comparison crossmap.xml @ 8:9750f8c1d3cb draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a-dirty

7:cb854f5d6a4b

    
    <requirements>
        <requirement type="package" version="0.1.9">crossmap</requirement>
    </requirements>
    
    <stdio></stdio>

    <command>
        CrossMap.py
            $multiple.input_format
            

                "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
            #else
                "$multiple.seq_source.input_chain"
            #end if
            
            #if $multiple.input_format == "bam"
                -m $multiple.insert_size
                -s $multiple.insert_size_stdev
                -t $multiple.insert_size_fold
            #end if
            
            "$multiple.seq_source.input"
            
            #if $multiple.input_format == "vcf"
                "$multiple.seq_source.input_fasta"

                            <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
                            <param type="data" name="input_chain" label="LiftOver chain file" />
                        </when>
                </conditional>
                
                <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]" />
                <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" />
                <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" />
            </when>
            <when value="bed">
                <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>

            </when>
        </conditional>
    </inputs>
    
    <outputs>
        <data format="text" name="output" label="Output file">
        </data>
    </outputs>
    
    <tests>
        <test>
            <param name="input" value="test1.hg19.txt"/>
            <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,
GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
and VCF, reading from remote servers and file compression are supported.
    </help>
    
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt730</citation>
    </citations>

8:9750f8c1d3cb

    
    <requirements>
        <requirement type="package" version="0.1.9">crossmap</requirement>
    </requirements>
    
    <stdio>
        <regex match="Usage: CrossMap.py" source="stdin" level="fatal"/>
        <regex match="^@ " source="stdin" level="warning" />
    </stdio>

    <command>
        CrossMap.py
            $multiple.input_format
            

                "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
            #else
                "$multiple.seq_source.input_chain"
            #end if
            
<!-- these arguments don't work
            #if $multiple.input_format == "bam"
                -m $multiple.insert_size
                -s $multiple.insert_size_stdev
                -t $multiple.insert_size_fold
            #end if
-->
            
            "$multiple.seq_source.input"
            
            #if $multiple.input_format == "vcf"
                "$multiple.seq_source.input_fasta"

                            <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]" />
                <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" />
                <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" />
-->
            </when>
            <when value="bed">
                <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>

            </when>
        </conditional>
    </inputs>
    
    <outputs>
        <data format="text" name="output" label="${tool.name} on ${input.hid}: ${input.name}" />
    </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,
GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
and VCF, reading from remote servers and file compression are supported.

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>