Mercurial > repos > brinkmanlab > parsnp

comparison ParSNP.xml @ 1:2e855db9b19b draft

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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/parsnp commit 3b0789f0a28a87952049d74a9250338221f9b286"
author brinkmanlab
date Thu, 12 Mar 2020 19:38:17 -0400
parents 932410434dd1
children 22bf5b566ce2
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0:932410434dd1 1:2e855db9b19b
12 <requirements> 12 <requirements>
13 <requirement type="package" version="1.2">parsnp</requirement> 13 <requirement type="package" version="1.2">parsnp</requirement>
14 </requirements> 14 </requirements>
15 <version_command><![CDATA[parsnp -V |& tail -n1]]></version_command> 15 <version_command><![CDATA[parsnp -V |& tail -n1]]></version_command>
16 <command detect_errors="aggressive"><![CDATA[ 16 <command detect_errors="aggressive"><![CDATA[
17 export MEMORY_LIMIT=`expr ${GALAXY_MEMORY_MB:-0} \* 1000`;
18 [[ $MEMORY_LIMIT -eq 0 ]] && export MEMORY_LIMIT=;
17 export GENOME_DIR=\$(mktemp -d -p `pwd`) 19 export GENOME_DIR=\$(mktemp -d -p `pwd`)
18 #for $genome in $genomes 20 #for $genome in $genomes
19 && ln -sf '$genome' 21 && ln -sf '$genome'
20 #if $adv.use_ids 22 #if $adv.use_ids
21 \$GENOME_DIR/'$genome.element_identifier' 23 \$GENOME_DIR/'$genome.element_identifier'
22 #else 24 #else
23 \$GENOME_DIR/\$(basename '$genome') 25 \$GENOME_DIR/\$(basename '$genome')
24 #end if 26 #end if
25 #end for 27 #end for
26 && parsnp -v -o `pwd` -p \${GALAXY_SLOTS:-1} -P \${GALAXY_MEMORY_MB:-15000000} -d "\$GENOME_DIR" 28 && parsnp -v -o `pwd` -p \${GALAXY_SLOTS:-1} -P \${MEMORY_LIMIT:-15000000} -d "\$GENOME_DIR"
27 #if $ref_or_gbk.ref_type == "fasta" 29 #if $ref_or_gbk.ref_type == "fasta"
28 #if $ref_or_gbk.ref_genome.random_ref 30 #if $ref_or_gbk.ref_genome.random_ref
29 -r '!' 31 -r '!'
30 #else 32 #else
31 -r '$ref_or_gbk.ref_genome.reference' 33 -r '$ref_or_gbk.ref_genome.reference'