diff rmarkdown_deseq2_count_matrix.xml @ 1:4a7131658ca6 draft

update tool

--- a/rmarkdown_deseq2_count_matrix.xml	Fri Dec 29 23:37:30 2017 -0500
+++ b/rmarkdown_deseq2_count_matrix.xml	Sat Dec 30 12:35:31 2017 -0500
@@ -1,54 +1,83 @@
 <tool id="rmarkdown_deseq2_count_matrix" name="DESeq2 (count matrix)" version="1.0.0">
-  <requirements>
-    <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
-    <requirement type="package" version="1.20.0">r-getopt</requirement>
-    <requirement type="package" version="1.3">r-rmarkdown</requirement>
-    <requirement type="package" version="0.3.5">r-htmltools</requirement>
-    <requirement type="package" version="0.5.0">r-dplyr</requirement>
-    <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
-    <requirement type="package" version="0.2">r-dt</requirement>
-  </requirements>
-  <description>deseq2 analysis given a count matrix input</description>
-  <stdio>
-    <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
-  </stdio>
-  <command><![CDATA[                    
-Rscript '${__tool_directory__}/rmarkdown_deseq2_count_matrx_render.R'
-                        -e $echo
-                        -c $count_matrix
-                        -r $report
-                        -d $report.files_path
-                        -s $sink_message
-                        -t '${__tool_directory__}/rmarkdown_deseq2_count_matrx.Rmd'
+    <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.3">r-rmarkdown</requirement>
+        <requirement type="package" version="0.3.5">r-htmltools</requirement>
+        <requirement type="package" version="0.5.0">r-dplyr</requirement>
+        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
+        <requirement type="package" version="0.2">r-dt</requirement>
+    </requirements>
+    <description>deseq2 analysis given a count matrix input</description>
+    <stdio>
+        <regex source="stderr" match="XXX" level="warning"
+               description="Check the warnings_and_errors.txt file for more details."/>
+    </stdio>
+    <command><![CDATA[
+Rscript '${__tool_directory__}/rmarkdown_deseq2_count_matrix_render.R'
+                        -e $echo
+                        -c $count_data
+                        -n '$count_matrix_column_names'
+                        -C $col_data
+                        -D '$design_formula'
+                        -k $contrast_condition
+                        -T $treatment
+                        -K $control
+                        -r $report
+                        -d $report.files_path
+                        -s $sink_message
+                        -t '${__tool_directory__}/rmarkdown_deseq2_count_matrix.Rmd'
                     ]]></command>
-  <inputs>
-    <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
-    <param type="data" name="count_matrix" label="count matrix" optional="False" format="txt,csv" multiple="False"/>
-  </inputs>
-  <outputs>
-    <data name="report" format="html" label="DESeq2 report" hidden="false"/>
-    <data name="differential_genes" format="csv" label="differential genes" from_work_dir="differential_genes.csv" hidden="false"/>
-    <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
-  </outputs>
-  <help><![CDATA[See http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html]]></help>
-  <citations>
-    <citation type="bibtex"><![CDATA[            @article{love2014moderated,
-            title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
-            author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
-            journal={Genome biology},
-            volume={15},
-            number={12},
-            pages={550},
-            year={2014},
-            publisher={BioMed Central}
+    <inputs>
+        <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False"
+               truevalue="TRUE" falsevalue="FALSE"/>
+        <param type="data" name="count_data" label="count data" optional="False" format="txt,csv" multiple="False"/>
+        <param type="text" name="count_matrix_column_names" label="column names"
+               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'"
+               optional="True" area="True" size="5x25"></param>
+        <param type="data" name="col_data" label="column data (from file)" optional="False" format="txt,csv" multiple="False"/>
+        <param type="text" name="design_formula" label="design formula"
+               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"
+               optional="False" value="~ condition_1 + condition_2">
+            <sanitizer>
+                <valid>
+                    <add value="~"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param type="text" name="contrast_condition" label="condition"
+               help="A condition name specified in the design formula" optional="False" value="condition_1"/>
+        <param type="text" name="treatment" label="treatment" help="the name of the numerator level for the fold change"
+               optional="False" value="treated"/>
+        <param type="text" name="control" label="control" help="the name of the denominator level for the fold change"
+               optional="False" value="untreated"/>
+    </inputs>
+    <outputs>
+        <data name="report" format="html" label="DESeq2 report" hidden="false"/>
+        <data name="differential_genes" format="csv" label="differential genes" from_work_dir="differential_genes.csv"
+              hidden="false"/>
+        <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"
+              hidden="false"/>
+    </outputs>
+    <help><![CDATA[See http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html]]></help>
+    <citations>
+        <citation type="bibtex"><![CDATA[            @article{love2014moderated,
+            title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
+            author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
+            journal={Genome biology},
+            volume={15},
+            number={12},
+            pages={550},
+            year={2014},
+            publisher={BioMed Central}
             }]]></citation>
-    <citation type="bibtex"><![CDATA[            @article{allaire2016rmarkdown,
-            title={rmarkdown: Dynamic Documents for R, 2016},
-            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
-            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
-            journal={R package version 0.9},
-            volume={6},
-            year={2016}
+        <citation type="bibtex"><![CDATA[            @article{allaire2016rmarkdown,
+            title={rmarkdown: Dynamic Documents for R, 2016},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
+            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
             }]]></citation>
-  </citations>
+    </citations>
 </tool>