enasearch_retrieve_run_report: generate

annotate generate_macros.py @ 2:3dd81790a236 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch commit a0adc28145cce02ecaed3a90156ed54c4385d1a0"

author	iuc
date	Tue, 21 Jan 2020 19:06:02 -0500
parents	c320e878909a
children

rev	line source
0 c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	1 #!/usr/bin/env python
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	2
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	3 import enasearch
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	4
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	5 spaces = ' '
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	6 operator_names = {
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	7 "=": "equal",
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	8 "!=": "different",
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	9 "<": "lower",
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	10 "<=": "equal or lower",
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	11 ">": "higher",
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	12 ">=": "equal or higher",
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	13 }
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	14
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	15
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	16 def format_name(name, alternative_name):
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	17 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	18 Format name to remove None name and & in name
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	19 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	20 if name is None:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	21 name = alternative_name
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	22 name = name.replace("&", "and")
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	23 return name
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	24
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	25
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	26 def sort_by_name(dict):
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	27 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	28 Sort a dictionary on the values
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	29 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	30 return sorted(dict, key=dict.get)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	31
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	32
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	33 def write_analysis_fields():
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	34 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	35 Write the analysis fields
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	36 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	37 s = '%s<xml name="analysis_fields">\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	38 fields = enasearch.get_returnable_fields(result="analysis", verbose=False)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	39 for f in fields:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	40 s += '%s<option value="%s">%s</option>\n' % (2 * spaces, f, f)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	41 s += '%s</xml>\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	42 return s
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	43
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	44
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	45 def write_display_options():
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	46 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	47 Write the display options
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	48 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	49 s = '%s<xml name="display_options">\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	50 when_s = '%s<xml name="when_display_options">\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	51 options = enasearch.get_display_options(verbose=False)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	52 for opt in options:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	53 s += '%s<option value="%s">%s</option>\n' % (2 * spaces, opt, options[opt]['description'])
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	54 when_s += '%s<when value="%s">\n' % (2 * spaces, opt)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	55 if opt == 'fasta' or opt == 'fastq':
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	56 when_s += '%s<param name="range_start" argument="--subseq_range" type="integer" optional="true" label="Start integer for subsequences"/>\n' % (3 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	57 when_s += '%s<param name="range_stop" argument="--subseq_range" type="integer" optional="true" label="Stop integer for subsequences"/>\n' % (3 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	58 else:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	59 when_s += '%s<param argument="--offset" type="integer" optional="true" label="First record to get"/>\n' % (3 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	60 when_s += '%s<param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>\n' % (3 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	61 when_s += '%s</when>\n' % (2 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	62 s += '%s</xml>\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	63 when_s += '%s</xml>\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	64 s += when_s
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	65 return s
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	66
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	67
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	68 def write_run_fields():
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	69 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	70 Write the run fields
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	71 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	72 s = '%s<xml name="run_fields">\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	73 fields = enasearch.get_returnable_fields(result="read_run", verbose=False)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	74 for f in fields:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	75 s += '%s<option value="%s">%s</option>\n' % (2 * spaces, f, f)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	76 s += '%s</xml>\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	77 return s
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	78
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	79
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	80 def write_taxonomy_results():
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	81 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	82 Write the possible taxonomy results
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	83 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	84 s = '%s<xml name="taxonomy_results">\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	85 fields = enasearch.get_taxonomy_results(verbose=False)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	86 for f in fields:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	87 s += '%s<option value="%s">%s</option>\n' % (2 * spaces, f, fields[f]['description'])
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	88 s += '%s</xml>\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	89 return s
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	90
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	91
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	92 def write_result_parameters(fts=False):
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	93 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	94 Write the parameters that are dependant of results
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	95 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	96 res = enasearch.get_results(verbose=False)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	97 options = enasearch.get_display_options(verbose=False)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	98 ft = enasearch.get_filter_types(verbose=False)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	99 # Format the filter type related parameters
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	100 ft_parameters = {}
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	101 for t in ft:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	102 s = ''
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	103 if 'operators' in ft[t]:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	104 s = '%s<param name="operation" type="select" label="Operator">\n' % (7 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	105 for o in ft[t]['operators']:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	106 on = o
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	107 if o in operator_names:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	108 on = operator_names[o]
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	109 s += '%s<option value="%s">%s</option>\n' % (8 * spaces, on, on)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	110 s += '%s</param>\n' % (7 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	111 if 'value' in ft[t]:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	112 value_format = 'float' if t == 'Number' else 'text'
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	113 s += '%s<param name="value" type="%s" value="" label="%s"/>\n' % (7 * spaces, value_format, ft[t]['value'])
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	114 elif 'values' in ft[t]:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	115 s += '%s<param name="value" type="select" label="Value">\n' % (7 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	116 for v in ft[t]['values']:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	117 s += '%s<option value="%s">%s</option>\n' % (8 * spaces, v, v)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	118 s += '%s</param>\n' % (7 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	119 else:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	120 s += '%s<conditional name="op">\n' % (7 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	121 s += '%s<param name="operation" type="select" label="Operation">\n' % (8 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	122 for op in ft[t]:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	123 s += '%s<option value="%s">%s</option>\n' % (9 * spaces, op, ft[t][op]['description'])
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	124 s += '%s</param>\n' % (8 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	125 for op in ft[t]:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	126 s += '%s<when value="%s">\n' % (8 * spaces, op)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	127 s += '%s<param name="values" type="text" value="" label="%s" help="Values separated by simple comma"/>\n' % (9 * spaces, ",".join(ft[t][op]['parameters']))
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	128 s += '%s</when>\n' % (8 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	129 s += '%s</conditional>\n' % (7 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	130 ft_parameters[t] = s
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	131 # Start adding the conditional
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	132 s = '%s<conditional name="res">\n' % (2 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	133 # Add result parameter
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	134 s += '%s<param argument="--result" type="select" label="Result to return">\n' % (3 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	135 for r in res:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	136 s += '%s<option value="%s">%s</option>\n' % (4 * spaces, r, res[r]['description'])
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	137 s += '%s</param>\n' % (3 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	138 for r in res:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	139 sf = enasearch.get_sortable_fields(r)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	140 ff = res[r]['filter_fields']
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	141 s += '%s<when value="%s">\n' % (3 * spaces, r)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	142 if not fts:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	143 s += '%s<repeat name="queries" title="Add a query">\n' % (4 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	144 # Add combination operator
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	145 s += '%s<param name="combination_operation" type="select" label="Combination operation">\n' % (5 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	146 s += '%s<option value="AND">AND</option>\n' % (6 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	147 s += '%s<option value="OR">OR</option>\n' % (6 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	148 s += '%s<option value="NOT">NOT</option>\n' % (6 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	149 s += '%s</param>\n' % (5 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	150 s += '%s<conditional name="filter_field">\n' % (5 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	151 s += '%s<param name="field" type="select" label="Field to query">\n' % (6 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	152 for f in ff:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	153 s += '%s<option value="%s">%s</option>\n' % (7 * spaces, f, ff[f]['description'])
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	154 s += '%s</param>\n' % (6 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	155 for f in ff:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	156 # Add the correct parameter given the type of field
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	157 typ = ff[f]['type'].capitalize()
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	158 if typ not in ft_parameters:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	159 if f == 'location':
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	160 typ = 'Geospatial'
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	161 else:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	162 continue
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	163 s += '%s<when value="%s">\n' % (6 * spaces, f)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	164 s += ft_parameters[typ]
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	165 s += '%s</when>\n' % (6 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	166 s += '%s</conditional>\n' % (5 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	167 s += '%s</repeat>\n' % (4 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	168 # Add display opt
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	169 s += '%s<conditional name="display_opt">\n' % (4 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	170 s += '%s<param argument="--display" type="select" label="Display option to specify the display format">\n' % (5 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	171 s += '%s<expand macro="display_options"/>\n' % (6 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	172 s += '%s</param>\n' % (5 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	173 for opt in options:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	174 s += '%s<when value="%s"' % (5 * spaces, opt)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	175 if opt != 'fasta' and opt != 'fastq':
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	176 s += '>\n'
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	177 s += '%s<param argument="--offset" type="integer" optional="true" label="First record to get"/>\n' % (6 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	178 s += '%s<param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>\n' % (6 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	179 if opt == 'report':
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	180 s += '%s<param argument="--fields" type="select" multiple="true" label="Fields to return">\n' % (6 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	181 for f in res[r]['returnable_fields']:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	182 s += '%s<option value="%s">%s</option>\n' % (7 * spaces, f, f)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	183 s += '%s</param>\n' % (6 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	184 s += '%s<param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">\n' % (6 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	185 for f in sf:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	186 s += '%s<option value="%s">%s</option>\n' % (7 * spaces, f, sf[f]['description'])
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	187 s += '%s</param>\n' % (6 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	188 s += '%s</when>\n' % (5 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	189 else:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	190 s += '/>\n'
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	191 s += '%s</conditional>\n' % (4 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	192 s += '%s</when>\n' % (3 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	193 s += '%s</conditional>\n' % (2 * spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	194 return s
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	195
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	196
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	197 def write_search_data_parameters():
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	198 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	199 Write the parameters for search_data
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	200 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	201 fts = '%s<xml name="free_text_search">\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	202 fts += write_result_parameters(True)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	203 fts += '%s</xml>\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	204 cts = '%s<xml name="conditional_text_search">\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	205 cts += write_result_parameters(False)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	206 cts += '%s</xml>\n' % (spaces)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	207 return fts + cts
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	208
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	209
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	210 def generate_search_macros(filepath):
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	211 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	212 Generate the content of the macro file
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	213 """
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	214 s = '<?xml version="1.0" ?>\n'
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	215 s += '<macros>\n'
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	216 s += write_analysis_fields()
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	217 s += write_display_options()
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	218 s += write_run_fields()
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	219 s += write_taxonomy_results()
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	220 s += write_search_data_parameters()
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	221 s += '</macros>\n'
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	222 with open(filepath, "w") as file:
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	223 file.write(s)
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	224
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	225
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	226 if __name__ == '__main__':
c320e878909a planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87 iuc parents: diff changeset	227 generate_search_macros("search_macros.xml")

Mercurial > repos > iuc > enasearch_retrieve_run_report

annotate generate_macros.py @ 2:3dd81790a236 draft default tip