Mercurial > repos > drosofff > repenrich

changeset 1:fa1e919fafed draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit e33b21484507981c2b8627a75cc5da3c1995b64a-dirty
author drosofff
date Tue, 23 May 2017 09:04:16 -0400
parents 041de602103e
children 7864d0421273
files repenrich.xml
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/repenrich.xml	Tue May 23 03:08:45 2017 -0400
+++ b/repenrich.xml	Tue May 23 09:04:16 2017 -0400
@@ -18,13 +18,13 @@
         ln -f -s '$input_fastq' '${input_base}.fastq' &&
         bowtie-build '$genome' ${baseReference} &&
         python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} &&
-        bowtie $baseReference -p 16 -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam &&
+        bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam &&
         samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam &&
         samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted &&
         mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam &&
         samtools index ${input_base}_unique.bam &&
         rm ${input_base}_unique.sam &&
-        python $__tool_directory__/RepEnrich.py $repeatmasker ${input_base} ${input_base} setup_folder_${baseReference} ${input_base}_multimap.fastq ${input_base}_unique.bam --cpus 16 &&
+        python $__tool_directory__/RepEnrich.py $repeatmasker ${input_base} ${input_base} setup_folder_${baseReference} ${input_base}_multimap.fastq ${input_base}_unique.bam --cpus "\${GALAXY_SLOTS:-4}" &&
         cp $input_base/${input_base}_class_fraction_counts.txt class_fraction_counts.tabular &&
         cp $input_base/${input_base}_family_fraction_counts.txt family_fraction_counts.tabular &&
         cp $input_base/${input_base}_fraction_counts.txt fraction_counts.tabular
@@ -117,7 +117,7 @@
 
 ]]>
 
-User may filter this file so that it contains only desired items (for instance only satellite, repeats and transposons)
+Users may filter this file so that it contains only desired items (for instance only satellites, repeats and transposons)
  
 **Outputs**