comparison mapper.xml @ 3:a8d24f4b6d95 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 3103ebed1a420c7d3415b67ef532ea579edf9faa

2:ab8cd78709e1

<tool id="rbc_mirdeep2_mapper" name="MiRDeep2 Mapper" version="2.0.0">
    <macros>
        <macro name="map_params">
            <conditional name="refGenomeSource">
                <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Map to genome. (-p)">
                    <option value="indexed">Use a built-in index</option>

                            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                        </options>
                    </param>
                </when> <!-- build-in -->
                <when value="history">
                    <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
                </when> <!-- history -->
            </conditional> <!-- refGenomeSource -->
            <param name="map_mismatch" type="boolean" truevalue="-q" falsevalue="" checked="false" label="Map with one mismatch in the seed (mapping takes longer)" help="(-q)"/>
            <param name="map_threshold" value="5" type="integer" optional="false" label="A read is allowed to map up to this number of positions in the genome" help="Map threshold. (-r)">
                <validator type="in_range" min="1" message="Minimum value is 1"/>
            </param>
        </macro>
    </macros>
    <description>
<![CDATA[
process and map reads to a reference genome
]]>
    </description>
    <requirements>
        <requirement type="package" version="2.0">mirdeep2_mapper</requirement>
        <requirement type="package" version="0.12.7">bowtie</requirement>
        <requirement type="package" version="5.18.1">perl</requirement>
    </requirements>

    <command>
<![CDATA[

        #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map"
            #if $operation.refGenomeSource.genomeSource == "history"

        #end if

        -v -n
]]>
    </command>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <!-- In case the return code has not been set propery check stderr too -->
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <inputs>
        <param format="fastq, fasta" name="reads" type="data" optional="false" label="Deep sequencing reads" help="Reads in fastq or FASTA format"/>
        <param name="remove_non_canon" type="boolean" truevalue="-j" falsevalue="" checked="false" label="Remove reads with non-standard nucleotides" help="Remove all entries that have a sequence that contains letters other than a,c,g,t,u,n,A,C,G,T,U,N. (-j)"/>
        <param name="convert_rna_dna" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Convert RNA to DNA alphabet (to map against genome)" help="(-i)"/>

3:a8d24f4b6d95

<tool id="rbc_mirdeep2_mapper" name="MiRDeep2 Mapper" version="2.0.0">
    <description>process and map reads to a reference genome</description>
    <macros>
        <macro name="map_params">
            <conditional name="refGenomeSource">
                <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Map to genome. (-p)">
                    <option value="indexed">Use a built-in index</option>

                            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                        </options>
                    </param>
                </when> <!-- build-in -->
                <when value="history">
                    <param name="ownFile" type="data" format="fasta" label="Select the reference genome" />
                </when> <!-- history -->
            </conditional> <!-- refGenomeSource -->
            <param name="map_mismatch" type="boolean" truevalue="-q" falsevalue="" checked="false" label="Map with one mismatch in the seed (mapping takes longer)" help="(-q)"/>
            <param name="map_threshold" value="5" type="integer" optional="false" label="A read is allowed to map up to this number of positions in the genome" help="Map threshold. (-r)">
                <validator type="in_range" min="1" message="Minimum value is 1"/>
            </param>
        </macro>
    </macros>
    <requirements>
        <requirement type="package" version="2.0.0.8">mirdeep2</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <!-- In case the return code has not been set propery check stderr too -->
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command>
<![CDATA[

        #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map"
            #if $operation.refGenomeSource.genomeSource == "history"

        #end if

        -v -n
]]>
    </command>
    <inputs>
        <param format="fastq, fasta" name="reads" type="data" optional="false" label="Deep sequencing reads" help="Reads in fastq or FASTA format"/>
        <param name="remove_non_canon" type="boolean" truevalue="-j" falsevalue="" checked="false" label="Remove reads with non-standard nucleotides" help="Remove all entries that have a sequence that contains letters other than a,c,g,t,u,n,A,C,G,T,U,N. (-j)"/>
        <param name="convert_rna_dna" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Convert RNA to DNA alphabet (to map against genome)" help="(-i)"/>