comparison cuffquant_wrapper.xml @ 4:679d93c99757 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"

3:6dc45faebc1d

    <description>Precompute gene expression levels</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command>cuffquant 2>&amp;1 | head -n 1</version_command>
    <command detect_errors="aggressive"><![CDATA[
        cuffquant
            --no-update-check
            --num-threads=\${GALAXY_SLOTS:-4}
            ## Set advanced SE data parameters?

  --no-length-correction         Disable all length correction.
  --library-type                 ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags
  --mask-file (gff3/gtf)         Ignore all alignment within transcripts in this file
  --max-bundle-frags             Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf.
    </help>
    <citations>
        <citation type="doi">10.1038/nbt.1621</citation>
    </citations>
</tool>

4:679d93c99757

    <description>Precompute gene expression levels</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command><![CDATA[cuffquant 2>&1 | head -n 1]]></version_command>
    <command detect_errors="aggressive"><![CDATA[
        cuffquant
            --no-update-check
            --num-threads=\${GALAXY_SLOTS:-4}
            ## Set advanced SE data parameters?

  --no-length-correction         Disable all length correction.
  --library-type                 ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags
  --mask-file (gff3/gtf)         Ignore all alignment within transcripts in this file
  --max-bundle-frags             Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf.
    </help>
    <expand macro="citations"/>
</tool>