Mercurial > repos > tyty > structurefold
diff Iterative_mapping/iterative_map.xml @ 56:9d26c2e4953e draft
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author | tyty |
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date | Tue, 18 Nov 2014 01:00:33 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Iterative_mapping/iterative_map.xml Tue Nov 18 01:00:33 2014 -0500 @@ -0,0 +1,96 @@ +<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>