Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filemerger/FileMerger/2.8+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filemerger/FileMerger/2.6+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filemerger/FileMerger/2.5+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filemerger/FileMerger/2.2.0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filemerger/FileMerger/2.1.0 |
FileMerger |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
openms | 2.8 | package |
openms-thirdparty | 2.8 | package |
omssa | 2.1.9 | package |
blast | 2.13.0 | package |
ctdopts | 1.4 | package |
Additional information about this tool |
#def quote(s): #set $s = [ _ for _ in $s.split(" ") if _ != "" ] #set $q = False #for $i, $p in enumerate($s): #if $p == "": #continue #end if #if $p.startswith('"'): #set $q = True #end if ## #if p.startswith('-'): ## #set p = "\\" + p ## #elif p.startswith('"-'): ## #set p = "\\" + p[1:] ## #end if #if not $q: #set $s[i] = '"%s"' % p #end if #if $p.endswith('"'): #set $q = False #end if #end for #return " ".join($s) #end def #def oms2gxyext(o) #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} #return m[o] #end def #def gxy2omsext(g) #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} #return m[g] #end def #import re ## Preprocessing mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir out && #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir rt_concat_trafo_out && mkdir ${' '.join(["'rt_concat_trafo_out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && #end if ## Main program call set -o pipefail && FileMerger -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' 'FileMerger.ctd' '$args_json' '$hardcoded_json' && FileMerger -ini FileMerger.ctd -in #if $in_cond.in_select == "no" ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' #end if -out 'out/output.${out_type}' #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -rt_concat:trafo_out ${' '.join(["'rt_concat_trafo_out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("trafoxml")) for i, f in enumerate($in_cond.in) if f])} #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' #end if ## Postprocessing && mv 'out/output.${out_type}' '$out' #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') ${' '.join(["&& mv -n 'rt_concat_trafo_out/%(bn)s/%(id)s.%(gext)s' 'rt_concat_trafo_out/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("trafoxml")} for i, f in enumerate($in_cond.in) if f])} #end if #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv 'FileMerger.ctd' '$ctd_out' #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
in_cond|in: ['FileMerger_2_input1.dta', 'FileMerger_2_input2.dta'] out_type: mzML annotate_file_origin: False append_method: append_rows rt_concat|gap: 0.0 raw|rt_auto: False raw|rt_custom: 5.0 10.0 raw|rt_filename: False raw|ms_level: 0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
FileMerger_2_input1.dta FileMerger_2_input2.dta value |
Test-2 |
in_cond|in: ['FileMerger_3_input1.dta', 'FileMerger_3_input2.dta'] out_type: mzML annotate_file_origin: False append_method: append_rows rt_concat|gap: 0.0 raw|rt_auto: True raw|rt_custom: raw|rt_filename: False raw|ms_level: 0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
FileMerger_3_input1.dta FileMerger_3_input2.dta value |
Test-3 |
in_cond|in: ['FileMerger_4_input1.dta2d', 'FileMerger_4_input2.dta2d'] out_type: mzML annotate_file_origin: False append_method: append_rows rt_concat|gap: 0.0 raw|rt_auto: False raw|rt_custom: raw|rt_filename: False raw|ms_level: 0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
FileMerger_4_input1.dta2d FileMerger_4_input2.dta2d value |
Test-4 |
in_cond|in: ['FileMerger_5_input_rt1023.331.dta', 'FileMerger_5_input_rt2044.334.dta', 'FileMerger_5_input_rt889.32.dta'] out_type: mzML annotate_file_origin: False append_method: append_rows rt_concat|gap: 0.0 raw|rt_auto: False raw|rt_custom: raw|rt_filename: True raw|ms_level: 2 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
FileMerger_5_input_rt1023.331.dta FileMerger_5_input_rt2044.334.dta FileMerger_5_input_rt889.32.dta value |
Test-5 |
in_cond|in: ['FileMerger_6_input1.mzML', 'FileMerger_6_input2.mzML'] out_type: mzML annotate_file_origin: False append_method: append_rows rt_concat|gap: 0.0 raw|rt_auto: False raw|rt_custom: raw|rt_filename: False raw|ms_level: 0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
FileMerger_6_input1.mzML FileMerger_6_input2.mzML value |
Test-6 |
in_cond|in: ['FileMerger_7_input1.featureXML', 'FileMerger_7_input2.featureXML'] out_type: featureXML annotate_file_origin: False append_method: append_rows rt_concat|gap: 0.0 raw|rt_auto: False raw|rt_custom: raw|rt_filename: False raw|ms_level: 0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
FileMerger_7_input1.featureXML FileMerger_7_input2.featureXML value |
Test-7 |
in_cond|in: ['FileMerger_8_input1.consensusXML', 'FileMerger_8_input2.consensusXML'] out_type: consensusXML annotate_file_origin: False append_method: append_rows rt_concat|gap: 0.0 raw|rt_auto: False raw|rt_custom: raw|rt_filename: False raw|ms_level: 0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
FileMerger_8_input1.consensusXML FileMerger_8_input2.consensusXML value |
Test-8 |
in_cond|in: ['FileMerger_9_input1.traML', 'FileMerger_9_input2.traML'] out_type: traML annotate_file_origin: False append_method: append_rows rt_concat|gap: 0.0 raw|rt_auto: False raw|rt_custom: raw|rt_filename: False raw|ms_level: 0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
FileMerger_9_input1.traML FileMerger_9_input2.traML value |
Test-9 |
in_cond|in: ['FileMerger_6_input2.mzML', 'FileMerger_6_input2_2.mzML'] out_type: mzML annotate_file_origin: False append_method: append_rows rt_concat|gap: 10.0 raw|rt_auto: False raw|rt_custom: raw|rt_filename: False raw|ms_level: 0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'trafo_out_FLAG'] |
name: value name: value |
FileMerger_6_input2.mzML FileMerger_6_input2_2.mzML value |
Test-10 |
in_cond|in: ['FileMerger_8_input1.consensusXML', 'FileMerger_8_input2.consensusXML'] out_type: consensusXML annotate_file_origin: False append_method: append_cols rt_concat|gap: 0.0 raw|rt_auto: False raw|rt_custom: raw|rt_filename: False raw|ms_level: 0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
FileMerger_8_input1.consensusXML FileMerger_8_input2.consensusXML value |