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comparison cuffquant_wrapper.xml @ 5:dd79e9e3aa10 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
author iuc
date Tue, 16 Jun 2020 16:59:04 +0000
parents d2daca60e139
children 1bb760457574
comparison
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4:d2daca60e139 5:dd79e9e3aa10
3 <description>Precompute gene expression levels</description> 3 <description>Precompute gene expression levels</description>
4 <macros> 4 <macros>
5 <import>cuff_macros.xml</import> 5 <import>cuff_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <version_command>cuffquant 2>&amp;1 | head -n 1</version_command> 8 <version_command><![CDATA[cuffquant 2>&1 | head -n 1]]></version_command>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 cuffquant 10 cuffquant
11 --no-update-check 11 --no-update-check
12 --num-threads=\${GALAXY_SLOTS:-4} 12 --num-threads=\${GALAXY_SLOTS:-4}
13 ## Set advanced SE data parameters? 13 ## Set advanced SE data parameters?
209 --no-length-correction Disable all length correction. 209 --no-length-correction Disable all length correction.
210 --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags 210 --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags
211 --mask-file (gff3/gtf) Ignore all alignment within transcripts in this file 211 --mask-file (gff3/gtf) Ignore all alignment within transcripts in this file
212 --max-bundle-frags Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. 212 --max-bundle-frags Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf.
213 </help> 213 </help>
214 <citations> 214 <expand macro="citations"/>
215 <citation type="doi">10.1038/nbt.1621</citation>
216 </citations>
217 </tool> 215 </tool>