view glimmer_glimmer_to_gff.xml @ 3:3d71ab1562d7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit a80e3e4aa3a40970af507bf9119cf7f1c2ffb336

<tool id="glimmer_glimmer_to_gff" name="Convert Glimmer to GFF" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command><![CDATA[
        python '$__tool_directory__/glimmer_glimmer_to_gff.py'
            '$input' > '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="txt" label="Glimmer Output File"/>
    </inputs>
    <outputs>
        <data name="output" format="gff"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="glimmer_w_icm_trans-table-11_genomic.out" />
            <output name="output" file='glimmer.gff'/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

Converts a Glimmer3 output File to an GFF Annotation File::

**Example**

Input::
    >contig00097 sbe.0.234
    orf00003     2869      497  -2     5.60
    orf00005     3894     2875  -1     7.05
    orf00007     4242     4826  +3     8.04
    orf00010     4846     5403  +1     8.57
    orf00012     6858     5413  -1    10.87
    orf00013     6857     7594  +2     3.61
    orf00014     7751     9232  +2    11.34
    orf00015     9374    10357  +2    10.66
    orf00017    10603    11196  +1    13.39
    orf00021    11303    11911  +2     8.81
    orf00025    14791    12050  -2    13.51
    orf00026    15216    16199  +3     6.37
    orf00028    16333    16935  +1     8.86


Output:
    contig00097 sbe.0.234	glimmer	gene	497	2869	.	-	.	-2     5.60
    contig00097 sbe.0.234	glimmer	gene	2875	3894	.	-	.	-1     7.05
    contig00097 sbe.0.234	glimmer	gene	4242	4826	.	+	.	+3     8.04
    contig00097 sbe.0.234	glimmer	gene	4846	5403	.	+	.	+1     8.57
    contig00097 sbe.0.234	glimmer	gene	5413	6858	.	-	.	-1    10.87
    contig00097 sbe.0.234	glimmer	gene	6857	7594	.	+	.	+2     3.61
    contig00097 sbe.0.234	glimmer	gene	7751	9232	.	+	.	+2    11.34
    contig00097 sbe.0.234	glimmer	gene	9374	10357	.	+	.	+2    10.66
    contig00097 sbe.0.234	glimmer	gene	10603	11196	.	+	.	+1    13.39
    contig00097 sbe.0.234	glimmer	gene	11303	11911	.	+	.	+2     8.81
    contig00097 sbe.0.234	glimmer	gene	12050	14791	.	-	.	-2    13.51
    contig00097 sbe.0.234	glimmer	gene	15216	16199	.	+	.	+3     6.37
    contig00097 sbe.0.234	glimmer	gene	16333	16935	.	+	.	+1     8.86

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