Mercurial > repos > bgruening > cp_relate_objects
diff relate_objects.xml @ 0:3a2cfcd7c38a draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
| author | bgruening |
|---|---|
| date | Thu, 26 Mar 2020 17:44:27 -0400 |
| parents | |
| children | b6f13e783ac5 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/relate_objects.xml Thu Mar 26 17:44:27 2020 -0400 @@ -0,0 +1,156 @@ +<tool id="cp_relate_objects" name="RelateObjects" version="@CP_VERSION@"> + <description>assigns relationships parent-children between objects</description> + <macros> + <import>macros.xml</import> + <xml name="distToOtherParents"> + <conditional name="con_other_parent_dist"> + <param name="calc_dist_to_others" label="Calculate distances to other parents?" display="radio" type="select"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <when value="Yes"> + <repeat name="rpt_parent_name" title="Parent Name"> + <param name="other_parent_name" type="text" label="Parent name"> + <expand macro="text_validator" /> + </param> + </repeat> + </when> + <when value="No" /> + </conditional> + </xml> + </macros> + + <expand macro="py_requirements"/> + <expand macro="cmd_modules" /> + + <configfiles> + <inputs name="inputs" /> + <configfile name="script_file"> +import json +import sys +import os + +FOURSPACES=@SPACES@ + +input_json_path = sys.argv[1] +input_pipeline= sys.argv[2] + +params = json.load(open(input_json_path, "r")) + +def writero(): + _str = "\nRelateObjects:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:5|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count + + _str += FOURSPACES + "Parent objects:%s\n" % params['parent_objects'] + + _str += FOURSPACES + "Child objects:%s\n" % params['child_objects'] + _str += FOURSPACES + "Calculate child-parent distances?:%s\n" % params['con_dist']['calc_dist'] + _str += FOURSPACES + "Calculate per-parent means for all child measurements?:%s\n" % params['means_for_all'] + + dist_others = params['con_dist']['con_other_parent_dist']['calc_dist_to_others'] + + _str += FOURSPACES + "Calculate distances to other parents?:%s\n" % dist_others + + name_flag = params['con_save_child']['save_child_as_new'] + _str += FOURSPACES + "Do you want to save the children with parents as a new object set?:%s\n" % name_flag + + if name_flag == "Yes": + _str += FOURSPACES + "Name the output object:%s\n" % params['con_save_child']['name_output'] + else: + _str += FOURSPACES + "Name the output object:None\n" + + if dist_others == "Yes": + for pname in params['con_dist']['con_other_parent_dist']['rpt_parent_name']: + _str += FOURSPACES + "Parent name:%s\n" % pname['other_parent_name'] + + return _str + +with open(input_pipeline) as fin: + lines = fin.readlines() + + k, v = lines[4].strip().split(':') + + module_count = int(v) + new_count = module_count + 1 + lines[4] = k + ":%d\n" % new_count + with open("output", "w") as f: + f.writelines(lines) + f.write(writero()) + +f.close() + </configfile> + </configfiles> + + <inputs> + <expand macro="input_pipeline_macro"/> + <param name="parent_objects" label="Parent objects" type="text"> + <expand macro="text_validator" /> + </param> + <param name="child_objects" label="Child objects" type="text" > + <expand macro="text_validator" /> + </param> + <param name="means_for_all" label="Calculate per-parent means for all child measurements?:" display="radio" type="select"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <conditional name="con_dist"> + <param name="calc_dist" label="Calculate child-parent distances?" type="select"> + <option value="None">None</option> + <option value="Centroid">Centroid</option> + <option value="Minimum">Minimum</option> + <option value="Both">Both</option> + </param> + <when value="Centroid"> + <expand macro="distToOtherParents" /> + </when> + <when value="Minimum"> + <expand macro="distToOtherParents" /> + </when> + <when value="Both"> + <expand macro="distToOtherParents" /> + </when> + <when value="None" /> + </conditional> + <conditional name="con_save_child"> + <param name="save_child_as_new" label="Do you want to save the children with parents as a new object set?" display="radio" type="select"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <when value="Yes"> + <param name="name_output" type="text" label="Name the output object"> + <expand macro="text_validator" /> + </param> + </when> + <when value="No" /> + </conditional> + </inputs> + + <outputs> + <expand macro="output_pipeline_macro" /> + </outputs> + + <tests> + <test> + <expand macro="test_input_pipeline_param" /> + + <param name="parent_objects" value="Nuclei" /> + <param name="child_objects" value="Nucleoli" /> + <param name="means_for_all" value="Yes" /> + <conditional name="con_dist"> + <param name="calc_dist" value="Both" /> + <conditional name="con_other_parent_dist"> + <param name="calc_dist_to_others" value="No" /> + </conditional> + </conditional> + <conditional name="con_save_child"> + <param name="save_child_as_new" value="Yes" /> + <param name="name_output" value="RelateObjects" /> + </conditional> + + <expand macro="test_out_file" file="relate_objects.txt" /> + </test> + </tests> + + <expand macro="help" module="RelateObjects" /> + <expand macro="citations" /> + +</tool>