diff hicDifferentialTAD.xml @ 2:77d8e0fd162a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9

--- a/hicDifferentialTAD.xml	Thu Jan 12 17:40:56 2023 +0000
+++ b/hicDifferentialTAD.xml	Wed Oct 18 11:06:49 2023 +0000
@@ -30,11 +30,11 @@
 ]]>
     </command>
     <inputs>
-        <param name='matrix_h5_cooler_target' type="data" format="h5,cool" label="Target matrix to compute on" />
-        <param name='matrix_h5_cooler_control' type="data" format="h5,cool" label="Control matrix to compute on" />
+        <param name="matrix_h5_cooler_target" type="data" format="h5,cool" label="Target matrix to compute on" />
+        <param name="matrix_h5_cooler_control" type="data" format="h5,cool" label="Control matrix to compute on" />
 
-        <param argument="--tadDomains" type="data" format='bed' optional='false' label="TAD domains file" help= "The TADs domain file computed by hicFindTADs." />
-        <param argument="--pValue" type="float" label="P-value" min='0.0' max='1.0' help= "H0 is considered as \'two regions are identical.\' i.e. all regions with a test result of smaller p-value are rejected and considered as differential." value='0.05' />
+        <param argument="--tadDomains" type="data" format="bed" optional="false" label="TAD domains file" help= "The TADs domain file computed by hicFindTADs." />
+        <param argument="--pValue" type="float" label="P-value" min="0.0" max="1.0" help= "H0 is considered as \'two regions are identical.\' i.e. all regions with a test result of smaller p-value are rejected and considered as differential." value="0.05" />
         <param name="mode_selector" type="select" label="Method to compute the differentail TAD expression">
             <option value="intra-TAD">intra-TAD</option>
             <option value="left-inter-TAD">left-inter-TAD</option>
@@ -48,15 +48,15 @@
         </param>
     </inputs>
     <outputs>
-        <data name='acceptedTADs' from_work_dir='galaxy_differential_tad_accepted.diff_tad' format='txt' label='Accepted TADs' />
-        <data name='rejectedTADs' from_work_dir='galaxy_differential_tad_rejected.diff_tad' format='txt' label='Rejected TADs' />
+        <data name="acceptedTADs" from_work_dir="galaxy_differential_tad_accepted.diff_tad" format="txt" label="Accepted TADs" />
+        <data name="rejectedTADs" from_work_dir="galaxy_differential_tad_rejected.diff_tad" format="txt" label="Rejected TADs" />
     </outputs>
     <tests>
         <test>
             <param name="matrix_h5_cooler_target" value="small_test_matrix.cool" />
             <param name="matrix_h5_cooler_control" value="small_test_matrix.cool" />
 
-            <param name="tadDomains" ftype='bed' value="hicDifferentialTAD/multiNone_domains.bed" />
+            <param name="tadDomains" ftype="bed" value="hicDifferentialTAD/multiNone_domains.bed" />
             <param name="pValue" value="1.0" />
             <param name="mode_selector" value="all" />
             <param name="modeReject" value="one" />