comparison epiviz_export.xml @ 0:78367907d256 draft default tip

planemo upload commit d56ec81d6c02ad971116dca44b22e02fb0a0ab30

0:78367907d256

<tool id="epiviz_export" name="Interactively visualize genomic data with Epiviz" version="0.1.0" python_template_version="3.5">
    <requirements>
    </requirements>
     <command detect_errors="exit_code"><![CDATA[
    	python $script_file 
    ]]></command>
    <configfiles>
	<configfile name="script_file">
import os
import sys
import json
file_location = []
file_type = []
file_annotations = [] 
#for $i, $s in enumerate($files)
tloc = '${s.input}'
tlocs = tloc.split("/")
file_location.append("/data/" + tlocs[len(tlocs)-1])
file_type.append('${s.format}')
tanno = '${s.fileanno}'
print(tanno)
tanno = tanno.split(",")
print(tanno)
ttanno = {}
for i in tanno:
	ti = i.split(":")
        ttanno[ti[0]] = ti[1]

file_annotations.append(ttanno)
#end for
epiviz_json = []
for i in range(0,len(file_location)):
	fdatatype = "bp" if file_type[i] == "BigWig" else "annotation"
	epiviz_json.append(
	   {
	     "url": file_location[i],
	     "file_type": file_type[i],
	     "datatype": fdatatype,
	     "name": file_location[i],
	     "id": file_location[i],
	     "annotation": file_annotations[i],
	     "metadata": []
	     }
	 )
print epiviz_json
fout = open('$output', "w")
json.dump(epiviz_json, fout)
fout.close()
</configfile>
    </configfiles>
    <inputs>
	<repeat name="files" title="Add File">
        	<param type="data" name="input" format="bigbed,bigwig"/>
		<param name="format" type="select" label="Data Format">
                	<option value="BigWig" selected="true">BigWig</option>
                	<option value="BigBed">BigBed</option>
                	<option value="tbx">tbx</option>
		</param>		
		<param type ="text" name="fileanno" format="json" /> 
	</repeat>
    </inputs>
    <outputs>
	<data name="output" format="json" from_work_dir="output.json" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="/test"/>
            <param name="format" value="bigbed"/>
            <param name="fileanno" value="annotation"/>
            <output name="output">
                <assert_contents>
                    <has_line line="datatype" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Usage: Choose files to interactively visualize with epiviz.
    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{epiviz,
  author = {epiviz},
  year = {2019},
  title = {epiviz},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/epiviz/epivizGalaxyTool},
}</citation>
    </citations>
</tool>