valid>
69 </sanitizer> 69 </sanitizer>
70 </param> 70 </param>
71 <param name="countsFile" type="data" multiple="true" label="Counts file"/> 71 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file"/>
72 </repeat> 72 </repeat>
73 </repeat> 73 </repeat>
74 <param name="report" type="boolean" truevalue="" falsevalue="" checked="true" 74 <param name="report" type="boolean" truevalue="" falsevalue="" checked="true"
75 label="Visualise the analysis results?" 75 label="Visualise the analysis results?"
76 help="output an additional html file" /> 76 help="output an additional html file" />
77 <param name="fdr_cutoff" type="float" min="0" max="1" value="0.05" label="All the genes under this FDR threshold will be shown in the html report."/> 77 <param name="fdr_cutoff" type="float" min="0" max="1" value="0.05" label="All the genes under this FDR threshold will be shown in the html report."/>
78 </inputs> 78 </inputs>
79
80 <outputs> 79 <outputs>
81 <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}"/> 80 <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}"/>
82 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}"> 81 <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
83 <filter>report == True</filter> 82 <filter>report == True</filter>
84 </data> 83 </data>
85 </outputs> 84 </outputs>
86
87 <code file="dexseq_helper.py" />
88 <tests> 85 <tests>
89 <test> 86 <test>
90 <param name="gtf" value="dexseq.gtf" ftype="bed"/> 87 <param name="gtf" value="dexseq.gtf" ftype="bed"/>
91 <repeat name="rep_factorName"> 88 <repeat name="rep_factorName">
92 <param name="factorName" value="condition" ftype="bed"/> 89 <param name="factorName" value="condition" ftype="bed"/>