Mercurial > repos > xuebing > sharplabtool
view tools/fastx_toolkit/fastx_clipper.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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<tool id="cshl_fastx_clipper" name="Clip" version="1.0.1" > <description>adapter sequences</description> <requirements><requirement type="package">fastx_toolkit</requirement></requirements> <command> zcat -f $input | fastx_clipper -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS #if $input.ext == "fastqsanger": -Q 33 #end if </command> <inputs> <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to clip" /> <param name="minlength" size="4" type="integer" value="15"> <label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label> </param> <conditional name="clip_source"> <param name="clip_source_list" type="select" label="Source"> <option value="prebuilt" selected="true">Standard (select from the list below)</option> <option value="user">Enter custom sequence</option> </param> <when value="user"> <param name="clip_sequence" size="30" label="Enter custom clipping sequence" type="text" value="AATTGGCC" /> </when> <when value="prebuilt"> <param name="clip_sequence" type="select" label="Choose Adapter"> <options from_file="fastx_clipper_sequences.txt"> <column name="name" index="1"/> <column name="value" index="0"/> </options> </param> </when> </conditional> <param name="keepdelta" size="2" type="integer" value="0"> <label>enter non-zero value to keep the adapter sequence and x bases that follow it</label> <help>use this for hairpin barcoding. keep at 0 unless you know what you're doing.</help> </param> <param name="KEEP_N" type="select" label="Discard sequences with unknown (N) bases"> <option value="">Yes</option> <option value="-n">No</option> </param> <param name="DISCARD_OPTIONS" type="select" label="Output options"> <option value="-c">Output only clipped sequences (i.e. sequences which contained the adapter)</option> <option value="-C">Output only non-clipped sequences (i.e. sequences which did not contained the adapter)</option> <option value="">Output both clipped and non-clipped sequences</option> </param> </inputs> <!-- #functional test with param value starting with - fails. <tests> <test> <param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/> <param name="maxmismatches" value="2" /> <param name="minlength" value="15" /> <param name="clip_source_list" value="user" /> <param name="clip_sequence" value="CAATTGGTTAATCCCCCTATATA" /> <param name="keepdelta" value="0" /> <param name="KEEP_N" value="-n" /> <param name="DISCARD_OPTIONS" value="-c" /> <output name="output" file="fastx_clipper1a.out" /> </test> </tests> --> <outputs> <data format="input" name="output" metadata_source="input" /> </outputs> <help> **What it does** This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. -------- **Clipping Illustration:** .. image:: ./static/fastx_icons/fastx_clipper_illustration.png **Clipping Example:** .. image:: ./static/fastx_icons/fastx_clipper_example.png **In the above example:** * Sequence no. 1 was discarded since it wasn't clipped (i.e. didn't contain the adapter sequence). (**Output** parameter). * Sequence no. 5 was discarded --- it's length (after clipping) was shorter than 15 nt (**Minimum Sequence Length** parameter). </help> </tool>