Mercurial > repos > iuc > masigpro
diff masigpro.xml @ 2:db04ba860dab draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231
author | iuc |
---|---|
date | Thu, 13 Jul 2017 18:23:17 -0400 |
parents | cc96abdef027 |
children | 83f8b5ceff43 |
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--- a/masigpro.xml Thu Jun 01 11:10:22 2017 -0400 +++ b/masigpro.xml Thu Jul 13 18:23:17 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="masigpro" name="maSigPro" version="1.49.3.0"> +<tool id="masigpro" name="maSigPro" version="1.49.3.1"> <description>Significant Gene Expression Profile Differences in Time Course Gene Expression Data</description> <requirements> <requirement type="package" version="1.49.3">bioconductor-masigpro</requirement> @@ -70,6 +70,7 @@ #if $pdf.pdf_selector: --cluster_data $pdf.seeGenes.clusterData -k $pdf.seeGenes.k + --print_cluster $pdf.seeGenes.print_cluster --cluster_method $pdf.seeGenes.clustering.clusterMethod #if str($pdf.seeGenes.clustering.clusterMethod) == "hclust": --distance $pdf.seeGenes.clustering.distance @@ -277,6 +278,9 @@ ‘c(sig.profiles,coefficients,t.score)’ of their list position (1,2 or 3)." /> <param name="k" type="integer" label="Number of clusters for data partioning" value="9" /> + <param name="print_cluster" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" + label="Add cluster information to summary file?" + help="Adds columns with the cluster assignment for each gene." /> <conditional name="clustering"> <param name="clusterMethod" label="Cluster Method" type="select" help="clustering method for data partioning. Currently @@ -313,6 +317,8 @@ <param name="iterMax" type="integer" label="Maximum number of iterations" value="500" help="Maximum number of iterations when ‘cluster.method’ is ‘kmeans’" /> </when> + <when value="Mclust"> + </when> </conditional> <param name="colorMode" label="Color Mode" type="select" help="Color scale for plotting profiles. Can be either ‘rainbow’ or ‘gray’"> <option selected="True" value="rainbow">Rainbow</option> @@ -328,10 +334,18 @@ help="Indicating whether legend must be added when plotting profiles" /> </section> </when> + <when value="0"> + </when> </conditional> </inputs> <outputs> - <data format="tabular" name="masigpro_out" label="maSigPro result file on ${on_string}"> + <data format="txt" name="data_out" label="maSigPro data file on ${on_string}"> + <filter> + (( + source['source_selector'] == 'advanced' and + source['enable_output'] == True + )) + </filter> </data> <data format="txt" name="edesign_out" label="maSigPro edesign file on ${on_string}"> <filter> @@ -341,14 +355,6 @@ )) </filter> </data> - <data format="txt" name="data_out" label="maSigPro data file on ${on_string}"> - <filter> - (( - source['source_selector'] == 'advanced' and - source['enable_output'] == True - )) - </filter> - </data> <data format="pdf" name="pdf_out" from_work_dir="Results.pdf" label="maSigPro Plot file on ${on_string}"> <filter> (( @@ -356,6 +362,8 @@ )) </filter> </data> + <data format="tabular" name="masigpro_out" label="maSigPro result file on ${on_string}"> + </data> </outputs> <tests> <test> @@ -397,6 +405,14 @@ <output name="masigpro_out" file="masigpro_out.tab" /> <output name="pdf_out" file="Results.pdf" /> </test> + <test> + <param name="source_selector" value="defaults" /> + <param name="edesign" value="edesign_out.txt" /> + <param name="data" value="data_out.txt" /> + <param name="print_cluster" value="FALSE" /> + <output name="masigpro_out" file="masigpro_out_no_cluster.tab" /> + <output name="pdf_out" file="Results.pdf" /> + </test> </tests> <help> <![CDATA[