comparison canongff3.xml @ 1:c45c9dd066e2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805

0:3f438bf5475d

<tool id='aegean_canongff3' name=' AEGeAn CanonGFF3' version='@TOOL_VERSION@' profile='20.01'>
    <description> pre-process GFF3 files, removing all features not directly related to protein-coding genes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='xrefs'/>
    <expand macro='edam_ontology'/>
    <expand macro='requirements'/>
    <version_command>canon-gff3 --version</version_command>
    <command detect_errors='exit_code'>
        <![CDATA[
            canon-gff3 '$gff3file'
            $infer
            #if $source
                -s '$source'
            #end if
            -o '$output'
            ]]>
    </command>
    <inputs>
        <param name='gff3file' type='data' format='gff3' label='GFF3 File'
            help="GFF3 annotation file" multiple='true' />
        <param argument='--infer' type='boolean'
            truevalue='--infer' falsevalue=''
            label='Infer gene feature for transcripts lacking it'            
            help='For transcript features lacking an explicitly declared gene feature as a parent, create this feature on-they-fly'/>
        <param argument='--source' type='text'
            value='' optional='true' 
            label='Reset the source of each feature'
            help='Reset the source of each feature to the given value. Source keywords can be a program (e.g. RepeatMasker) or an organization (like TAIR)'>
          <validator type="regex" message="Please only use letters, numbers or underscores in sample label">^[\w]+$</validator>
        </param>
    </inputs>
    <outputs>
        <data name='output' format='gff3' />
    </outputs>
    <tests>
        <test>
            <param name='gff3file' value='TAIR10_GFF3_genes.gff'/>
            <output name='output' file='canon-output_test1.gff3'/>
        </test>
        <test>
            <param name='gff3file' value='TAIR10_GFF3_genes.gff'/>
            <param name='source' value='test_source'/>
            <output name='output' file='canon-output_test2.gff3'/>
        </test>
        <test>
            <param name='gff3file' value='TAIR10_GFF3_genes.gff'/>
            <param name='infer' value='true'/>
            <output name='output' file='canon-output_test3.gff3'/>
        </test>
    </tests>
    <help>
        <![CDATA[        
.. class:: infomark

            
CanonGFF3 output is a GFF3 file containing protein-coding genes from the provided input file(s).
            
]]>
    </help>
    <expand macro='citations'/>
</tool>

1:c45c9dd066e2

<tool id="aegean_canongff3" name="AEGeAn CanonGFF3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description> pre-process GFF3 files, removing all features not directly related to protein-coding genes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <version_command>canon-gff3 --version</version_command>
    <command detect_errors="exit_code">
        <![CDATA[
            canon-gff3 "$gff3file"
            $infer
            #if $source
                -s "$source"
            #end if
            -o "$output"
            ]]>
    </command>
    <inputs>
        <param name="gff3file" type="data" format="gff3" label="GFF3 File"
            help="GFF3 annotation file" multiple="true" />
        <param argument="--infer" type="boolean"
            truevalue="--infer" falsevalue=""
            label="Infer gene feature for transcripts lacking it"            
            help="For transcript features lacking an explicitly declared gene feature as a parent, create this feature on-they-fly"/>
        <param argument="--source" type="text"
            value="" optional="true" 
            label="Reset the source of each feature"
            help="Reset the source of each feature to the given value. Source keywords can be a program (e.g. RepeatMasker) or an organization (like TAIR)">
          <validator type="regex" message="Please only use letters, numbers or underscores in sample label">^[\w]+$</validator>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="gff3" />
    </outputs>
    <tests>
        <test>
            <param name="gff3file" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
            <output name="output" file="canon-output_test1.gff3"/>
        </test>
        <test>
            <param name="gff3file" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
            <param name="source" value="test_source"/>
            <output name="output" file="canon-output_test2.gff3"/>
        </test>
        <test>
            <param name="gff3file" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>
            <param name="infer" value="true"/>
            <output name="output" file="canon-output_test3.gff3"/>
        </test>
    </tests>
    <help>
        <![CDATA[        
.. class:: infomark

            
CanonGFF3 output is a GFF3 file containing protein-coding genes from the provided input file(s).
            
]]>
    </help>
    <expand macro="citations"/>
</tool>