comparison macros.xml @ 12:f2000bc73102 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664
author bgruening
date Wed, 07 Dec 2022 19:32:02 +0000
parents e661a3269313
children e32b215b7c04
comparison
equal deleted inserted replaced
11:e661a3269313 12:f2000bc73102
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.9.0</token> 2 <token name="@TOOL_VERSION@">1.9.0</token>
3 <token name="@VERSION_SUFFIX@">1</token> 3 <token name="@VERSION_SUFFIX@">2</token>
4 <token name="@IDX_VERSION@">q7</token> 4 <token name="@IDX_VERSION@">q7</token>
5 <token name="@PROFILE_VERSION@">20.01</token> 5 <token name="@PROFILE_VERSION@">20.01</token>
6 <xml name="requirements"> 6 <xml name="requirements">
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">salmon</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
169 <param argument="--writeQualities" type="boolean" truevalue="--writeQualities" falsevalue="" checked="false" label="Write qualities" help="If this flag is 169 <param argument="--writeQualities" type="boolean" truevalue="--writeQualities" falsevalue="" checked="false" label="Write qualities" help="If this flag is
170 provided, then the output SAM file will contain quality strings as well as read sequences." /> 170 provided, then the output SAM file will contain quality strings as well as read sequences." />
171 </when> 171 </when>
172 <when value=""/> 172 <when value=""/>
173 </conditional> 173 </conditional>
174 <param name="writeMappings" type="boolean" truevalue="" falsevalue="" checked="False" 174 <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
175 label="Write Mappings to Bam File"
176 help="If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead"/>
177 <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
178 label="Consistent Hits" 175 label="Consistent Hits"
179 help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/> 176 help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/>
180 <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage" 177 <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage"
181 help="[Experimental]: The fraction of the read that must be covered by MMPs (of length >= 31) if this read is to be considered as 'mapped'. This may help to avoid 'spurious' mappings. A value of 0 (the default) denotes no coverage threshold (a single 31-mer can yield a mapping). Since coverage by exact matching, large, MMPs is a rather strict condition, this value should likely be set to something low, if used."/> 178 help="[Experimental]: The fraction of the read that must be covered by MMPs (of length >= 31) if this read is to be considered as 'mapped'. This may help to avoid 'spurious' mappings. A value of 0 (the default) denotes no coverage threshold (a single 31-mer can yield a mapping). Since coverage by exact matching, large, MMPs is a rather strict condition, this value should likely be set to something low, if used."/>
182 </xml> 179 </xml>