Mercurial > repos > mingchen0919 > rmarkdown_deseq2_count_matrix

comparison rmarkdown_deseq2_count_matrix.xml @ 1:629323b5fc0c draft

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update tool
author mingchen0919
date Sat, 30 Dec 2017 16:39:39 -0500
parents c1f718dd6c7a
children 8ceda5896765
comparison
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0:c1f718dd6c7a 1:629323b5fc0c
15 </stdio> 15 </stdio>
16 <command><![CDATA[ 16 <command><![CDATA[
17 Rscript '${__tool_directory__}/rmarkdown_deseq2_count_matrix_render.R' 17 Rscript '${__tool_directory__}/rmarkdown_deseq2_count_matrix_render.R'
18 -e $echo 18 -e $echo
19 -c $count_data 19 -c $count_data
20 -n '$count_matrix_column_names'
20 -C $col_data 21 -C $col_data
21 -D '$design_formula' 22 -D '$design_formula'
22 -k $contrast_condition 23 -k $contrast_condition
23 -T $treatment 24 -T $treatment
24 -k $control 25 -K $control
25 -r $report 26 -r $report
26 -d $report.files_path 27 -d $report.files_path
27 -s $sink_message 28 -s $sink_message
28 -t '${__tool_directory__}/rmarkdown_deseq2_count_matrix.Rmd' 29 -t '${__tool_directory__}/rmarkdown_deseq2_count_matrix.Rmd'
29 ]]></command> 30 ]]></command>
30 <inputs> 31 <inputs>
31 <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" 32 <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False"
32 truevalue="TRUE" falsevalue="FALSE"/> 33 truevalue="TRUE" falsevalue="FALSE"/>
33 <param type="data" name="count_data" label="count data" optional="False" format="txt,csv" multiple="False"/> 34 <param type="data" name="count_data" label="count data" optional="False" format="txt,csv" multiple="False"/>
34 <param type="data" name="col_data" label="column data" optional="False" format="txt,csv" multiple="False"/> 35 <param type="text" name="count_matrix_column_names" label="column names"
36 help="This field is used to update the column names of count data matrix. Column names are separated by comma (,). For example, 'column_1, column_2, column_3, column_4'"
37 optional="True" area="True" size="5x25"></param>
38 <param type="data" name="col_data" label="column data (from file)" optional="False" format="txt,csv" multiple="False"/>
35 <param type="text" name="design_formula" label="design formula" 39 <param type="text" name="design_formula" label="design formula"
36 help="The simplest design formula for differential expression would be ~ condition, where condition&#13;&#10; is a column in colData(dds) that specifies which of two (or more groups) the samples belong to" 40 help="The simplest design formula for differential expression would be ~ condition, where condition&#13;&#10; is a column in colData(dds) that specifies which of two (or more groups) the samples belong to"
37 optional="False" value="~ condition_1 + condition_2"/> 41 optional="False" value="~ condition_1 + condition_2">
42 <sanitizer>
43 <valid>
44 <add value="~"/>
45 </valid>
46 </sanitizer>
47 </param>
38 <param type="text" name="contrast_condition" label="condition" 48 <param type="text" name="contrast_condition" label="condition"
39 help="A condition name specified in the design formula" optional="False" value="condition_1"/> 49 help="A condition name specified in the design formula" optional="False" value="condition_1"/>
40 <param type="text" name="treatment" label="treatment" help="the name of the numerator level for the fold change" 50 <param type="text" name="treatment" label="treatment" help="the name of the numerator level for the fold change"
41 optional="False"/> 51 optional="False" value="treated"/>
42 <param type="text" name="control" label="control" help="the name of the denominator level for the fold change" 52 <param type="text" name="control" label="control" help="the name of the denominator level for the fold change"
43 optional="False"/> 53 optional="False" value="untreated"/>
44 </inputs> 54 </inputs>
45 <outputs> 55 <outputs>
46 <data name="report" format="html" label="DESeq2 report" hidden="false"/> 56 <data name="report" format="html" label="DESeq2 report" hidden="false"/>
47 <data name="differential_genes" format="csv" label="differential genes" from_work_dir="differential_genes.csv" 57 <data name="differential_genes" format="csv" label="differential genes" from_work_dir="differential_genes.csv"
58 hidden="false"/>
59 <data name="deseq2" format="rdata" label="DESeq2 R objects" from_work_dir="deseq2.RData"
48 hidden="false"/> 60 hidden="false"/>
49 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" 61 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"
50 hidden="false"/> 62 hidden="false"/>
51 </outputs> 63 </outputs>
52 <help><![CDATA[See http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html]]></help> 64 <help><![CDATA[See http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html]]></help>