Mercurial > repos > yhoogstrate > crossmap
changeset 9:0cae6e3273a8 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd
| author | yhoogstrate |
|---|---|
| date | Wed, 05 Aug 2015 02:58:35 -0400 |
| parents | 9750f8c1d3cb |
| children | 4f280582a2fc |
| files | crossmap.xml |
| diffstat | 1 files changed, 8 insertions(+), 5 deletions(-) [+] |
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--- a/crossmap.xml Tue Aug 04 09:43:29 2015 -0400 +++ b/crossmap.xml Wed Aug 05 02:58:35 2015 -0400 @@ -7,7 +7,7 @@ <stdio> <regex match="Usage: CrossMap.py" source="stdin" level="fatal"/> - <regex match="^@ " source="stdin" level="warning" /> + <regex match=".*" source="both" level="log" description="tool progress"/> </stdio> <command> @@ -35,7 +35,10 @@ "$multiple.seq_source.input_fasta" #end if - $output + <!-- BED format does not write to the output file, but does write fails to stdout --> + > "$output" + + 2>/dev/null </command> <inputs> @@ -101,8 +104,8 @@ </param> </when> <when value="history"> - <param format="bed" name="input" type="data" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." /> - <param type="data" name="input_chain" label="LiftOver chain file" /> + <param type="data" format="bed" name="input" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." /> + <param type="data" name="input_chain" label="LiftOver chain file" /> </when> </conditional> </when> @@ -243,7 +246,7 @@ </inputs> <outputs> - <data format="text" name="output" label="${tool.name} on ${input.hid}: ${input.name}" /> + <data format="text" name="output" label="${tool.name} on " /> </outputs> <tests>