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galaxyproject · Apr 10, 2024 · dbccfcd · dbccfcd
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diff --git a/tools/meryl/arithmetic-kmers.xml b/tools/meryl/arithmetic-kmers.xml
@@ -1,5 +1,5 @@
-<tool id="meryl_arithmetic_kmers" name="Meryl: arithmetic-kmers" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="20.01">
-    <description>a genomic k-mer counter and sequence utility</description>
+<tool id="meryl_arithmetic_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="20.01">
+    <description>apply arithmetic operations to k-mer counts</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -10,7 +10,7 @@
     <expand macro="requirements"/>
     <version_command>meryl --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
+    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
     mkdir  -p ./temp_db/ &&
     tar -zxf $input_meryldb_02 -C ./temp_db/ &&
     mv ./temp_db/* tmp.meryl &&
@@ -19,7 +19,8 @@
     $X
     tmp.meryl
     output read-db.meryl &&
-    tar -zcf read-db.meryldb read-db.meryl]]></command>
+    tar -zcf read-db.meryldb read-db.meryl
+    ]]></command>
     <inputs>
         <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>
@@ -104,58 +105,14 @@
 
 **Purpose**
 
-Meryl is the k-mer counter. It is built into the Celera assembler and is also available as a stand-alone application.
-Meryl uses a sorting-based approach that sorts the k-mers in lexicographical order.
-
-In addition of generating count-databases, meryl can perform simple operations on it. 
-
------
-
-.. class:: infomark
-
-**Basic functions**
-
-The functions that meryl includes are described below: 
-
-    ::
-
-        COUNT OPERATIONS
-        - Count: count the occurrences of canonical k-mers
-        - Count-forward: count the occurreces of forward k-mers
-        - Count-reverse: count the occurreces of reverse k-mers
-        FILTERING OPERATIONS
-        - Less-than: return k-mers that occur fewer than N times in the input
-        - Greater-than: return k-mers that occur more than N times in the input
-        - Equal-to: return k-mers that occur exactly N times in the input
-        - Not-equal-to: return k-mers that do not occur exactly N times in the input
-        ARITHMETIC OPERATIONS
-        - Increase: add x to the count of each k-mer
-        - Decrease: subsctract x from the count of each k-mer
-        - Multiply: multiply the count of each k-mer by x
-        - Divide: divide the count of each k-mer by x
-        - Divide-round: divide the count of each k-mer by x and round th results
-        - Modulo: set the count of each k-mer to the remainder of the count divided by x
-        OPERATIONS ON SETS
-        - Union-min: return k-mers that occur in any input, set the count to the minimum count
-        - Union-max: return k-mers that occur in any input, set the count to the maximum count
-        - Union-sum: return k-mers that occur in any input, set the count to the sum of the counts
-        - Intersect: return k-mers that occur in all inputs, set the count to the count in the first input
-        - Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count
-        - Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count
-        - Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts
-        - Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs
-        - Difference: return k-mers that occur in the first input, but none of the other inputs
-        - Symmetric-difference: return k-mers that occur in exactly one input
-
------
-
-.. class:: infomark
-
-**Additional function: build hap-mers dbs for trios**
-
-In addition of the basic operations, this wrapper allows to build the hap-mers databases for trios, in accordance
-with `merqury's recommended guidelines. &lt;https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs#3-build-hap-mer-dbs-for-trios&gt;`_
+Meryl is the k-mer counter. This tool applies arithmetic operations on k-mer counts: 
 
+- Increase: add x to the count of each k-mer
+- Decrease: subsctract x from the count of each k-mer
+- Multiply: multiply the count of each k-mer by x
+- Divide: divide the count of each k-mer by x
+- Divide-round: divide the count of each k-mer by x and round th results
+- Modulo: set the count of each k-mer to the remainder of the count divided by x
         </help>
     <expand macro="citations"/>
 </tool>
diff --git a/tools/meryl/count-kmers.xml b/tools/meryl/count-kmers.xml
@@ -1,5 +1,5 @@
-<tool id="meryl_count_kmers" name="Meryl: count-kmers" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="20.01">
-    <description>a genomic k-mer counter and sequence utility</description>
+<tool id="meryl_count_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="20.01">
+    <description>count k-mers</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -10,7 +10,7 @@
     <expand macro="requirements"/>
     <version_command>meryl --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
+    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
     #if $options_kmer_size.kmer_size == 'estimate'
         #from math import log
         #set size=int(log(int($options_kmer_size.genome_size)*(1-float($options_kmer_size.collision_rate))/float($options_kmer_size.collision_rate))/log(4))
@@ -27,9 +27,10 @@
     ./input.${operation_type.input_reads.ext}
     output read-db.meryl &&
     echo 'K-mer size: ${size}' &&
-    tar -zcf read-db.meryldb read-db.meryl]]></command>
+    tar -zcf read-db.meryldb read-db.meryl
+    ]]></command>
     <inputs>
-        <param name="count_operation" type="select" label="Count operation" help="Select an operation to be executed">
+        <param name="count_operation" type="select" label="Count operations" help="Select an operation to be executed">
             <option value="count">Count: count the occurrences of canonical k-mers</option>
             <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option>
             <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option>
@@ -93,58 +94,11 @@
 
 **Purpose**
 
-Meryl is the k-mer counter. It is built into the Celera assembler and is also available as a stand-alone application.
-Meryl uses a sorting-based approach that sorts the k-mers in lexicographical order.
-
-In addition of generating count-databases, meryl can perform simple operations on it. 
-
------
-
-.. class:: infomark
-
-**Basic functions**
-
-The functions that meryl includes are described below: 
-
-    ::
-
-        COUNT OPERATIONS
-        - Count: count the occurrences of canonical k-mers
-        - Count-forward: count the occurreces of forward k-mers
-        - Count-reverse: count the occurreces of reverse k-mers
-        FILTERING OPERATIONS
-        - Less-than: return k-mers that occur fewer than N times in the input
-        - Greater-than: return k-mers that occur more than N times in the input
-        - Equal-to: return k-mers that occur exactly N times in the input
-        - Not-equal-to: return k-mers that do not occur exactly N times in the input
-        ARITHMETIC OPERATIONS
-        - Increase: add x to the count of each k-mer
-        - Decrease: subsctract x from the count of each k-mer
-        - Multiply: multiply the count of each k-mer by x
-        - Divide: divide the count of each k-mer by x
-        - Divide-round: divide the count of each k-mer by x and round th results
-        - Modulo: set the count of each k-mer to the remainder of the count divided by x
-        OPERATIONS ON SETS
-        - Union-min: return k-mers that occur in any input, set the count to the minimum count
-        - Union-max: return k-mers that occur in any input, set the count to the maximum count
-        - Union-sum: return k-mers that occur in any input, set the count to the sum of the counts
-        - Intersect: return k-mers that occur in all inputs, set the count to the count in the first input
-        - Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count
-        - Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count
-        - Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts
-        - Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs
-        - Difference: return k-mers that occur in the first input, but none of the other inputs
-        - Symmetric-difference: return k-mers that occur in exactly one input
-
------
-
-.. class:: infomark
-
-**Additional function: build hap-mers dbs for trios**
-
-In addition of the basic operations, this wrapper allows to build the hap-mers databases for trios, in accordance
-with `merqury's recommended guidelines. &lt;https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs#3-build-hap-mer-dbs-for-trios&gt;`_
+Meryl is the k-mer counter. This tool can be used to count kmers. 
 
+- Count: count the occurrences of canonical k-mers
+- Count-forward: count the occurreces of forward k-mers
+- Count-reverse: count the occurreces of reverse k-mers
         </help>
     <expand macro="citations"/>
 </tool>
diff --git a/tools/meryl/filter-kmers.xml b/tools/meryl/filter-kmers.xml
@@ -1,5 +1,5 @@
-<tool id="meryl_filter_kmers" name="Meryl: filter-kmers" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="20.01">
-    <description>a genomic k-mer counter and sequence utility</description>
+<tool id="meryl_filter_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="20.01">
+    <description>filter k-mers</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -10,7 +10,7 @@
     <expand macro="requirements"/>
     <version_command>meryl --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
+    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
     mkdir  -p ./temp_db/ &&
     tar -zxf $input_meryldb_02 -C ./temp_db/ &&
     mv ./temp_db/* tmp.meryl &&
@@ -23,7 +23,8 @@
     #end if
     tmp.meryl
     output read-db.meryl &&
-    tar -zcf read-db.meryldb read-db.meryl]]></command>
+    tar -zcf read-db.meryldb read-db.meryl
+    ]]></command>
     <inputs>
         <param name="filter_operations" type="select" label="Filter operations" help="Select an operation to be executed">
             <option value="less-than">Less-than: return k-mers that occur fewer than a threshold value</option>
@@ -117,57 +118,12 @@
 
 **Purpose**
 
-Meryl is the k-mer counter. It is built into the Celera assembler and is also available as a stand-alone application.
-Meryl uses a sorting-based approach that sorts the k-mers in lexicographical order.
+Meryl is the k-mer counter. This tool can be used to filter k-mers.
 
-In addition of generating count-databases, meryl can perform simple operations on it. 
-
------
-
-.. class:: infomark
-
-**Basic functions**
-
-The functions that meryl includes are described below: 
-
-    ::
-
-        COUNT OPERATIONS
-        - Count: count the occurrences of canonical k-mers
-        - Count-forward: count the occurreces of forward k-mers
-        - Count-reverse: count the occurreces of reverse k-mers
-        FILTERING OPERATIONS
-        - Less-than: return k-mers that occur fewer than N times in the input
-        - Greater-than: return k-mers that occur more than N times in the input
-        - Equal-to: return k-mers that occur exactly N times in the input
-        - Not-equal-to: return k-mers that do not occur exactly N times in the input
-        ARITHMETIC OPERATIONS
-        - Increase: add x to the count of each k-mer
-        - Decrease: subsctract x from the count of each k-mer
-        - Multiply: multiply the count of each k-mer by x
-        - Divide: divide the count of each k-mer by x
-        - Divide-round: divide the count of each k-mer by x and round th results
-        - Modulo: set the count of each k-mer to the remainder of the count divided by x
-        OPERATIONS ON SETS
-        - Union-min: return k-mers that occur in any input, set the count to the minimum count
-        - Union-max: return k-mers that occur in any input, set the count to the maximum count
-        - Union-sum: return k-mers that occur in any input, set the count to the sum of the counts
-        - Intersect: return k-mers that occur in all inputs, set the count to the count in the first input
-        - Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count
-        - Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count
-        - Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts
-        - Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs
-        - Difference: return k-mers that occur in the first input, but none of the other inputs
-        - Symmetric-difference: return k-mers that occur in exactly one input
-
------
-
-.. class:: infomark
-
-**Additional function: build hap-mers dbs for trios**
-
-In addition of the basic operations, this wrapper allows to build the hap-mers databases for trios, in accordance
-with `merqury's recommended guidelines. &lt;https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs#3-build-hap-mer-dbs-for-trios&gt;`_
+- Less-than: return k-mers that occur fewer than N times in the input
+- Greater-than: return k-mers that occur more than N times in the input
+- Equal-to: return k-mers that occur exactly N times in the input
+- Not-equal-to: return k-mers that do not occur exactly N times in the input
 
         </help>
     <expand macro="citations"/>

diff --git a/tools/meryl/groups-kmers.xml b/tools/meryl/groups-kmers.xml
@@ -1,5 +1,5 @@
-<tool id="meryl_groups_kmers" name="Meryl: groups-kmers" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="20.01">
-    <description>a genomic k-mer counter and sequence utility</description>
+<tool id="meryl_groups_kmers" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="20.01">
+    <description>apply operations on k-mer databases</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -10,14 +10,15 @@
     <expand macro="requirements"/>
     <version_command>meryl --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
+    export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
     #for $i,$mdb in enumerate($input_meryldb_02)
         mkdir -p ./tmp_folder_$i/ &&
         tar -zxf $mdb -C ./tmp_folder_$i &&
         mv ./tmp_folder_$i/* db_'${i}'.meryl &&
     #end for
     meryl $groups_operations output read-db.meryl db_*  &&
-    tar -zcf read-db.meryldb read-db.meryl]]></command>
+    tar -zcf read-db.meryldb read-db.meryl
+    ]]></command>
     <inputs>
         <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>
@@ -145,57 +146,18 @@
 
 **Purpose**
 
-Meryl is the k-mer counter. It is built into the Celera assembler and is also available as a stand-alone application.
-Meryl uses a sorting-based approach that sorts the k-mers in lexicographical order.
+Meryl is the k-mer counter. Apply operations on multiple k-mer databases.
 
-In addition of generating count-databases, meryl can perform simple operations on it. 
-
------
-
-.. class:: infomark
-
-**Basic functions**
-
-The functions that meryl includes are described below: 
-
-    ::
-
-        COUNT OPERATIONS
-        - Count: count the occurrences of canonical k-mers
-        - Count-forward: count the occurreces of forward k-mers
-        - Count-reverse: count the occurreces of reverse k-mers
-        FILTERING OPERATIONS
-        - Less-than: return k-mers that occur fewer than N times in the input
-        - Greater-than: return k-mers that occur more than N times in the input
-        - Equal-to: return k-mers that occur exactly N times in the input
-        - Not-equal-to: return k-mers that do not occur exactly N times in the input
-        ARITHMETIC OPERATIONS
-        - Increase: add x to the count of each k-mer
-        - Decrease: subsctract x from the count of each k-mer
-        - Multiply: multiply the count of each k-mer by x
-        - Divide: divide the count of each k-mer by x
-        - Divide-round: divide the count of each k-mer by x and round th results
-        - Modulo: set the count of each k-mer to the remainder of the count divided by x
-        OPERATIONS ON SETS
-        - Union-min: return k-mers that occur in any input, set the count to the minimum count
-        - Union-max: return k-mers that occur in any input, set the count to the maximum count
-        - Union-sum: return k-mers that occur in any input, set the count to the sum of the counts
-        - Intersect: return k-mers that occur in all inputs, set the count to the count in the first input
-        - Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count
-        - Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count
-        - Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts
-        - Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs
-        - Difference: return k-mers that occur in the first input, but none of the other inputs
-        - Symmetric-difference: return k-mers that occur in exactly one input
-
------
-
-.. class:: infomark
-
-**Additional function: build hap-mers dbs for trios**
-
-In addition of the basic operations, this wrapper allows to build the hap-mers databases for trios, in accordance
-with `merqury's recommended guidelines. &lt;https://github.com/marbl/merqury/wiki/1.-Prepare-meryl-dbs#3-build-hap-mer-dbs-for-trios&gt;`_
+- Union-min: return k-mers that occur in any input, set the count to the minimum count
+- Union-max: return k-mers that occur in any input, set the count to the maximum count
+- Union-sum: return k-mers that occur in any input, set the count to the sum of the counts
+- Intersect: return k-mers that occur in all inputs, set the count to the count in the first input
+- Intersect-min: return k-mers that occur in all inputs, set the count to the minimum count
+- Intersect-max: return k-mers that occur in all inputs, set the count to the maximum count
+- Intersect-sum: return k-mers that occur in all inputs, set the count to the sum of the counts
+- Subtract: return k-mers that occur in the first input, subtracting counts from the other inputs
+- Difference: return k-mers that occur in the first input, but none of the other inputs
+- Symmetric-difference: return k-mers that occur in exactly one input
 
         </help>
     <expand macro="citations"/>