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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa |
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modified:
salmon.xml |
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| diff -r 570e7e9c19a5 -r 53e9709776a0 salmon.xml --- a/salmon.xml Fri Jun 30 05:45:09 2017 -0400 +++ b/salmon.xml Wed Jul 12 14:05:10 2017 -0400 |
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| @@ -132,7 +132,6 @@ #if $adv.forgettingFactor: --forgettingFactor $adv.forgettingFactor #end if - $adv.writeMappings #if str($adv.maxOcc): --maxOcc $adv.maxOcc #end if @@ -167,6 +166,9 @@ --vbPrior $adv.vbPrior #end if $adv.writeUnmappedNames + #if str($adv.writeMappings): + $adv.writeMappings > ${output_sam} + #end if ]]> </command> @@ -239,7 +241,7 @@ <section name="adv" title="Additional Options"> <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False" label="Write Mappings" - help=" Setting this option then the quasi-mapping results will be written out in SAM-cpmpatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead." /> + help="If this option is set to 'Yes', then the quasi-mapping results will be written out in SAM-compatible format. By default, output is directed to stdout." /> <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21" label="Incompatible Prior" help="This option sets the prior probability that an alignment that disagrees with the specified library type (--libType) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do" /> @@ -336,6 +338,9 @@ <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)"> <filter>geneMap</filter> </data> + <data name="output_sam" format="sam" label="${tool.name} on ${on_string} (SAM format)"> + <filter>adv['writeMappings']</filter> + </data> </outputs> <tests> |