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author | xilinxu |
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date | Thu, 14 Aug 2014 04:52:17 -0400 |
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<tool id="cshl_fastx_collapser" name="Collapse"> <description>sequences</description> <command>zcat -f '$input' | fastx_collapser -v -o '$output' </command> <inputs> <param format="fastqsolexa,fasta" name="input" type="data" label="Library to collapse" /> <!-- <param name="GZIPOUT" type="select" label="Compress output file (using GZIP) "> <option value="">no</option> <option value="-g">yes</option> </param> --> </inputs> <tests> <test> <param name="input" value="fasta_collapser1.fasta" /> <param name="GZIPOUT" value=""/> <output name="output" file="fasta_collapser1.out" /> </test> </tests> <outputs> <data format="fasta" name="output" metadata_source="input" label="$input.tag collapsed" /> </outputs> <help> **What it does** This tool collapses identical sequences in a FASTA file into a single sequence. -------- **Example** Example Input File (Sequence "ATAT" appears multiple times):: >CSHL_2_FC0042AGLLOO_1_1_605_414 TGCG >CSHL_2_FC0042AGLLOO_1_1_537_759 ATAT >CSHL_2_FC0042AGLLOO_1_1_774_520 TGGC >CSHL_2_FC0042AGLLOO_1_1_742_502 ATAT >CSHL_2_FC0042AGLLOO_1_1_781_514 TGAG >CSHL_2_FC0042AGLLOO_1_1_757_487 TTCA >CSHL_2_FC0042AGLLOO_1_1_903_769 ATAT >CSHL_2_FC0042AGLLOO_1_1_724_499 ATAT Example Output file:: >1-1 TGCG >2-4 ATAT >3-1 TGGC >4-1 TGAG >5-1 TTCA .. class:: infomark Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. The output seqeunce name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value. The following output:: >2-4 ATAT means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file. </help> </tool>