Mercurial > repos > iuc > sinto_fragments
changeset 1:02f96be6c3c9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit 3c8b3c4132aae6131854e2b5ef5cdcb7b30c4f0f
author | iuc |
---|---|
date | Tue, 18 Apr 2023 09:28:12 +0000 |
parents | b6009d0098d7 |
children | 29e6bfb2cf49 |
files | sinto_fragments.xml |
diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/sinto_fragments.xml Thu Apr 13 11:03:34 2023 +0000 +++ b/sinto_fragments.xml Tue Apr 18 09:28:12 2023 +0000 @@ -27,7 +27,7 @@ <param argument="--bam" type="data" format="bam" label="Input BAM file" /> <param argument="--min_mapq" type="integer" value="30" min="0" label="Minimum MAPQ required to retain fragment" /> <param argument="--barcodetag" type="text" value="CB" label="Read tag storing cell barcode information" /> - <param argument="--barcode_regex" type="text" value="[^:]*" label="Read tag storing cell barcode information" + <param argument="--barcode_regex" type="text" value="[^:]*" label="Regular expression used to extract cell barcode from read name" help="[^:]* matches all characters up to the first colon" > <sanitizer> <valid initial="string.printable"> @@ -36,17 +36,17 @@ </sanitizer> </param> <param argument="--max_distance" type="integer" value="5000" min="0" label="Maximum distance between integration sites for the fragment to be retained" - help="Allows filtering of implausible fragments that likely result from incorrect mapping positions. Default is 5000 bp."/> + help="Allows filtering of implausible fragments that likely result from incorrect mapping positions."/> <param argument="--min_distance" type="integer" value="10" min="0" label="Minimum distance between integration sites for the fragment to be retained" - help="Allows filtering of implausible fragments that likely result from incorrect mapping positions. Default is 5000 bp."/> - <param argument="--shift_plus" type="integer" value="4" label="Minimum MAPQ required to retain fragment" /> - <param argument="--shift_minus" type="integer" value="-5" label="Minimum MAPQ required to retain fragment" /> + help="Allows filtering of implausible fragments that likely result from incorrect mapping positions."/> + <param argument="--shift_plus" type="integer" value="4" label=" Number of bases to shift Tn5 insertion position by on the forward strand" /> + <param argument="--shift_minus" type="integer" value="-5" label="Number of bases to shift Tn5 insertion position by on the reverse strand" /> <param argument="--collapse_within" type="boolean" truevalue="--collapse_within" falsevalue="" label="Take cell barcode into account when collapsing duplicate fragments" help="Setting this flag means that fragments with the same coordinates can be identified provided they originate from a different cell barcode." /> </inputs> <outputs> - <data name='fragments' format='bed' label="${tool.name} on ${on_string}: fragments" /> + <data name='fragments' format='bed' label="${tool.name} on ${on_string}: fragments BED" /> </outputs> <tests> <test expect_num_outputs="1">