Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts

diff hicPlotDistVsCounts.xml @ 20:6326cd29c1c3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:16:53 +0000
parents e2971589184b
children 11f39d7f6c64
line wrap: on
line diff
--- a/hicPlotDistVsCounts.xml	Tue Jan 10 18:59:41 2023 +0000
+++ b/hicPlotDistVsCounts.xml	Wed Oct 18 10:16:53 2023 +0000
@@ -30,7 +30,9 @@
             #if $chromosomeExclude:
                 --chromosomeExclude '$chroms'
             #end if
-
+            #if $domains:
+                --domains '$domains'
+            #end if
             #if $outFileData_Boolean:
                 $outFileData_Boolean ./outFileData
             #end if
@@ -50,7 +52,9 @@
                 <validator type="empty_field" />
             </param>
         </repeat>
-        <param name='outFileData_Boolean' type='boolean' truevalue='--outFileData' falsevalue="" checked="false" label="Save data underlying the plots as BAM" help="A bam file containing all data underlying the plots is saved on this file." />
+        <param argument="--domains" type="data" format="bed" optional="True" label="Bed file with domains coordinates" help="Bed file with domains coordinates: instead of evaluating the distance vs. Hi-C counts for intra chromosomal counts, compute it for intra-domains." />
+
+        <param name="outFileData_Boolean" type="boolean" truevalue="--outFileData" falsevalue="" checked="false" label="Save data underlying the plots as BAM" help="A bam file containing all data underlying the plots is saved on this file." />
     </inputs>
     <outputs>
         <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot" />
@@ -59,19 +63,19 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrices" ftype="h5" value="small_test_matrix.h5" />
             <param name="skipDiagonal" value="False" />
             <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="matrices" ftype="h5" value="small_test_matrix.h5" />
             <param name="skipDiagonal" value="False" />
-            <param name='outFileData_Boolean' value='True' />
+            <param name="outFileData_Boolean" value="True" />
             <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size" />
             <output name="outFileData" file="distVsCounts.txt" ftype="txt" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="matrices" ftype="h5" value="small_test_matrix.h5,small_test_matrix.h5" />
             <param name="skipDiagonal" value="False" />
             <param name="perchr" value="True" />