Mercurial > repos > iuc > meryl

changeset 6:31fa26c0692b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3"
author iuc
date Tue, 08 Jun 2021 07:20:29 +0000
parents d63739222f68
children 51c2360aa807
files macros.xml meryl.xml
diffstat 2 files changed, 20 insertions(+), 35 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Sun May 23 18:09:41 2021 +0000
+++ b/macros.xml	Tue Jun 08 07:20:29 2021 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3</token>
-    <token name="@GALAXY_TOOL_VERSION@">galaxy1</token>
+    <token name="@GALAXY_TOOL_VERSION@">galaxy2</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0196</edam_topic>
--- a/meryl.xml	Sun May 23 18:09:41 2021 +0000
+++ b/meryl.xml	Tue Jun 08 07:20:29 2021 +0000
@@ -49,16 +49,12 @@
             output read-db.meryl &&
             tar -zcf read-db.meryldb read-db.meryl
         #elif $operation_type.command_type == 'groups-kmers'
-            mkdir  -p ./temp_db/ &&
-            tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ &&
-            mv ./temp_db/* tmp_01.meryl &&
-            tar -zxf  $operation_type.input_meryldb_03 -C ./temp_db/ &&
-            mv ./temp_db/* tmp_02.meryl &&
-            meryl
-            $operation_type.groups_operations
-            tmp_01.meryl
-            tmp_02.meryl
-            output read-db.meryl &&
+            #for $i,$mdb in enumerate($operation_type.input_meryldb_02)
+                mkdir -p ./tmp_folder_$i/ &&
+                tar -zxf $mdb -C ./tmp_folder_$i &&
+                mv ./tmp_folder_$i/* db_'${i}'.meryl &&
+            #end for
+            meryl $operation_type.groups_operations output read-db.meryl db_*  &&
             tar -zcf read-db.meryldb read-db.meryl
         #elif $operation_type.command_type == 'histogram-kmers'
             mkdir  -p ./temp_db/ &&
@@ -220,8 +216,7 @@
                     <option value="difference">Difference: return k-mers that occur in the first input, but none of the other inputs</option>
                     <option value="symmetric-difference">Symmetric-difference: return k-mers that occur in exactly one input</option>
                 </param>
-                <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" />
-                <param name="input_meryldb_03" type="data" format="meryldb" label="Input meryldb" />
+                <param name="input_meryldb_02" type="data" multiple="true" format="meryldb" label="Input meryldb" />
             </when>
             <when value="histogram-kmers">
                 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" />
@@ -450,8 +445,8 @@
             <conditional name="operation_type">
                 <param name="command_type" value="groups-kmers" />
                 <param name="groups_operations" value="union" />
-                <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" />
-                <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
+                <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
+                <param name="input_meryldb_03" value="" ftype="meryldb" />
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
@@ -463,8 +458,7 @@
             <conditional name="operation_type">
                 <param name="command_type" value="groups-kmers" />
                 <param name="groups_operations" value="union-min" />
-                <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" />
-                <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
+                <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
@@ -476,8 +470,7 @@
             <conditional name="operation_type">
                 <param name="command_type" value="groups-kmers" />
                 <param name="groups_operations" value="union-max" />
-                <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" />
-                <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
+                <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
@@ -489,8 +482,7 @@
             <conditional name="operation_type">
                 <param name="command_type" value="groups-kmers" />
                 <param name="groups_operations" value="union-sum" />
-                <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" />
-                <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
+                <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
@@ -502,8 +494,7 @@
             <conditional name="operation_type">
                 <param name="command_type" value="groups-kmers" />
                 <param name="groups_operations" value="intersect" />
-                <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" />
-                <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
+                <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
@@ -515,8 +506,7 @@
             <conditional name="operation_type">
                 <param name="command_type" value="groups-kmers" />
                 <param name="groups_operations" value="intersect-min" />
-                <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" />
-                <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
+                <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
@@ -528,8 +518,7 @@
             <conditional name="operation_type">
                 <param name="command_type" value="groups-kmers" />
                 <param name="groups_operations" value="intersect-max" />
-                <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" />
-                <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
+                <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
@@ -541,8 +530,7 @@
             <conditional name="operation_type">
                 <param name="command_type" value="groups-kmers" />
                 <param name="groups_operations" value="intersect-sum" />
-                <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" />
-                <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
+                <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
@@ -555,8 +543,7 @@
             <conditional name="operation_type">
                 <param name="command_type" value="groups-kmers" />
                 <param name="groups_operations" value="subtract" />
-                <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" />
-                <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
+                <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
@@ -568,8 +555,7 @@
             <conditional name="operation_type">
                 <param name="command_type" value="groups-kmers" />
                 <param name="groups_operations" value="difference" />
-                <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" />
-                <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
+                <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
@@ -581,8 +567,7 @@
             <conditional name="operation_type">
                 <param name="command_type" value="groups-kmers" />
                 <param name="groups_operations" value="symmetric-difference" />
-                <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" />
-                <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" />
+                <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" />
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>