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diff fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit_with_gzip_and_output_label/fastx_clipper.xml @ 3:997f5136985f draft default tip
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author | xilinxu |
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date | Thu, 14 Aug 2014 04:52:17 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit_with_gzip_and_output_label/fastx_clipper.xml Thu Aug 14 04:52:17 2014 -0400 @@ -0,0 +1,116 @@ +<tool id="cshl_fastx_clipper" name="Clip" version="1.0.1" > + <description>adapter sequences</description> + <command> + zcat -f $input | fastx_clipper $GZIPOUT -s $maxmismatches -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS + </command> + + <inputs> + <param format="fasta,fastqsolexa" name="input" type="data" label="Library to clip" /> + + <param name="maxmismatches" size="4" type="integer" value="2"> + <label>Maximum number of mismatches allowed (when matching the adapter sequence)</label> + </param> + + <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 seqeunces (i.e. sequences which contained the adapter)</option> + <option value="-C">Output only non-clipped seqeunces (i.e. sequences which did not contained the adapter)</option> + <option value="">Output both clipped and non-clipped sequences</option> + </param> + + <param name="GZIPOUT" type="select" label="Compress output file (using GZIP) "> + <option value="-z">yes</option> + <option value="">no</option> + </param> + + + </inputs> + + <tests> + <test> + <!-- Clip a FASTQ file --> + <param name="input" value="fastx_clipper1.fastq" /> + <param name="maxmismatches" value="2" /> + <param name="minlength" value="15" /> + <param name="clip_source.clip_source_list" value="user" /> + <param name="clip_source.clip_sequence" value="CAATTGGTTAATCCCCCTATATA" /> + <param name="keepdelta" value="0" /> + <param name="KEEP_N" value="-n" /> + <param name="DISCARD_OPTIONS" value="-c" /> + <param name="GZIPOUT" value=""/> + <output name="output" file="fastx_clipper1a.out" /> + </test> + </tests> + + <outputs> + <data format="input" name="output" label="$input.tag clipped" 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>