diff rmarkdown_deseq2_count_matrix.xml @ 0:c1f718dd6c7a draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmarkdown_deseq2_count_matrix.xml	Sat Dec 30 00:25:38 2017 -0500
@@ -0,0 +1,73 @@
+<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_matrix_render.R'
+                        -e $echo
+                        -c $count_data
+                        -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_data" label="count data" optional="False" format="txt,csv" multiple="False"/>
+        <param type="data" name="col_data" label="column data" 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"/>
+        <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"/>
+        <param type="text" name="control" label="control" help="the name of the denominator level for the fold change"
+               optional="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}
+            }]]></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>
+    </citations>
+</tool>