Repository revision
15:c44f824c051a

Repository 'cactus_export'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export

Cactus: export tool metadata
Miscellaneous
Cactus: export
whole-genome multiple sequence alignment to other formats
cactus_export
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.7.1+galaxy0
2.7.1+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.7.1+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.6.7+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.6.4+galaxy1
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.5.1+galaxy1
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.5.1+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.4.4+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.4.3+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.4.2+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.4.1+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.4.0+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.2.4+galaxy1
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.2.4+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.2.1+galaxy1
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.2.1+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.1.1+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxy-australia/cactus_export/cactus_export/2.0.5+galaxy0
cactus_export
Requirements (dependencies defined in the <requirements> tag set)
No requirements defined
Additional information about this tool
## check if the reference level was specified
        #if $export_select.format in ['maf_selector', 'vg_selector']:
            #if $export_select.ref_level == '':
                echo "You must provide a reference level" &&
                exit 1 ;
            #end if
        #end if

        ln -s '$hal_file' alignment.hal 

        ## make a MAF
        #if $export_select.format == 'maf_selector':
            &&
            hal2maf 
            --refGenome $export_select.ref_level
            alignment.hal
            alignment.maf
        #end if

        ## make an assemblyHub
        #if $export_select.format == 'ah_selector':
            &&
            hal2assemblyHub.py 
            --maxCores  \${GALAXY_SLOTS:-4}
            --maxMemory \${GALAXY_MEMORY_MB:-8196}M
            ./jobStore
            alignment.hal
            assemblyhub
            &&
            tar -cv assemblyhub > assemblyhub.tar
        #end if

        ## make a VG
        #if $export_select.format == 'vg_selector':
            &&
            hal2vg alignment.hal
            --progress 
            > alignment.pg
        #end if
None
False
Functional tests
No functional tests defined