diff hicFindTADs.xml @ 20:ec4b948dc6f0 draft default tip

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

--- a/hicFindTADs.xml	Tue Jan 10 19:07:55 2023 +0000
+++ b/hicFindTADs.xml	Wed Oct 18 12:47:13 2023 +0000
@@ -50,13 +50,13 @@
         #end if
     ]]>    </command>
     <inputs>
-        <expand macro='matrix_h5_cooler_macro' />
-        <conditional name='precomputedZscore_conditional'>
-            <param name='precomputedZscore_selector' type="select" label="Compute from scratch or use precomputed data">
-                <option value='scratch' selected='True'>From scratch</option>
-                <option value='precomputed'>Precomputed z-score matrix</option>
+        <expand macro="matrix_h5_cooler_macro" />
+        <conditional name="precomputedZscore_conditional">
+            <param name="precomputedZscore_selector" type="select" label="Compute from scratch or use precomputed data">
+                <option value="scratch" selected="True">From scratch</option>
+                <option value="precomputed">Precomputed z-score matrix</option>
             </param>
-            <when value='scratch'>
+            <when value="scratch">
                 <param argument="--minDepth" type="integer" value="5000" label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin." help="This number should be at least 3 times as large as the bin size of the Hi-C matrix." />
                 <param argument="--maxDepth" type="integer" value="10000" label="Maximum window length (in bp) to be considered to the left and to the right of each Hi-C bin." help="This number should around 6-10 times as large as the bin size of the Hi-C matrix." />
                 <param argument="--step" type="integer" value="10000" label="Step size when moving from minDepth to maxDepth" help="The step size grows exponentially as maxDeph + (step * int(x)**1.5) for x in [0, 1, ...]
@@ -64,9 +64,9 @@
                         and maxDepth=150,000 will compute TAD-scores for window sizes:
                         20,000, 30,000, 40,000, 70,000 and 100,000" />
             </when>
-            <when value='precomputed'>
-                <param name="scoreFile" type="data" format='bedgraph' label="Precomputed TAD score file (bm)" />
-                <param name="zscoreMatrix" type="data" format='cool,h5' label="Precomputed z-score matrix" />
+            <when value="precomputed">
+                <param name="scoreFile" type="data" format="bedgraph" label="Precomputed TAD score file (bm)" />
+                <param name="zscoreMatrix" type="data" format="cool,h5" label="Precomputed z-score matrix" />
             </when>
         </conditional>
         <conditional name="multiple_comparison_conditional">
@@ -91,7 +91,7 @@
                         can be given." />
         <param argument="--minBoundaryDistance" type="integer" value="" optional="True" label="Minimum distance between boundaries (in bp)." help="This parameter can be used to reduce spurious boundaries caused by noise. " />
         <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
-            <param name="chromosome" type="text" label='chromosome (one per field)'>
+            <param name="chromosome" type="text" label="chromosome (one per field)">
                 <validator type="empty_field" />
             </param>
         </repeat>
@@ -102,17 +102,17 @@
         <data name="domains" from_work_dir="galaxy_tad_prefix_domains.bed" format="bed" label="${tool.name} on ${on_string}: TAD domains" />
         <data name="boundaries_bin" from_work_dir="galaxy_tad_prefix_boundaries.gff" format="gff" label="${tool.name} on ${on_string}: Boundary information plus score" />
         <data name="tad_score" from_work_dir="galaxy_tad_prefix_tad_score.bm" format="bedgraph" label="${tool.name} on ${on_string}: TAD information in bm file">
-            <filter>precomputedZscore_conditional.precomputedZscore_selector == 'scratch'</filter>
+            <filter>precomputedZscore_conditional['precomputedZscore_selector'] == 'scratch'</filter>
         </data>
         <data name="matrix_output" from_work_dir="matrix" format="h5" label="${tool.name} z-score matrix on ${on_string}">
-            <filter>precomputedZscore_conditional.precomputedZscore_selector == 'scratch'</filter>
+            <filter>precomputedZscore_conditional['precomputedZscore_selector'] == 'scratch'</filter>
             <change_format>
                 <when input="matrix_h5_cooler.ext" value="cool" format="cool" />
             </change_format>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="6">
             <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
             <conditional name="precomputedZscore_conditional">
                 <param name="precomputedZscore_selector" value="scratch" />
@@ -140,11 +140,11 @@
             <output name="tad_score" file="find_TADs/multiFDR_tad_score.bm" ftype="bedgraph" />
             <output name="matrix_output" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='intervals,matrix' />
+                    <has_h5_keys keys="intervals,matrix" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
             <conditional name="precomputedZscore_conditional">
                 <param name="precomputedZscore_selector" value="precomputed" />