Repository revision
17:f6e09a37bc8b

Repository 'apollo_export'
hg clone https://toolshed.g2.bx.psu.edu/repos/gga/apollo_export

Retrieve Data tool metadata
Miscellaneous
from Apollo into Galaxy
export
toolshed.g2.bx.psu.edu/repos/gga/apollo_export/export/4.2.13+galaxy0
4.2.13+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/gga/apollo_export/export/4.2.13+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/gga/apollo_export/export/4.2.13
toolshed.g2.bx.psu.edu/repos/gga/apollo_export/export/4.2.5
toolshed.g2.bx.psu.edu/repos/gga/apollo_export/export/4.2.3
toolshed.g2.bx.psu.edu/repos/gga/apollo_export/export/4.2.1
toolshed.g2.bx.psu.edu/repos/gga/apollo_export/export/4.1
toolshed.g2.bx.psu.edu/repos/gga/apollo_export/export/4.0.0
toolshed.g2.bx.psu.edu/repos/gga/apollo_export/export/3.1
toolshed.g2.bx.psu.edu/repos/gga/apollo_export/export/3.0
export
Requirements (dependencies defined in the <requirements> tag set)
name version type
apollo 4.2.13 package
Additional information about this tool
if [ -z "\$ARROW_GLOBAL_CONFIG_PATH" ]; then
        echo "__default: local" > '.auth.yml' &&
        echo "local:" >> '.auth.yml' &&
        echo "    url: \"\$GALAXY_WEBAPOLLO_URL\"" >> '.auth.yml' &&
        echo "    username: \"\$GALAXY_WEBAPOLLO_USER\"" >> '.auth.yml' &&
        echo "    password: \"\$GALAXY_WEBAPOLLO_PASSWORD\"" >> '.auth.yml' &&

        export ARROW_GLOBAL_CONFIG_PATH='.auth.yml'
      ; fi &&
  
python '$__tool_directory__/export.py'





#if $org_source.source_select == "auto_json":
    --org_json '${org_source.org_file}'
#elif $org_source.source_select == "select":
    --org_id '${org_source.org_select}'
#else:
    --org_raw '${org_source.org_raw}'
#end if

  

#if $cn_source.source_select == "auto":
    #if str($cn_source.cn_file) != "None":
        --seq_fasta '$cn_source.cn_file'
    #end if
#else
    #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0:
        --seq_raw
        #for $item in $cn_source.refseqs:
            '${item.refseq}'
        #end for
    #end if
#end if

  

--gff '$gff_out'
$gff_with_fasta
--fasta_pep '$fasta_pep'
--fasta_cds '$fasta_cds'
--fasta_cdna '$fasta_cdna'
--vcf '$vcf_out'
--json '$json_out'
$die

'$__user_email__'

None
False
Functional tests
name inputs outputs required files
Test-1 org_source|org_raw: test_organism
org_source|source_select: direct
cn_source|source_select: all
name: value
name: value
name: value
name: value
name: value
name: value
value