changeset 2:2e773e00ceb0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d

--- a/macros.xml	Tue Mar 10 15:13:23 2020 -0400
+++ b/macros.xml	Fri Apr 14 14:29:46 2023 +0000
@@ -1,10 +1,11 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@WRAPPER_VERSION@">4</token>
+    <token name="@TOOL_VERSION@">4</token>
+    <token name="@PROFILE@">22.05</token>
 
      <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@WRAPPER_VERSION@">schicexplorer</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">schicexplorer</requirement>
             <yield />
         </requirements>
         <version_command>@BINARY@ --version</version_command>

--- a/scHicAdjustMatrix.xml	Tue Mar 10 15:13:23 2020 -0400
+++ b/scHicAdjustMatrix.xml	Fri Apr 14 14:29:46 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="schicexplorer_schicadjustmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="schicexplorer_schicadjustmatrix" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@">
     <description>clusters single-cell Hi-C interaction matrices on the raw data</description>
     <macros>
         <token name="@BINARY@">scHicAdjustMatrix</token>
@@ -8,10 +8,10 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
 
-        --matrix '$matrix_scooler'
+        --matrix "$matrix_scooler"
         --action $action_selector
         #if $chromosomes:
-            #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
+            #set $chromosome = " ".join([ "\"%s\"" % $chrom for $chrom in str($chromosomes).split(" ") ])
             --chromosomes $chromosome
         #end if
 
@@ -19,30 +19,27 @@
         --outFileName adjusted_matrix.scool
 
         --threads @THREADS@
-
-
-
     ]]></command>
     <inputs>
         
         <expand macro="matrix_scooler_macro"/>
         <param name="action_selector" type="select" label="Action to take apply on matrices:">
-                <option value="keep" selected="True">Keep the listed chromosomes</option>
+                <option value="keep" selected="true">Keep the listed chromosomes</option>
                 <option value="remove" >Remove the listed chromosomes</option>
         </param>
-        <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
+        <param name="chromosomes" type="text" label="List of chromosomes to consider" help="Please separate the chromosomes by space"/>
     </inputs>
     <outputs>
         <data name="outFileName" from_work_dir="adjusted_matrix.scool" format="scool" label="${tool.name} on ${on_string}: Adjusted matrix"/>
     </outputs>
     <tests>
         <test>
-            <param name='matrix_scooler' value='test_matrix.scool' />
-            <param name='clusterMethod_selector' value='keep' />
-            <param name='chromosomes' value='chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX' />
+            <param name="matrix_scooler" value="test_matrix.scool" />
+            <param name="action_selector" value="keep" />
+            <param name="chromosomes" value="chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX" />
             <output name="outFileName" ftype="scool">
                 <assert_contents>
-                    <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, 
+                    <has_h5_keys keys="Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, 
                     Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, 
                     Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/start, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms, 
                     Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/length, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/chroms/name, 
@@ -190,7 +187,7 @@
                     Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/indexes, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/indexes/bin1_offset,
                     Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/indexes/chrom_offset, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels, 
                     Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/bin1_id, Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/bin2_id, 
-                    Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/count'/>
+                    Diploid_2_AGGCAGAA_AAGGAGTA_R1fastqgz/pixels/count"/>
                 </assert_contents>
             </output>
         </test>