# HG changeset patch
# User iuc
# Date 1741201593 0
# Node ID 3ec2cd53b6759399154ffc5c2a18ed98708701c3
# Parent  2fbd93fe4a6f7771100bb1cf4284f0da25aa9846
planemo upload for repository https://github.com/thegenemyers/MERQURY.FK commit f02f3754424a68a1463fa75e9523d49e60d68373

diff -r 2fbd93fe4a6f -r 3ec2cd53b675 hapmaker.xml
--- a/hapmaker.xml	Tue Feb 25 13:34:19 2025 +0000
+++ b/hapmaker.xml	Wed Mar 05 19:06:33 2025 +0000
@@ -11,19 +11,19 @@
         && tar -xf maternal.tar
         && mv ktabfiles ktabfiles_maternal
         && mv ktabfiles_maternal/output.ktab input_files/maternal.ktab
-        && mv "\$(find ktabfiles_maternal -type f -name '*.ktab.1')" "input_files/.maternal.ktab.1"
+        && mv ktabfiles_maternal/.*.ktab* input_files/.maternal.ktab.1
         && ln -s '$paternal_ktab_tar' paternal.tar
         && tar -xf paternal.tar
         && mv ktabfiles ktabfiles_paternal
         && mv ktabfiles_paternal/output.ktab input_files/paternal.ktab
-        && mv "\$(find ktabfiles_paternal -type f -name '*.ktab.1')" "input_files/.paternal.ktab.1"
+        && mv ktabfiles_paternal/.*.ktab* input_files/.paternal.ktab.1
         && ln -s '$child_ktab_tar' child.tar
         && tar -xf child.tar
         && mv ktabfiles ktabfiles_child
         && mv ktabfiles_child/output.ktab input_files/child.ktab
-        && mv "\$(find ktabfiles_child -type f -name '*.ktab.1')" "input_files/.child.ktab.1"
+        && mv ktabfiles_child/.*.ktab* input_files/.child.ktab.1
         && HAPmaker -v 
-        -T\${GALAXY_SLOTS:-4}
+        -T\${GALAXY_SLOTS:-1}
         input_files/maternal.ktab
         input_files/paternal.ktab
         input_files/child.ktab
@@ -36,22 +36,30 @@
         <param name="child_ktab_tar" type="data" format="fastk_ktab_tar" label="Select the TAR file consisting of child ktab file from FastK"/>
     </inputs>
     <outputs>
-        <data name="paternal_out" format="fastk_ktab" from_work_dir="paternal.hap.ktab" label="${tool.name} on ${on_string}: paternal hap-mers"/>
-        <data name="maternal_out" format="fastk_ktab" from_work_dir="maternal.hap.ktab" label="${tool.name} on ${on_string}: maternal hap-mers"/>
+        <data name="paternal_out" format="fastk_ktab" from_work_dir="input_files/paternal.hap.ktab" label="${tool.name} on ${on_string}: paternal hap-mers"/>
+        <data name="maternal_out" format="fastk_ktab" from_work_dir="input_files/maternal.hap.ktab" label="${tool.name} on ${on_string}: maternal hap-mers"/>
         <data name="intermediate_ktab" format="fastk_ktab_tar" from_work_dir="HapK_ktab_files.tar.gz" label="${tool.name} on ${on_string}: HapMaker Intermediate Ktab files"/>
     </outputs>
     <tests>
         <test expect_num_outputs="3">
-            <param name="maternal_ktab_tar" ftype="fastk_ktab_tar" value="maternal.tar"/>
-            <param name="paternal_ktab_tar" ftype="fastk_ktab_tar" value="paternal.tar"/>
-            <param name="child_ktab_tar" ftype="fastk_ktab_tar" value="child.tar"/>
-            <output name="paternal_out" value="paternal.hap.ktab"/>
-            <output name="maternal_out" value="maternal.hap.ktab"/>
+            <param name="maternal_ktab_tar" ftype="fastk_ktab_tar" location="https://zenodo.org/records/14965629/files/maternal.fastk_ktab_tar"/>
+            <param name="paternal_ktab_tar" ftype="fastk_ktab_tar" location="https://zenodo.org/records/14965629/files/paternal.fastk_ktab_tar"/>
+            <param name="child_ktab_tar" ftype="fastk_ktab_tar" location="https://zenodo.org/records/14965629/files/child.fastk_ktab_tar"/>
+            <output name="paternal_out" ftype="fastk_ktab">
+                <assert_contents>
+                    <has_size value="524304" delta="2000"/>
+                </assert_contents>
+            </output>
+            <output name="maternal_out" ftype="fastk_ktab">
+                <assert_contents>
+                    <has_size value="524304" delta="2000"/>
+                </assert_contents>
+            </output>
             <output name="intermediate_ktab" ftype="fastk_ktab_tar">
-                <assert_contents>
+                 <assert_contents>
                     <has_archive_member path="hapmaker_ktabs/.maternal.hap.ktab.1"/>
                     <has_archive_member path="hapmaker_ktabs/.paternal.hap.ktab.1"/>
-                </assert_contents>
+                </assert_contents> 
             </output>
         </test>
     </tests>
diff -r 2fbd93fe4a6f -r 3ec2cd53b675 test-data/HapK_ktab_files.tar.gz
Binary file test-data/HapK_ktab_files.tar.gz has changed
diff -r 2fbd93fe4a6f -r 3ec2cd53b675 test-data/maternal.hap.ktab
Binary file test-data/maternal.hap.ktab has changed
diff -r 2fbd93fe4a6f -r 3ec2cd53b675 test-data/paternal.hap.ktab
Binary file test-data/paternal.hap.ktab has changed