annotate Iterative_mapping/iterative_map.xml @ 66:d2817a631a7b draft

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<tool id="iterative_map_pipeline" name="Iterative Mapping" version="1.0">
	<description></description>
	<command interpreter="python">
        #if $mapping_file.type == "user"
            iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $t_end $mapping_file.type $output $mapping_file.param_v $mapping_file.param_five $mapping_file.param_three $mapping_file.param_k $mapping_file.param_a $mapping_file.param_m $mapping_file.param_best  
        #else
            iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $t_end $mapping_file.type $output
        #end if
    </command>
        <requirements>
                <requirement type="package" version="1.61">biopython</requirement>
                <requirement type="package" version="1.7.1">numpy</requirement>
                <requirement type="package" version="0.1.18">samtools</requirement>
                <requirement type="package" version="0.12.7">bowtie</requirement>
        </requirements>
	<inputs>
                <conditional name="file_format">
                  <param name="type" type="select" label="File format of the reads (Default FASTQ)">
                    <option value="fastq">FASTQ</option>
                    <option value="fasta">FASTA</option>
                  </param>
                  <when value="fastq">
                    <param name="seq_file" type="data" format="fastq" label="Fastq file"/>
                  </when>
                  <when value="fasta">
                    <param name="seq_file" type="data" format="fasta" label="Fasta file"/>
                  </when>
                </conditional>
		        <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
                <param name="shift" type="integer" value="1" label="Number of nucleotides trimmed each round"/>
                <param name="length" type="integer" value="21" label="Minimum requirement of read length for mapping"/>
                <param name="t_end" type="select" label="Trim from 5' or 3' end">
                    <option value="five_end">5' end</option>
                    <option value="three_end">3' end</option>
                </param>
                
                <conditional name="mapping_file">
                  <param name="type" type="select" label="Bowtie mapping flags (Default -v 0 -a --best --strata)">
                    <option value="default">Default</option>
                    <option value="user">User specified</option>
                  </param>
                  <when value="default"/>
                  <when value="user"> 
                    <param name="param_v" type="integer" value="0" label="Number of mismatches for SOAP-like alignment policy (-v)"/>
                    <param name="param_five" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)"/>
                    <param name="param_three" type="integer" value="0" label="Trim n bases from high-quality (right) end of each read before alignment (-3)"/>
                    <param name="param_k" type="integer" value="1" label="Report up to n valid alignments per read (-k)"/>
                    <param name="param_a" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to report all valid alignments per read (-a)"/>
                    <param name="param_m" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m), -1 for unlimited"/>
                    <param name="param_best" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best --strata)"/>
                  </when>
                </conditional>

	</inputs>
	<outputs>
		<data name="output" type="data" format="bam"/>
	</outputs>
    <tests>
        <test>
            <param name="file_format.type" value="fasta" />
            <param name="file_format.seq_file" value="sample.fasta" />
	        <param name="reference_file" value="rRNA.txt" />
            <param name="shift" value="1" />
            <param name="length" value="21" />
            <param name="mapping_file.type" value="default" />
	        <output name="output" file="mapped.out" />
        </test>
    </tests>

	<help>


**TIPS**:

-----

**Input**:

* 1. Sequence file type (FASTA/FASTQ)
* 2. Sequence file (fasta/fastq format)
* 3. Reference file (fasta) used to map the reads to
* 4. “Shift” (The length of the sequence that will be trimmed at the 3’end of the reads before each round of mapping)
* 5. “Length” (The minimum length of the reads for mapping after trimming)
* [Optional]
* 1. Bowtie mapping flags (options) [Default: -v 0 -a --best --strata] (-v flag indicates the number of allowed mismatches. Use -5/-3 flag to trim the nucleotides from 5'/3' end of the reads)

-----

**Output**:

A bam file with all of the reads that are mapped	



	</help>
</tool>