comparison je-clip.xml @ 5:8b4ccdf5f7dd draft

planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6

4:9d85f5915da9

<tool id="je_clip" name="Je-Clip" version="@VERSION_STRING@">
    <description>clips Unique Molecular Identifiers (UMIs) from fastq files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>
    <version_command>echo '1.0'</version_command>
    <command interpreter="bash">
<![CDATA[
    je clip

    ## Fastq inputs
    @single_or_paired_cmd@

            <output name="OF1" file="clip_dataset1_PE.fastq"/>
            <output name="OF2" file="clip_dataset2_PE.fastq"/>
        </test>
    </tests>


  <help>
<![CDATA[
**What it does**

Je clip: Clips barcodes or Unique Molecular Identifiers (UMIs) from the input fastq files
Input files are fastq files, and can be in gzip compressed format.

    + barcode + quality from read_2 (col 4 and 5 respectively) when relevant.
    Can either be a name (in which case the file will be created in the output dir) or a full path.
    Default value: null.

]]>
  </help>

</tool>

5:8b4ccdf5f7dd

<tool id="je_clip" name="Je-Clip" version="@VERSION_STRING@">
    <description>clips Unique Molecular Identifiers (UMIs) from fastq files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>
    <expand macro="version_command" />
    <command>
<![CDATA[
    je clip

    ## Fastq inputs
    @single_or_paired_cmd@

            <output name="OF1" file="clip_dataset1_PE.fastq"/>
            <output name="OF2" file="clip_dataset2_PE.fastq"/>
        </test>
    </tests>

    <help>
<![CDATA[
**What it does**

Je clip: Clips barcodes or Unique Molecular Identifiers (UMIs) from the input fastq files
Input files are fastq files, and can be in gzip compressed format.

    + barcode + quality from read_2 (col 4 and 5 respectively) when relevant.
    Can either be a name (in which case the file will be created in the output dir) or a full path.
    Default value: null.

]]>
    </help>
    <expand macro="citations"/>
</tool>