I wrote five tools to process genetic data. All them were verified to work correctly out of galaxy and also as isolated tools inside galaxy. Also, the intermediate results, produced by a tool and used as an input of the next one, are ok. In short, everything works well when using the tools in isolation, but not when they are laid in sequence in a workflow. To illustrate, I show here the xml files of the first two tools.
Tool1: reads a paired collection of genetic data where the genes are identified by Gene Symbol and changes the identification to UniProt Id.
Current xml file is as below:
<tool id="gs2up" name="GS2UP: Gene Symbol to UniProt" version="0.1.0"> <description>-</description> <command> <![CDATA[ perl $__tool_directory__/GS2UP.pl $gstcga $gstcga.name $uptcga ]]> </command> <inputs> <param type="data" name="gstcga" format="tabular" /> </inputs> <outputs> <data format="tabular" name="uptcga" label="up_$(gstcga.name)" /> </outputs> </tool>
Tool 2: reads a paired collection of genetic data, where the genes are identified by UniProt Id and for each dataset generates three output datasets. That is to say, this tool uses a paired collection as input and generates a triplet list.
The xml file is as below:
<tool id="urgel" name="URGEL" version="0.1.0"> <description>-</description> <command> <![CDATA[perl $__tool_directory__/URGEL.pl $tcga.forward $tcga.reverse $triplet.thrsh $triplet.diffrn $triplet.upreg ]]> </command> <inputs> <param name="tcga" type="data_collection" collection_type="paired" format="txt" /> </inputs> <outputs> <collection name="triplet" type="list" label="ur_$(tcga.name)" > <data name="thrsh" format="txt" /> <data name="diffrn" format="txt" /> <data name="upreg" format="txt" /> </collection> </outputs> </tool>
As a newbie to Galaxy, I may be incurring an error. However, I can’t find it alone and would appreciate any help.