diff meryl.xml @ 5:d63739222f68 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit b30f2a9974c569de148c3791d42ff7dc8d9b018c"

--- a/meryl.xml	Fri Apr 30 06:40:29 2021 +0000
+++ b/meryl.xml	Sun May 23 18:09:41 2021 +0000
@@ -7,6 +7,7 @@
     <expand macro='requirements' />
     <version_command>meryl --version</version_command>
     <command detect_errors='exit_code'><![CDATA[
+        export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
         #if $operation_type.command_type == 'count-kmers'
             #if $operation_type.options_kmer_size.kmer_size == 'estimate'
                 #from math import log
@@ -17,7 +18,7 @@
             meryl
             $operation_type.count_operations
             k=$size
-            memory=\${GALAXY_MEMORY_GB:-1}
+            memory=\$GALAXY_MEMORY_GB
             threads=\${GALAXY_SLOTS:-1}
             $operation_type.input_reads
             output read-db.meryl &&
@@ -79,17 +80,17 @@
             #end if
             #for $i, $read in enumerate($paternal_reads):
                 mkdir 'paternal{$i}.meryl' &&
-                meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'paternal{$i}.meryl' &&
+                meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'paternal{$i}.meryl' &&
             #end for
             meryl union-sum paternal*.meryl output pat.meryl &&
             #for $i, $read in enumerate($maternal_reads):
                 mkdir 'maternal{$i}.meryl' &&
-                meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'maternal{$i}.meryl' &&
+                meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'maternal{$i}.meryl' &&
             #end for
             meryl union-sum maternal*.meryl output mat.meryl &&
             #for $i, $read in enumerate($child_reads):
                 mkdir 'child{$i}.meryl' &&
-                meryl count k=$size memory=\${GALAXY_MEMORY_GB:-1} threads=\${GALAXY_SLOTS:-1} '${read}' output 'child{$i}.meryl' &&
+                meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'child{$i}.meryl' &&
             #end for
             meryl union-sum child*.meryl output child.meryl &&
             ## mat specific kmers
@@ -144,10 +145,10 @@
             <param name="command_type" type="select" label="Operation type selector" help="Select a type of operation">
                 <option value="count-kmers">Count operations</option>
                 <option value="filter-kmers">Filter operations</option>
-                <option value="arithmetic-kmers">Arithmetic operations on kmer counts</option>
+                <option value="arithmetic-kmers">Arithmetic operations on k-mer counts</option>
                 <option value="groups-kmers">Operations on sets of k-mers</option>
                 <option value="histogram-kmers">Generate histogram dataset</option>
-                <option value="print">Print kmer counts to a tabular file</option>
+                <option value="print">Print k-mer counts to a tabular file</option>
                 <option value="trio-mode">Build hap-mer dbs for trios</option>
             </param>
             <when value="count-kmers">
@@ -182,21 +183,21 @@
                 
                 <conditional name="filter_type">
                     <param name="type" type="select" label="Type of filtering">
-                        <option value="times">Return kmers that occur N times in the input</option>
-                        <option value="frequency">Return kmers occurring at specific frequencies</option>
+                        <option value="times">Return k-mers that occur N times in the input</option>
+                        <option value="frequency">Return k-mers occurring at specific frequencies</option>
                     </param>
                     <when value="times">
-                        <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Number of times in the input" help="Return kmers that occur N times in the input."/>
+                        <param name="N" type="integer" min="0" max="50000000000" value="" optional="true" label="Number of times in the input" help="Return k-mers that occur N times in the input."/>
                     </when>
                     <when value="frequency">
-                        <param name="distinct" type="float" min="0" max="1" value="0.9998" optional="true" label="Frequency" help="Return kmers that at specific frequency (e.g. frequency = 0.9998 returns top 0.02% most frequent)"/>
+                        <param name="distinct" type="float" min="0" max="1" value="0.9998" optional="true" label="Frequency" help="Return k-mers that at specific frequency (e.g. frequency = 0.9998 returns top 0.02% most frequent)"/>
                     </when>
                 </conditional>
             </when>
             <when value="arithmetic-kmers">
                 <param name="arithmetic_operations" type="select" label="Arithmetic operations" help="Select an operation to be executed">
                     <option value="increase">Increase: add x to the count of each k-mer</option>
-                    <option value="decrease">Decrease: subsctract x from the count of each k-mer</option>
+                    <option value="decrease">Decrease: subtract x from the count of each k-mer</option>
                     <option value="multiply">Multiply: multiply the count of each k-mer by x</option>
                     <option value="divide">Divide: divide the count of each k-mer by x</option>
                     <option value="divide-round">Divide-round: divide the count of each k-mer by x and round th results</option>
@@ -206,7 +207,7 @@
                 <param name="X" type="integer" min="1" max="1000000" value="" optional="true" label="Operand" />
             </when>
             <when value="groups-kmers">
-                <param name="groups_operations" type="select" label="Operations on sets of kmers" help="Select an operation to be executed">
+                <param name="groups_operations" type="select" label="Operations on sets of k-mers" help="Select an operation to be executed">
                     <option value="union">Union: return k-mers that occur in any input</option>
                     <option value="union-min">Union-min: return k-mers that occur in any input, set the count to the minimum count</option>
                     <option value="union-max">Union-max: return k-mers that occur in any input, set the count to the maximum count</option>
@@ -362,7 +363,7 @@
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="59378" delta="300" />
+                    <has_size value="59100" delta="300" />
                 </assert_contents>
             </output>
         </test>
@@ -375,7 +376,7 @@
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="59822" delta="300" />
+                    <has_size value="59500" delta="300" />
                 </assert_contents>
             </output>
         </test>
@@ -401,7 +402,7 @@
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="60531" delta="300" />
+                    <has_size value="60530" delta="300" />
                 </assert_contents>
             </output>
         </test>
@@ -414,7 +415,7 @@
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="56569" delta="300" />
+                    <has_size value="56200" delta="300" />
                 </assert_contents>
             </output>
         </test>
@@ -427,7 +428,7 @@
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="56539" delta="300" />
+                    <has_size value="56100" delta="300" />
                 </assert_contents>
             </output>
         </test>
@@ -454,7 +455,7 @@
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="36417" delta="300" />
+                    <has_size value="36100" delta="300" />
                 </assert_contents>
             </output>
         </test>
@@ -493,7 +494,7 @@
             </conditional>
             <output name="read_db" ftype="meryldb">
                 <assert_contents>
-                    <has_size value="59004" delta="350" />
+                    <has_size value="58600" delta="300" />
                 </assert_contents>
             </output>
         </test>