Mercurial > repos > iuc > crossmap_bed
diff crossmap_bed.xml @ 9:ee86b27291b5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"
author | iuc |
---|---|
date | Thu, 20 Jan 2022 04:31:56 +0000 |
parents | f4a70882a71b |
children | 50b7875a49d0 |
line wrap: on
line diff
--- a/crossmap_bed.xml Thu Jul 15 16:19:05 2021 +0000 +++ b/crossmap_bed.xml Thu Jan 20 04:31:56 2022 +0000 @@ -18,15 +18,15 @@ <command><![CDATA[ CrossMap.py bed '${chain_source.input_chain}' - '${input}' #if $merge_unmapped_entries: > '${output_combined}' #else: output + --unmap-file output.unmap #end if - +--chromid $chromid ]]></command> @@ -35,7 +35,11 @@ help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/> <expand macro="chain" /> - + <param name="chromid" type="select" label="Style of chromosome IDs"> + <option value="a" selected="true">As-is</option> + <option value="l">Long style, e.g. chr1, chrX</option> + <option value="s">Short style, e.g. 1, X</option> + </param> <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/> </inputs> @@ -76,6 +80,7 @@ <param name="index_source" value="history"/> <param name="input_chain" value="aToB.over.chain" ftype="txt"/> <param name="merge_unmapped_entries" value="false" /> + <param name="chromid" value="s" /> <output name="output_valid" file="test_bed_02_output_a__only-matches.bed"/> <output name="output_failed" file="test_bed_02_output_a__only_fails.bed"/> @@ -85,6 +90,7 @@ <param name="index_source" value="history"/> <param name="input_chain" value="aToB.over.chain" ftype="txt"/> <param name="merge_unmapped_entries" value="true" /> + <param name="chromid" value="s" /> <output name="output_combined" file="test_bed_02_output_a__all.bed"/> </test>