Hi,
Tools with "change_format" in the <outputs> tag aren't working well in workflows:
I have a tool which uses the "change_format" option to output different types of files. The XML definition is similar to this:
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<outputs> <data format="fasta" name="output" metadata_source="input" label="$input.tag (FASTA)" > <change_format> <when input="wanttype" value="coordinates" format="bed" label="$input.tag (BED)" /> </change_format> </data> </outputs>
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The tool allows the user to select the output file type: FASTA or BED (the variable "wanttype"). This works fine when running the tool manually, but the tool can't be used in a workflow: the output type is always "FASTA" (the "change_format" is ignored) and so the tool can not be connected to other tools which need "bed" input.
-gordon