comparison crispr_studio.xml @ 1:a227c05e0a55 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ commit 539468c8c39e3024f000110b16718c40a363f9e5

0:7346619ad005

<?xml version="1.0"?>
<tool id="crispr_studio" name="CRISPR Studio" version="1+galaxy0">
    <description>
        facilitate and accelerate CRISPR array visualization from a GFF3 file generated with CRISPRDetect
    </description>
    <requirements>
        <requirement type="package" version="1">crispr_studio</requirement>
    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[

            </when>
            <when value="File">
                 <param name="isolate_list" type="data" format="txt" optional="true" label="List of Isolates to show" help="Generate the figure with the subset of isolates listed in the file"/>
            </when>
        </conditional>
        <param name="n" argument="-n" truevalue="-n" falsevalue="" type="boolean" label="Show the size of the spacers over the boxed diamonds?" help="We recommend to use this option only for experimental analysis of the data"/>
        <param argument="-f" truevalue="-f" falsevalue="" type="boolean" label="Skip the verification of the fasta file generated from the GFF file?" help="The verification is mainly based on the length of the spacer sequences. If a spacer is 1.5 time shorter or longer than the average spacer size of the dataset, a warning is raised and the script stops (Verification is ran by default)."/>
        <param name="cut_off" type="integer" optional="true" label="Score cutoff for pairing of the spacers"/>
        <param argument="-gU" truevalue="-gU" falsevalue="" type="boolean" label="Gray out unique?" help="The unique spacers will be grayed"/>
        <param argument="-gS" truevalue="-gS" falsevalue="" type="boolean" label="Gray out similar?" help="The conserved spacers will be grayed"/>
        <conditional name="rerun">

1:a227c05e0a55

<?xml version="1.0"?>
<tool id="crispr_studio" name="CRISPR Studio" version="1+galaxy0">
    <description>
        facilitate and accelerate CRISPR array visualization from a GFF3 file generated with CRISPRDetect
    </description>
    <xrefs>
        <xref type="bio.tools">crisprstudio</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="1">crispr_studio</requirement>
    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[

            </when>
            <when value="File">
                 <param name="isolate_list" type="data" format="txt" optional="true" label="List of Isolates to show" help="Generate the figure with the subset of isolates listed in the file"/>
            </when>
        </conditional>
        <param argument="-n" truevalue="-n" falsevalue="" type="boolean" label="Show the size of the spacers over the boxed diamonds?" help="We recommend to use this option only for experimental analysis of the data"/>
        <param argument="-f" truevalue="-f" falsevalue="" type="boolean" label="Skip the verification of the fasta file generated from the GFF file?" help="The verification is mainly based on the length of the spacer sequences. If a spacer is 1.5 time shorter or longer than the average spacer size of the dataset, a warning is raised and the script stops (Verification is ran by default)."/>
        <param name="cut_off" type="integer" optional="true" label="Score cutoff for pairing of the spacers"/>
        <param argument="-gU" truevalue="-gU" falsevalue="" type="boolean" label="Gray out unique?" help="The unique spacers will be grayed"/>
        <param argument="-gS" truevalue="-gS" falsevalue="" type="boolean" label="Gray out similar?" help="The conserved spacers will be grayed"/>
        <conditional name="rerun">