diff sr_bowtie_dataset_annotation.xml @ 10:fd4a60fc3fca draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit cf30b4fab90cf7910bb2900a05b85ca3344aae59

--- a/sr_bowtie_dataset_annotation.xml	Mon Apr 11 00:27:41 2022 +0000
+++ b/sr_bowtie_dataset_annotation.xml	Tue Nov 15 00:45:36 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.7">
+<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.8">
   <description>by iterative alignments with sRbowtie</description>
   <requirements>
         <requirement type="package" version="1.3.1">bowtie</requirement>
@@ -8,14 +8,14 @@
   </requirements>
   <command  detect_errors="exit_code"><![CDATA[
         #if $refGenomeSource1.genomeSource == "history":
-            bowtie-build -f $refGenomeSource1.ownFile genome  1>/dev/null &&
+            bowtie-build --threads \${GALAXY_SLOTS:-4} -f $refGenomeSource1.ownFile genome  1>/dev/null &&
             #set index_path = 'genome'
         #else:
             #set index_path = $refGenomeSource1.index.fields.path
         #end if
         
         #for $i in $AdditionalQueries:
-            bowtie-build -f $i.ownFile $i.ownFile.name  1>/dev/null &&
+            bowtie-build --threads \${GALAXY_SLOTS:-4} -f $i.ownFile $i.ownFile.name  1>/dev/null &&
         #end for
                 
         #set method_prefix = "-v %s -k 1 --best" % str($mismatches)
@@ -121,11 +121,11 @@
             <output name="output" ftype="tabular" file="multisample5_output.tab" />
             <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" />
             <output_collection name="unmatched" type="list" count="5">
-                <element name="sample5.fa_unmatched" file="unmatched_5.fa" ftype="fasta"/>
-                <element name="sample4.fa_unmatched" file="unmatched_4.fa" ftype="fasta"/>
-                <element name="sample3.fa_unmatched" file="unmatched_3.fa" ftype="fasta"/>
-                <element name="sample2.fa_unmatched" file="unmatched_2.fa" ftype="fasta"/>
-                <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta"/>
+                <element name="sample5.fa_unmatched" file="unmatched_5.fa" ftype="fasta" compare="sim_size" delta="0"/>
+                <element name="sample4.fa_unmatched" file="unmatched_4.fa" ftype="fasta"  compare="sim_size" delta="0"/>
+                <element name="sample3.fa_unmatched" file="unmatched_3.fa" ftype="fasta"  compare="sim_size" delta="0"/>
+                <element name="sample2.fa_unmatched" file="unmatched_2.fa" ftype="fasta"  compare="sim_size" delta="0"/>
+                <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta"  compare="sim_size" delta="0"/>
             </output_collection>
         </test>
         <test>
@@ -137,7 +137,7 @@
             <output name="output" ftype="tabular" file="sample1_output.tab" />
             <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/>
             <output_collection name="unmatched" type="list">
-                <element name="sample1.fa_unmatched" file="unmatched_1.fa" ftype="fasta"/>
+                <element name="sample1.fa_unmatched" file="unmatched_6.fa" ftype="fasta" compare="sim_size" delta="0"/>
             </output_collection>
         </test>
         <test>