comparison crossmap.xml @ 11:a5eb1023fc34 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty

10:4f280582a2fc

    <requirements>
        <requirement type="package" version="0.1.9">crossmap</requirement>
    </requirements>
    
    <stdio>
        <regex match="Usage: CrossMap.py" source="stdin" level="fatal"/>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

    <command>
        CrossMap.py

            
            #if $multiple.input_format == "vcf"
                "$multiple.seq_source.input_fasta"
            #end if 
            
            <!-- BED format does not write to the output file, but does write fails to stdout -->
            > "$output"
            
            2>/dev/null
    </command>

    <inputs>
        <conditional name="multiple">
            <param name="input_format" type="select" label="Convert a file of the following format">

                                </options>
                            </param>
                        </when>
                        <when value="history">
                            <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
                            <param type="data" name="input_chain" label="LiftOver chain file" />
                        </when>
                </conditional>
                
<!-- These parameters don't work
                <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" />

                                </options>
                            </param>
                        </when>
                        <when value="history">
                            <param type="data" format="bed" name="input"       label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." />
                            <param type="data"              name="input_chain" label="LiftOver chain file" />
                        </when>
                </conditional>
            </when>
            <when value="bigwig">
                <conditional name="seq_source">
                    <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
                        <option value="cached">Local data (in galaxy)</option>

                                    <filter type="data_meta" ref="input" key="dbkey" column="0" />
                                </options>
                            </param>
                        </when>
                        <when value="history">
                            <param format="bigwig" name="input" type="data" label="BigWig file" />
                            <param type="data" name="input_chain" label="LiftOver chain file" />
                        </when>
                </conditional>
            </when>
            <when value="gff">
                <conditional name="seq_source">

                                    <filter type="data_meta" ref="input" key="dbkey" column="0" />
                                </options>
                            </param>
                        </when>
                        <when value="history">
                            <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file" />
                            <param type="data" name="input_chain" label="LiftOver chain file" />
                        </when>
                </conditional>
            </when>
            <when value="vcf">
                <conditional name="seq_source">

                        <when value="history_chain">
                            <param type="data" format="vcf" name="input" label="VCF file">
                                <validator type="unspecified_build" />
                                <validator type="dataset_metadata_in_file" filename="all_fasta.loc" metadata_name="dbkey" metadata_column="1" message="LiftOver mapping (FASTA file) is not available for the specified build." />
                            </param>
                            <param type="data"  name="input_chain" multiple="false" label="LiftOver chain file" />
                            <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
                                <options from_file="all_fasta.loc">
                                    <column name="name" index="2"/>
                                    <column name="value" index="3"/>
                                    <column name="dbkey" index="1"/>

                            </param>
                        </when>
                        
                        <when value="history_all">
                            <param type="data" format="vcf"   name="input" label="VCF file" />
                            <param type="data"                name="input_all_chain" multiple="false" label="LiftOver chain file" />
                            <param type="data" format="fasta" name="input_all_fasta" multiple="false" label="Full genome FASTA file" />
                        </when>
                </conditional>
            </when>
            <when value="wig">
                <conditional name="seq_source">

                                </options>
                            </param>
                        </when>
                        <when value="history">
                            <param format="wig" name="input" type="data" label="Wiggle file" />
                            <param type="data" name="input_chain" label="LiftOver chain file" />
                        </when>
                </conditional>
            </when>
        </conditional>
    </inputs>

        <data format="text" name="output" label="${tool.name} on " />
    </outputs>
    
    <tests>
        <test>
            <param name="input" value="test1.hg19.txt"/>
            <param name="input" value="hg18tohg19.chain"/>
            <output name="output" file="test1.hg18.txt"/>
        </test>
    </tests>
    
    <help>
CrossMap is versatile tool to convert genome coordinates or annotation files between genome
assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,

CrossMap bed
------------
BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1

    </help>
    
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt730</citation>
    </citations>

11:a5eb1023fc34

    <requirements>
        <requirement type="package" version="0.1.9">crossmap</requirement>
    </requirements>
    
    <stdio>
        <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

    <command>
        CrossMap.py

            
            #if $multiple.input_format == "vcf"
                "$multiple.seq_source.input_fasta"
            #end if 
            
            #if $multiple.include_fails == "true"
            >
            #end if
            
            "$output"
    </command>

    <inputs>
        <conditional name="multiple">
            <param name="input_format" type="select" label="Convert a file of the following format">

                                </options>
                            </param>
                        </when>
                        <when value="history">
                            <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
                            <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
                        </when>
                </conditional>
                
<!-- These parameters don't work
                <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" />

                                </options>
                            </param>
                        </when>
                        <when value="history">
                            <param type="data" format="bed" name="input"       label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." />
                            <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
                        </when>
                </conditional>
                <param name="include_fails" type="boolean" truevalue="true" falsevalue="false" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')" />
            </when>
            <when value="bigwig">
                <conditional name="seq_source">
                    <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
                        <option value="cached">Local data (in galaxy)</option>

                                    <filter type="data_meta" ref="input" key="dbkey" column="0" />
                                </options>
                            </param>
                        </when>
                        <when value="history">
                            <param type="data" format="bigwig" name="input"       label="BigWig file" />
                            <param type="data" format="csv"    name="input_chain" label="LiftOver chain file" />
                        </when>
                </conditional>
            </when>
            <when value="gff">
                <conditional name="seq_source">

                                    <filter type="data_meta" ref="input" key="dbkey" column="0" />
                                </options>
                            </param>
                        </when>
                        <when value="history">
                            <param type="data" format="gtf,gff,gff3" name="input"       label="GTF/GFF file" />
                            <param type="data" format="csv"          name="input_chain" label="LiftOver chain file" />
                        </when>
                </conditional>
            </when>
            <when value="vcf">
                <conditional name="seq_source">

                        <when value="history_chain">
                            <param type="data" format="vcf" name="input" label="VCF file">
                                <validator type="unspecified_build" />
                                <validator type="dataset_metadata_in_file" filename="all_fasta.loc" metadata_name="dbkey" metadata_column="1" message="LiftOver mapping (FASTA file) is not available for the specified build." />
                            </param>
                            <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" />
                            <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
                                <options from_file="all_fasta.loc">
                                    <column name="name" index="2"/>
                                    <column name="value" index="3"/>
                                    <column name="dbkey" index="1"/>

                            </param>
                        </when>
                        
                        <when value="history_all">
                            <param type="data" format="vcf"   name="input" label="VCF file" />
                            <param type="data" format="csv"   name="input_chain" multiple="false" label="LiftOver chain file" />
                            <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file" />
                        </when>
                </conditional>
            </when>
            <when value="wig">
                <conditional name="seq_source">

                                </options>
                            </param>
                        </when>
                        <when value="history">
                            <param format="wig" name="input" type="data" label="Wiggle file" />
                            <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
                        </when>
                </conditional>
            </when>
        </conditional>
    </inputs>

        <data format="text" name="output" label="${tool.name} on " />
    </outputs>
    
    <tests>
        <test>
            <param name="input_format" value="bed"/>
            <param name="index_source" value="history"/>
            <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
            <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
            <param name="include_fails" value="false"/>
            
            <output name="output" file="test_bed_01_output_a__only-matches.bed"/>
        </test>
        <!--<test>
            <param name="input_format" value="bed"/>
            <param name="index_source" value="history"/>
            <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
            <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
            <param name="include_fails" value="true"/>
            
            <output name="output" file="test_bed_02_output_a__all.bed"/>
        </test>
        <test>
            <param name="input_format" value="bed"/>
            <param name="index_source" value="history"/>
            <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
            <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
            <param name="include_fails" value="false"/>
            
            <output name="output" file="test_bed_02_output_a__only-matches.bed"/>
        </test>
        <test>
            <param name="input_format" value="bed"/>
            <param name="index_source" value="history"/>
            <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
            <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
            <param name="include_fails" value="true"/>
            
            <output name="output" file="test_bed_02_output_a__all.bed"/>
        </test>-->
    </tests>
    
    <help>
CrossMap is versatile tool to convert genome coordinates or annotation files between genome
assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,

CrossMap bed
------------
BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
    </help>
    
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt730</citation>
    </citations>