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comparison stringtie.xml @ 19:333a6e13b622 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a586aaa6ef561527cda9e922a2260aa591f43938"
author iuc
date Tue, 30 Nov 2021 11:01:34 +0000
parents 258d696dbd7e
children cef79931dda5
comparison
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18:258d696dbd7e 19:333a6e13b622
1 <tool id="stringtie" name="StringTie" version="@TOOL_VERSION@"> 1 <tool id="stringtie" name="StringTie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>transcript assembly and quantification</description> 2 <description>transcript assembly and quantification</description>
3 <xrefs> 3 <xrefs>
4 <xref type="bio.tools">stringtie</xref> 4 <xref type="bio.tools">stringtie</xref>
5 </xrefs> 5 </xrefs>
6 <macros> 6 <macros>
76 -c '$adv.min_bundle_cov' 76 -c '$adv.min_bundle_cov'
77 -g '$adv.bdist' 77 -g '$adv.bdist'
78 -M '$adv.bundle_fraction' 78 -M '$adv.bundle_fraction'
79 $adv.disable_trimming 79 $adv.disable_trimming
80 $adv.multi_mapping 80 $adv.multi_mapping
81 #if $adv.point_features
82 --ptf $adv.point_features
83 #end if
81 #if $adv.abundance_estimation: 84 #if $adv.abundance_estimation:
82 -A '$gene_abundance_estimation' 85 -A '$gene_abundance_estimation'
83 #end if 86 #end if
84 #if str($adv.omit_sequences).strip() != "": 87 #if str($adv.omit_sequences).strip() != "":
85 -x '$adv.omit_sequences' 88 -x '$adv.omit_sequences'
224 <param name="min_bundle_cov" argument="-c" type="integer" min="0" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" help="Sets the minimum read coverage allowed for the predicted transcripts. A transcript with a lower coverage than this value is not shown in the output. Default: 2"/> 227 <param name="min_bundle_cov" argument="-c" type="integer" min="0" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" help="Sets the minimum read coverage allowed for the predicted transcripts. A transcript with a lower coverage than this value is not shown in the output. Default: 2"/>
225 <param name="bdist" argument="-g" type="integer" min="0" value="50" label="Gap between read mappings triggering a new bundle" help="Minimum locus gap separation value. Reads that are mapped closer than this distance are merged together in the same processing bundle. Default: 50 (bp)"/> 228 <param name="bdist" argument="-g" type="integer" min="0" value="50" label="Gap between read mappings triggering a new bundle" help="Minimum locus gap separation value. Reads that are mapped closer than this distance are merged together in the same processing bundle. Default: 50 (bp)"/>
226 <param name="bundle_fraction" argument="-M" type="float" min="0.0" max="1.0" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads" help="Sets the maximum fraction of muliple-location-mapped reads that are allowed to be present at a given locus. Default: 0.95"/> 229 <param name="bundle_fraction" argument="-M" type="float" min="0.0" max="1.0" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads" help="Sets the maximum fraction of muliple-location-mapped reads that are allowed to be present at a given locus. Default: 0.95"/>
227 <param name="disable_trimming" argument="-t" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Disable trimming of predicted transcripts based on coverage" help="This parameter disables trimming at the ends of the assembled transcripts. By default StringTie adjusts the predicted transcript's start and/or stop coordinates based on sudden drops in coverage of the assembled transcript. Default: No" /> 230 <param name="disable_trimming" argument="-t" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Disable trimming of predicted transcripts based on coverage" help="This parameter disables trimming at the ends of the assembled transcripts. By default StringTie adjusts the predicted transcript's start and/or stop coordinates based on sudden drops in coverage of the assembled transcript. Default: No" />
228 <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Disable multi-mapping correction" help="Default: No"/> 231 <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Disable multi-mapping correction" help="Default: No"/>
229 <param name="point_features" type="data" format="tabular" optional="True" label="Input point-features dataset" help="Loads a list of point-features from a text feature file to guide the transcriptome assembly. Accepted point features are transcription start sites (TSS) and polyadenylation sites (CPAS). There are four tab-delimited columns in the feature file. The first three define the location of the point feature on the cromosome (sequence name, coordinate and strand), and the last is the type of the feature (TSS or CPAS)."/> 232 <param name="point_features" type="data" format="tabular" optional="true" label="Input point-features dataset" help="Loads a list of point-features from a text feature file to guide the transcriptome assembly. Accepted point features are transcription start sites (TSS) and polyadenylation sites (CPAS). There are four tab-delimited columns in the feature file. The first three define the location of the point feature on the cromosome (sequence name, coordinate and strand), and the last is the type of the feature (TSS or CPAS)."/>
230 </section> 233 </section>
231 </inputs> 234 </inputs>
232 <outputs> 235 <outputs>
233 <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" /> 236 <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" />
234 <data name="gene_abundance_estimation" format="tabular" label="${tool.name} on ${on_string}: Gene abundance estimates"> 237 <data name="gene_abundance_estimation" format="tabular" label="${tool.name} on ${on_string}: Gene abundance estimates">