comparison nugen_nudup.xml @ 2:57a00c4e43ec draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup commit c3b2bf5ee64db2e334711d6f012190f9f7b4ea28

1:24693e595caf

<tool id="nugen_nudup" name="NuDUP" version="2.3.1" profile="17.01">
    <description>
        mark/remove PCR duplicates based on molecular tags
    </description>
    <requirements>
        <requirement type="package" version="2.3.1">nudup</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <version_command>nudup.py --version</version_command>

        #else:
            #set umi_file = 'umi.fastq'
        #end if
        ln -f -s '$umi_fastq' '$umi_file' &&
        nudup.py
        -T \$PWD'/tmp'
        $paired_end
        -f '$umi_file'
        --start $start
        --length $length
        $rmdup_only

        ]]></help>
    <citations>
        <citation type="bibtex">@misc{Patel2017,
  author = {Patel, Anand},
  title = {NuDUP},
  year = {2017},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/nugentechnologies/nudup}},
  commit = {7451de86680d24f19638ed6ac88f6504f0817753}
}
        </citation>
    </citations>
</tool>

2:57a00c4e43ec

<tool id="nugen_nudup" name="NuDUP" version="2.3.2" profile="17.01">
    <description>
        mark/remove PCR duplicates based on molecular tags
    </description>
    <requirements>
        <requirement type="package" version="2.3.2">nudup</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <version_command>nudup.py --version</version_command>

        #else:
            #set umi_file = 'umi.fastq'
        #end if
        ln -f -s '$umi_fastq' '$umi_file' &&
        nudup.py
        -T 'tmp'
        $paired_end
        -f '$umi_file'
        --start $start
        --length $length
        $rmdup_only

        ]]></help>
    <citations>
        <citation type="bibtex">@misc{Patel2017,
  author = {Patel, Anand},
  title = {NuDUP},
  version = {2.3.2},
  year = {2017},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/nugentechnologies/nudup}},
  commit = {7a126eb5a4ccc2bacb426c7cf58b351962798093}
}
        </citation>
    </citations>
</tool>