Mercurial > repos > iuc > presto_maskprimers
diff presto_maskprimers.xml @ 0:14e648d05cce draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
| author | iuc |
|---|---|
| date | Wed, 30 May 2018 15:34:53 -0400 |
| parents | |
| children | 61c1ae41a6bd |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/presto_maskprimers.xml Wed May 30 15:34:53 2018 -0400 @@ -0,0 +1,123 @@ +<tool id="presto_maskprimers" name="pRESTO MaskPrimers" version="@PRESTO_VERSION@"> + <description>Removes primers and annotates sequences with primer and barcode identifiers.</description> + + <macros> + <import>presto_macros.xml</import> + </macros> + + <expand macro="requirements"/> + + <version_command>MaskPrimers.py --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$fastq_in' in.fastq && + ln -s '$primers_in' primers.fasta && + MaskPrimers.py '$cc.command' + --nproc "\${GALAXY_SLOTS:-1}" + -s in.fastq + -p primers.fasta + --mode '$mode' + --maxerror '$maxerror' + $revpr + $barcode + + #if $cc.command == "align" + --maxlen '$cc.maxlen' + --gap '$cc.gap_open' '$cc.gap_extend' + $cc.skiprc + #end if + + #if $cc.command == "score" + --start '$cc.start' + #end if + + --outdir=. + --outname=tmp_mask + #if $capture_log + --log '$log_out' + #end if + ]]></command> + <inputs> + <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file"/> + <param argument="-p" name="primers_in" type="data" format="fasta" label="Primer FASTA file"/> + <param argument="--mode" type="select" value="mask" label="Mode" help="Specifies how identified primer sequences will be handled."> + <option value="cut">Remove primer and preceding sequence (cut)</option> + <option value="mask">Mask primer to Ns and remove preceding sequence (mask)</option> + <option value="trim">Leave primer intact and remove preceding sequence (trim)</option> + <option value="tag">Leave primer and preceding sequence intact (tag)</option> + </param> + <conditional name="cc"> + <param name="command" type="select" label="Command"> + <option value="align">Find primer matches using pairwise local alignment (align)</option> + <option value="score">Find primer matches by scoring primers at a fixed position (score)</option> + </param> + <when value="align"> + <param argument="--maxlen" type="integer" value="50" label="Max Length" help="Maximum length of sequence window to search for primers."/> + <param argument="--skiprc" type="boolean" value="false" truevalue="--skiprc" falsevalue="" label="Skip Reverse Complement" help="Skip checking of reverse complement sequences."/> + <param name="gap_open" type="integer" value="1" label="Gap Open Penalty" help="Positive value of the gap open penalty."/> + <param name="gap_extend" type="integer" value="1" label="Gap Extension Penalty" help="Positive value of the gap extension penalty."/> + </when> + <when value="score"> + <param argument="--start" type="integer" value="0" label="Start Position" help="The starting position of the primer."/> + </when> + </conditional> + <param argument="--revpr" type="boolean" value="false" truevalue="--revpr" falsevalue="" label="Reverse Match" help="Match the reverse complement of primer sequences against the ends of reads."/> + <param argument="--barcode" type="boolean" value="false" truevalue="--barcode" falsevalue="" label="Extract Barcodes (UMIs)" help="Capture the sequence preceding the primer as a UMI."/> + <param argument="--maxerror" type="float" value="0.2" label="Max Error Rate" help="Maximum allowable rate between read and primer sequence."/> + <expand macro="presto-log-param"/> + </inputs> + + <outputs> + <data name="fastq_out" format="fastq" from_work_dir="tmp_mask_primers-pass.fastq"/> + <expand macro="presto-log-output"/> + </outputs> + + <tests> + <test> + <param name="command" value="score"/> + <param name="fastq_in" value="presto_maskprimers_without_barcode_test_in.fastq"/> + <param name="start" value="0"/> + <param name="primers_in" value="read1_primers.fasta"/> + <param name="mode" value="cut"/> + <param name="maxerror" value="0.15"/> + <output name="fastq_out" file="presto_maskprimers_without_barcode_test_score_out.fastq" sort="true"/> + </test> + <test> + <param name="command" value="score"/> + <param name="fastq_in" value="presto_maskprimers_with_barcode_test_in.fastq"/> + <param name="start" value="17"/> + <param name="barcode" value="true"/> + <param name="primers_in" value="read2_primers.fasta"/> + <param name="mode" value="cut"/> + <param name="maxerror" value="0.15"/> + <output name="fastq_out" file="presto_maskprimers_with_barcode_test_score_out.fastq" sort="true"/> + </test> + <test> + <param name="command" value="align"/> + <param name="fastq_in" value="presto_maskprimers_without_barcode_test_in.fastq"/> + <param name="primers_in" value="read1_primers.fasta"/> + <param name="mode" value="cut"/> + <param name="maxerror" value="0.15"/> + <param name="maxlen" value="25"/> + <output name="fastq_out" file="presto_maskprimers_without_barcode_test_align_out.fastq" sort="true"/> + </test> + <test> + <param name="command" value="align"/> + <param name="fastq_in" value="presto_maskprimers_with_barcode_test_in.fastq"/> + <param name="barcode" value="true"/> + <param name="primers_in" value="read2_primers.fasta"/> + <param name="mode" value="cut"/> + <param name="maxerror" value="0.15"/> + <param name="maxlen" value="25"/> + <output name="fastq_out" file="presto_maskprimers_with_barcode_test_align_out.fastq" sort="true"/> + </test> + </tests> + + <help><![CDATA[ +Removes primers and annotates sequences with primer and barcode identifiers + +See the `pRESTO online help <@PRESTO_URL_BASE@/MaskPrimers.html>`_ for more information. + +@HELP_NOTE@ + ]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file