comparison orfipy.xml @ 1:45d4d26e01b5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5

0:c147914c9f02

<tool id="orfipy" name="ORFipy" version="@TOOL_VERSION@+galaxy0" profile="21.05">
    <description>a versatile ORF finder</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>

    #end if
#end for
--strand $strand
#if $min:
    --min $min
#end if
--table $table
#if $start:
    --start '$start'
#end if

            <option value="f">Forward</option>
            <option value="r">Reverse</option>
        </param>
        <param argument="--min" type="integer" min="0" optional="true" label="Minimum length of ORFs"
               help="No ORFs below this value will be reported. All ORFs will be reported if this parameter is not set. Default is 30"/>
        <param argument="--start" type="text" optional="true" label="Start codon(s) to use"
               help="A comma-separated list without spaces. Only ATCG and comma are allowed">
            <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator>
        </param>
        <param argument="--stop" type="text" optional="true" label="Stop codon(s) to use"

            <param name="input1" value="orfipy.fa.gz"/>
            <param name="out_files" value="DNA"/>
            <param name="min" value="100"/>
            <param name="partial_5" value="true"/>
            <output name="out_dna" file="test2.fa"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

1:45d4d26e01b5

<tool id="orfipy" name="ORFipy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>a versatile ORF finder</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>

    #end if
#end for
--strand $strand
#if $min:
    --min $min
#end if
#if $max:
    --max $max
#end if
--table $table
#if $start:
    --start '$start'
#end if

            <option value="f">Forward</option>
            <option value="r">Reverse</option>
        </param>
        <param argument="--min" type="integer" min="0" optional="true" label="Minimum length of ORFs"
               help="No ORFs below this value will be reported. All ORFs will be reported if this parameter is not set. Default is 30"/>
        <param argument="--max" type="integer" min="0" optional="true" label="Maximum length of ORFs"
               help="This value doesn't take in account the STOP codon. No ORFs over this value will be reported. Default is 1.000.000.000."/>
        <param argument="--start" type="text" optional="true" label="Start codon(s) to use"
               help="A comma-separated list without spaces. Only ATCG and comma are allowed">
            <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator>
        </param>
        <param argument="--stop" type="text" optional="true" label="Stop codon(s) to use"

            <param name="input1" value="orfipy.fa.gz"/>
            <param name="out_files" value="DNA"/>
            <param name="min" value="100"/>
            <param name="partial_5" value="true"/>
            <output name="out_dna" file="test2.fa"/>
        </test>
        <test expect_num_outputs="1">
            <param name="input1" value="orfipy.fa.gz"/>
            <param name="out_files" value="DNA"/>
            <param name="max" value="100000000"/>
            <output name="out_dna" file="test3.fa"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**