view vmap_rnamap.xml @ 60:7352fecc9860 draft default tip

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<tool id="vmap_rnamap" name="Virana RNAMap">

<description>Map input reads against a STAR index. </description>

	<requirements>
        <requirement type="package" version="2.3.0">STAR</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="package" version="1.0">virana_python</requirement>

    </requirements>

    <command interpreter="python">vmap.py rnamap
    
    
    
    --reads $reads
    
    #if $paired.select_paired == "paired"
        --reads $paired.paired_read
    #end if
    
    #if $refseq
        #set $groups = str($refseq).split(",")
        #for $ref in $groups:
            --virana_hit_filter $ref
        #end for
    #end if
        

        #if $bam
            --bam $bam_output
        #end if
        
        #if $sam
            --sam $sam_output
        #end if
        
        #if $output_type.hit
            --virana_hits $hit_output
            
            $output_type.filter_complexity
            
            #if $output_type.max_mismatches
                --max_mismatches $output_type.max_mismatches
            #end if
            
            #if $output_type.max_relative_mismatches
                --max_relative_mismatches $output_type.max_relative_mismatches
            #end if
            
            #if $output_type.min_alignment_score
                --min_alignment_score $output_type.min_alignment_score
            #end if
            
            #if $output_type.min_continiously_matching
                --min_continiously_matching $output_type.min_continiously_matching
            #end if
            
            #if $output_type.min_mapping_score
                --min_mapping_score $output_type.min_mapping_score
            #end if
       #end if
       #if $qual
            --qual $qual_output
       #end if
        
       #if $tax
            --taxonomy $tax_output
       #end if
        #if $chimeric
            --chimeric_mappings $chimeric_output
        #end if
        #if $unmapped
            --unmapped_end_1 $unmapped1_output
            #if $paired.select_paired == "paired"
                --unmapped_end_2 $unmapped2_output
            #end if
        #end if
    
    #if $sample_id:
        --sample_id $sample_id
    #end if 
        
    #if $splice_junctions:
        --splice_junctions $splice_junctions
    #end if
    
    --index_dir $index.extra_files_path
    
    $sensitive
    
    2&gt;&amp;1
        
    </command>
    
    <inputs>
        <param name="reads" type="data" format="fastq" label="Read file" help="input read file"/>
        
        <conditional name="paired">
            <param name="select_paired" type="select" label="Paired end reads?" >
                <option value="single">single end</option>
                <option value="paired">paired end</option>
            </param>
            
           <when value="paired">
                <param name="paired_read" type="data" format="fastq" label="Paired end read file" />
           </when>
        
        </conditional>
        <conditional name="output_type">
            <param name="hit" type="boolean" label="Hit Output"/>
                           
            <when value="true">
                <param name="max_mismatches" type="integer" min="0" max="10000000"  optional="true" label="Maximum number of mismatches for saved hits"/>
                <param name="max_relative_mismatches" type="float" min="0" max="1" optional="true" label="Maximum number of mismatches relative to read length for saved hits " />
                <param name="min_continiously_matching" type="integer" min="0" max="10000000" optional="true" label="Minimum number of continious matches for saved hits"  />
                <param name="min_mapping_score" type="integer" min="1" max="255"  optional="true" label="Mimimum mapping score for saved hit"  />        
                <param name="filter_complexity" type="boolean" truevalue="--filter_complexity" falsevalue="" label="Discard low-complexity reads"/>
                <param name="min_alignment_score" type="integer" min="0" max="255" optional="true" label="Mimimum alignment score for reported hits"/>

            </when>
        
        </conditional>
        
        <param name="bam" type="boolean" label="BAM Output"/>
        <param name="sam" type="boolean" label="SAM Output"/>
        <param name="qual" type="boolean"  label="Quality Output"/>
        <param name="tax" type="boolean"  label="Taxonomy Output"/>
        <param name="chimeric" type="boolean" label="Chimeric Mapping Ouput" />
        <param name="unmapped" type="boolean" label="Unmapped Reads Output" />
        
        <param name="refseq" type="select" label="Set RefSeq taxonomic groups" multiple="true" display="checkboxes" optional="true">
            <option value="UniVec">UniVec</option>
            <option value="rRNA">rRNA</option>
            <option value="Homo_sapiens">Homo sapiens</option>
            <option value="Fungi">Fungi</option>
            <option value="Plasmids">Plasmids</option>
            <option value="Protozoa">Protozoa</option>
            <option value="Viruses">Viruses</option>
            <option value="Homo_sapiens_cDNA">Homo sapiens cDNA</option>
            <option value="Fungi_DRAFT">Fungi DRAFT</option>
            <option value="Bacteria">Bacteria</option>
            <option value="Bacteria_DRAFT">Bacteria DRAFT</option>
        </param>
        
        <param name="splice_junctions" type="data" format="txt" optional="true" label="splice junction file"/>
        
        <param name="index" type="data" format="star_index" label="STAR Index files"/>
        
        <param name="sample_id" type="text" optional="true" label="String used to designate sample information within the hit file"/>
        
        <param name="sensitive" type="boolean" truevalue="--sensitive" falsevalue="" label="If given, mapping will process slower and more sensitive"/>

    </inputs>
    
    
    <outputs>
        <data format="hit_bz2" name="hit_output" label="">
            <filter>output_type['hit']</filter>
        </data>
        <data format="bam" name="bam_output" label="" >
            <filter>bam</filter>
        </data>
        <data format="sam" name="sam_output" label="">
            <filter>sam</filter>
        </data>
        <data format="qual" name="qual_output" label="" >
            <filter>qual</filter>
        </data>
        <data format="tax" name="tax_output" label="" >
            <filter>tax</filter>
        </data>
        <data format="sam" name="chimeric_output" label="" >
            <filter>chimeric</filter>
        </data>
        <data format="fastq" name="unmapped1_output" label="" >
            <filter>unmapped</filter>
        </data>
        <data format="fastq" name="unmapped2_output" label="" >
            <filter>unmapped</filter>
            <filter> paired['select_paired'] == 'paired'</filter>
        </data>
    </outputs>
</tool>