| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/customize_metaphlan_database/customize_metaphlan_database/3.0.14+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/customize_metaphlan_database/customize_metaphlan_database/3.0.13+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/customize_metaphlan_database/customize_metaphlan_database/3.0.9+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/customize_metaphlan_database/customize_metaphlan_database/3.0.8+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/customize_metaphlan_database/customize_metaphlan_database/3.0.7+galaxy0 |
| customize_metaphlan_database |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| metaphlan | 3.0.13 | package |
| seqtk | 1.3 | package |
| Additional information about this tool |
python '$__tool_directory__/customizemetadata.py'
$op.operation
#if $op.operation == "add_marker"
--in_json '$in_json'
--out_json '$out_json'
--name $op.name
--m_length $op.m_length
#for $s in $op.genomes
--g_length $s.g_length
#if str($s.gca) != ''
--gca '$s.gca'
#else
--gca ''
#end if
--k_name '$s.k_name'
--k_id $s.k_id
--p_name '$s.p_name'
--p_id $s.p_id
--c_name '$s.c_name'
--c_id $s.c_id
--o_name '$s.o_name'
--o_id $s.o_id
--f_name '$s.f_name'
--f_id $s.f_id
--g_name '$s.g_name'
--g_id $s.g_id
--s_name '$s.s_name'
--s_id $s.s_id
--t_name '$s.t_name'
#end for
&&
cat
'$in_fasta'
'$op.marker_seq'
> '$out_fasta'
#else if $op.operation == "remove_markers"
--in_json '$in_json'
--markers '$op.markers'
--out_json '$out_json'
--kept_markers 'kept_makers'
&&
seqtk subseq
'$in_fasta'
'kept_makers'
> '$out_fasta'
#else if $op.operation == "keep_markers"
--in_json '$in_json'
--markers '$op.markers'
--out_json '$out_json'
&&
seqtk subseq
'$in_fasta'
'$op.markers'
> '$out_fasta'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
in_fasta: test-db-without-one-marker.fasta in_json: test-db-without-one-marker.json op|marker_seq: marker_sequence.fasta op|name: 13076__A0A2I1PE66__CYJ72_10760 op|m_length: 540 op|genomes_0|g_length: 2411251 op|genomes_0|gca: GCA_002847845 op|genomes_0|k_name: Bacteria op|genomes_0|k_id: 2 op|genomes_0|p_name: Bacilli op|genomes_0|p_id: 1239 op|genomes_0|c_name: Negativicutes op|genomes_0|c_id: 91061 op|genomes_0|o_name: Lactobacillales op|genomes_0|o_id: 186826 op|genomes_0|f_name: Aerococcaceae op|genomes_0|f_id: 186827 op|genomes_0|g_name: Globicatella op|genomes_0|g_id: 13075 op|genomes_0|s_name: Globicatella_sanguinis op|genomes_0|s_id: 13076 op|genomes_0|t_name: GCA_002847845 op|operation: add_marker |
name: value name: value |
test-db-without-one-marker.fasta test-db-without-one-marker.json marker_sequence.fasta value |
| Test-2 |
in_fasta: test-db.fasta in_json: test-db.json op|markers: marker.txt op|operation: remove_markers |
name: value name: value |
test-db.fasta test-db.json marker.txt value |
| Test-3 |
in_fasta: test-db.fasta in_json: test-db.json op|markers: marker.txt op|operation: keep_markers |
name: value name: value |
test-db.fasta test-db.json marker.txt value |