annotate relate_objects.xml @ 0:3a2cfcd7c38a draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"

<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>