diff bbmerge.xml @ 2:16db2a5b73c5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb

--- a/bbmerge.xml	Tue May 30 09:01:10 2023 +0000
+++ b/bbmerge.xml	Tue Aug 27 10:13:32 2024 +0000
@@ -4,11 +4,9 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="edam_ontology"/>
+    <expand macro="bio.tools"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-#import os
-#import re
-
 #if str($input_type_cond.input_type) in ['single', 'pair']:
     #set read1 = $input_type_cond.read1
     ## bbmerge uses the file extension to determine the input format.
@@ -25,21 +23,24 @@
     #end if
 #else:
     #set read1 = $input_type_cond.reads_collection['forward']
-    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
     ## bbmap uses the file extension to determine the input format.
-    #set ext = $read1_identifier + '.fastq'
+    #set ext = '.fastq'
     #if $read1.ext.endswith('.gz'):
         #set ext = $ext + '.gz'
     #end if
-    #set read1_file = $read1_identifier + $ext
+    #set read1_file = 'forward' + $ext
     ln -s '${read1}' '${read1_file}' &&
     #set read2 = $input_type_cond.reads_collection['reverse']
-    #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
-    #set read2_file = $read2_identifier + $ext
+    #set read2_file = 'reverse' + $ext
     ln -s '${read2}' '${read2_file}' &&
 #end if
 
-bbmerge.sh
+if [[ "\${_JAVA_OPTIONS}" != *-Xmx* && "\${JAVA_TOOL_OPTIONS}" != *-Xmx* ]]; then
+    export _JAVA_OPTIONS="\${_JAVA_OPTIONS} -Xmx\${GALAXY_MEMORY_MB:-4096}m -Xms256m";
+fi &&
+
+bbmerge.sh tmpdir="\$TMPDIR" t="\${GALAXY_SLOTS:-2}"
+
 #### Input parameters
 #if str($input_type_cond.input_type) == 'single':
     in='${read1_file}'
@@ -97,7 +98,6 @@
 ]]></command>
     <inputs>
         <expand macro="input_type_cond"/>
-        
         <section name="qt_options" title="Quality and trimming options">
             <param name="qtrim" type="select" label="Select option for quality trimming ends before mapping">
                 <option value="f" selected="true">No trimming</option>
@@ -109,7 +109,6 @@
             <param argument="minlength_after_trim" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
             <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
         </section>
-        
         <section name="merge_options" title="Merging parameters">
             <param name="strictness" type="select" label="Select option for quality trimming ends before mapping">
                 <option value="xstrict">max strict</option>
@@ -127,16 +126,13 @@
             <param argument="trimnonoverlapping" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim all non-overlapping portions, leaving only consensus sequence. By default, only sequence to the right of the overlap (adapter sequence) is trimmed."/>
             <param argument="mininsert" type="integer" value="35" label="Minimum insert size to merge reads"/>
             <param argument="minoverlap" type="integer" value="12" label="Minimum number of overlapping bases to allow merging"/>
-            
             <param argument="minq" type="integer" value="9" label="Ignore bases with quality below this"/>
             <param argument="maxq" type="integer" value="41" label="Cap output quality scores at this"/>
-            
             <param argument="entropy" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Increase the minimum overlap requirement for low-complexity reads"/>
             <param argument="efilter" type="integer" value="6" label="Ban overlaps with over this many times the expected number of errors." help="Lower is more strict, -1 disables."/>
             <param argument="pfilter" type="float" value="0.00004" label="Probability filter to disallow improbable overlaps." help="Higher is stricter. 0 will disable the filter; 1 will allow only perfect overlaps."/>
             <param argument="kfilter" type="integer" value="41" label="Ban overlaps that create kmers with count below this value" help="Requires good coverage, 0 disables."/>
             <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Take quality factors into account" help="If disabled, quality values are completely ignored, both for overlap detection and filtering. May be useful for data with inaccurate quality values."/>
-            
             <conditional name="adapters">
                 <param name="selector" type="select" label="Provide adapter sequences to improve accuracy?">
                     <option value="wout_adapters" selected="true">No</option>
@@ -148,7 +144,6 @@
                     <param argument="adapter2" type="text" value="" label="Right adapter sequence"/>
                 </when>
             </conditional>
-
             <conditional name="merge_mode">
                 <param name="selector" type="select" label="Evaluate overlaps via..." help="In the ratio mode, overlaps are decided based on the ratio of matching to mismatching bases. Flat mode scores overlaps based on the total number of mismatching bases only.">
                     <option value="Ratio mode" selected="true">Ratio mode</option>
@@ -252,4 +247,3 @@
     </help>
     <expand macro="citations"/>
 </tool>
-