Mercurial > repos > bgruening > bionano_scaffold
diff bionano_scaffold.xml @ 3:295c0e28f4ee draft
"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit 8afc84a2ccaa084b4eedb01a0b76e4c463931db3"
| author | bgruening |
|---|---|
| date | Sun, 23 May 2021 17:23:03 +0000 |
| parents | 9bd94d9a1b2e |
| children | 8cc3862f8b8e |
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--- a/bionano_scaffold.xml Mon May 17 21:26:16 2021 +0000 +++ b/bionano_scaffold.xml Sun May 23 17:23:03 2021 +0000 @@ -5,23 +5,24 @@ </macros> <expand macro="edam_ontology"/> <expand macro="requirements"/> - <version_command>perl /HybridScaffold/hybridScaffold.pl --version</version_command> <command detect_errors="exit_code"><![CDATA[ #set RefAligner = '/usr/local/bin/RefAligner' ## softlinks do not work cp '${ngs_fasta}' ./ngs.fasta && cp '${bionano_cmap}' ./bionano.cmap + && export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) + ## return max out of GALAXY_SLOTS and 2 --> use a minimum 2 slots + && export SLOTS=\$(( \${GALAXY_SLOTS:-2} > 2 ? \${GALAXY_SLOTS:-2} : 2 )) #if $configuration_options.configuration == 'vgp' && cp '${vgp_mode}' ./config.xml + && sed -i "s|__MEMORY__|\$GALAXY_MEMORY_GB|" ./config.xml + && sed -i "s|__CORES__|\$SLOTS|" ./config.xml #else - #import os - #set cores = os.environ.get('GALAXY_SLOTS', 2) - #set memory = os.environ.get('GALAXY_MEMORY_MB', 4000) / 1000 && cp '${configuration_file}' ./config.xml - && sed -i 's|attr="maxmem" val0=.* display|attr="maxmem" val0="$memory" display|' ./config.xml - && sed -i 's|attr="maxthreads" val0=.* display|attr="maxthreads" val0="$cores" display|' ./config.xml - && sed -i 's|attr="maxvirtmem" val0=.*/>|attr="maxvirtmem" val0="$cores"/>|' ./config.xml - && sed -i 's|attr="insertThreads" val0=.*/>|attr="insertThreads" val0="$cores"/>|' ./config.xml + && sed -i "s|attr=\"maxmem\" val0=.* display|attr=\"maxmem\" val0=\"\$GALAXY_MEMORY_GB\" display|" ./config.xml + && sed -i "s|attr=\"maxthreads\" val0=.* display|attr=\"maxthreads\" val0=\"\$SLOTS\" display|" ./config.xml + && sed -i "s|attr=\"maxvirtmem\" val0=.*/>|attr=\"maxvirtmem\" val0=\"\$GALAXY_MEMORY_GB\"/>|" ./config.xml + && sed -i "s|attr=\"insertThreads\" val0=.*/>|attr=\"insertThreads\" val0=\"\$SLOTS\"/>|" ./config.xml #end if ## output the configuration file on stdout && cat ./config.xml @@ -53,24 +54,19 @@ -f $zip_file -o ./ - ##; - ##sleep 1000000 ]]> </command> <configfiles> <configfile name="vgp_mode"><![CDATA[ #if $configuration_options.configuration == 'vgp' - #import os - #set cores = os.environ.get('GALAXY_SLOTS', 2) - #set memory = os.environ.get('GALAXY_MEMORY_MB', 4000) / 1000 <hybridScaffold> <version> <flag attr="version" val0="\$Id: hybridScaffold_DLE1_config.xml 7702 2018-06-25 20:53:51Z apang \$"/> </version> <global> - <flag attr="maxmem" val0="$memory" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/> - <flag attr="maxthreads" val0="$cores" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/> - <flag attr="maxvirtmem" val0="$memory"/> + <flag attr="maxmem" val0="__MEMORY__" display="Maximum memory (GB)" group="Global options" description="Define the maximum amount of RAM in gigabytes to be used by each process."/> + <flag attr="maxthreads" val0="__CORES__" display="Max threads" group="Global options" description="Define maximum number of threads to be used by each process."/> + <flag attr="maxvirtmem" val0="__MEMORY__"/> <flag attr="RAmem" val0="3" val1="1"/> </global> <fasta2cmap> @@ -100,7 +96,7 @@ <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/> <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/> <flag attr="hashMultiMatch" val0="30" val1="10"/> - <flag attr="insertThreads" val0="$cores"/> + <flag attr="insertThreads" val0="__CORES__"/> <flag attr="nosplit" val0="2"/> <flag attr="biaswt" val0="0"/> <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/> @@ -136,7 +132,7 @@ <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/> <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/> <flag attr="hashMultiMatch" val0="30" val1="10"/> - <flag attr="insertThreads" val0="$cores"/> + <flag attr="insertThreads" val0="__CORES__"/> <flag attr="nosplit" val0="2"/> <flag attr="biaswt" val0="0"/> <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output initial alignments. Recommended starting value of 1e-5/genome size in Mb."/> @@ -178,7 +174,7 @@ <flag attr="RepeatMask" val0="4" val1="0.01" display=""/> <flag attr="RepeatRec" val0="0.7" val1="0.6" val2="1.4" display=""/> <flag attr="pairmerge" val0="80" val1="0.2" display="Min alignment length and Max endoutlier" group="Merging" description="Minimum alignment length required for pair merge, and the maximum endoutlier allowed."/> - <flag attr="maxmem" val0="$memory" display=""/> + <flag attr="maxmem" val0="__MEMORY__" display=""/> <flag attr="pairmergeRepeat"/> <flag attr="NoBpp"/> <flag attr="first" val0="-1" display=""/> @@ -201,7 +197,7 @@ <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/> <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/> <flag attr="hashMultiMatch" val0="30" val1="10"/> - <flag attr="insertThreads" val0="$cores"/> + <flag attr="insertThreads" val0="__CORES__"/> <flag attr="nosplit" val0="2"/> <flag attr="biaswt" val0="0"/> <flag attr="T" val0="1e-10" display="P-value" group="Initial alignment" description="Minimum confidence value to output intial alignments. Recommended starting value of 1e-5/genome size in Mb."/> @@ -238,7 +234,7 @@ <flag attr="hashgen" val0="5" val1="3" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/> <flag attr="hash" val0="-hashdelta" val1="50"/> <flag attr="hashMultiMatch" val0="30" val1="10" val2="3"/> - <flag attr="insertThreads" val0="$cores"/> + <flag attr="insertThreads" val0="__CORES__"/> <flag attr="nosplit" val0="2"/> <flag attr="biaswt" val0="0"/> <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/> @@ -275,7 +271,7 @@ <flag attr="hashgen" val0="5" val1="7" val2="2.4" val3="1.5" val4="0.05" val5="5.0" val6="1" val7="1" val8="4"/> <flag attr="hash" val0="-hashdelta" val1="26" val2="10" val3="46"/> <flag attr="hashMultiMatch" val0="30" val1="10"/> - <flag attr="insertThreads" val0="$cores"/> + <flag attr="insertThreads" val0="__CORES__"/> <flag attr="nosplit" val0="2"/> <flag attr="biaswt" val0="0"/> <flag attr="T" val0="1e-10" display="P-value" group="Final alignment" description="Minimum confidence score used to align NGS contigs back to hybrid scaffold."/> @@ -348,7 +344,7 @@ <flag attr="HSDrange" val0="1.0"/> <flag attr="hashoffset" val0="1"/> <flag attr="hashMultiMatch" val0="15"/> - <flag attr="insertThreads" val0="$cores"/> + <flag attr="insertThreads" val0="__CORES__"/> <flag attr="BestRef" val0="1"/> <flag attr="BestRefPV" val0="1"/> <flag attr="ChimQuality"/> @@ -453,16 +449,16 @@ </assert_contents> </output> <assert_stdout> - <has_text text='attr="maxmem" val0="4.0"'/> + <has_text text='attr="maxmem" val0="8"'/> </assert_stdout> <assert_stdout> - <has_text text='attr="maxthreads" val0="2"'/> + <has_text text='attr="maxthreads" val0="1"'/> </assert_stdout> <assert_stdout> - <has_text text='attr="insertThreads" val0="2"'/> + <has_text text='attr="insertThreads" val0="1"'/> </assert_stdout> <assert_stdout> - <has_text text='attr="maxvirtmem" val0="4.0"'/> + <has_text text='attr="maxvirtmem" val0="8"'/> </assert_stdout> <assert_stdout> <has_text text="hybridScaffold"/> @@ -488,16 +484,16 @@ <output name="ngs_contigs_scaffold_gap" file="test_02.gap" ftype="txt"/> <output name="report" file="test_02_report.txt" ftype="txt"/> <assert_stdout> - <has_text text='attr="maxmem" val0="4.0"'/> + <has_text text='attr="maxmem" val0="8"'/> </assert_stdout> <assert_stdout> - <has_text text='attr="maxthreads" val0="2"'/> + <has_text text='attr="maxthreads" val0="1"'/> </assert_stdout> <assert_stdout> - <has_text text='attr="insertThreads" val0="2"'/> + <has_text text='attr="insertThreads" val0="1"'/> </assert_stdout> <assert_stdout> - <has_text text='attr="maxvirtmem" val0="4.0"'/> + <has_text text='attr="maxvirtmem" val0="8"'/> </assert_stdout> <assert_stdout> <has_text text="hybridScaffold"/> @@ -531,16 +527,16 @@ </assert_contents> </output> <assert_stdout> - <has_text text='attr="maxmem" val0="4.0"'/> + <has_text text='attr="maxmem" val0="8"'/> </assert_stdout> <assert_stdout> - <has_text text='attr="maxthreads" val0="2"'/> + <has_text text='attr="maxthreads" val0="1"'/> </assert_stdout> <assert_stdout> - <has_text text='attr="insertThreads" val0="2"'/> + <has_text text='attr="insertThreads" val0="1"'/> </assert_stdout> <assert_stdout> - <has_text text='attr="maxvirtmem" val0="4.0"'/> + <has_text text='attr="maxvirtmem" val0="8"'/> </assert_stdout> <assert_stdout> <has_text text="hybridScaffold"/> @@ -572,16 +568,16 @@ </assert_contents> </output> <assert_stdout> - <has_text text='attr="maxmem" val0="4.0"'/> + <has_text text='attr="maxmem" val0="8"'/> </assert_stdout> <assert_stdout> - <has_text text='attr="maxthreads" val0="2"'/> + <has_text text='attr="maxthreads" val0="1"'/> </assert_stdout> <assert_stdout> - <has_text text='attr="insertThreads" val0="2"'/> + <has_text text='attr="insertThreads" val0="1"'/> </assert_stdout> <assert_stdout> - <has_text text='attr="maxvirtmem" val0="4.0"'/> + <has_text text='attr="maxvirtmem" val0="8"'/> </assert_stdout> <assert_stdout> <has_text text="hybridScaffold"/>