Mercurial > repos > iuc > presto_assemblepairs
diff presto_assemblepairs.xml @ 0:44c980933450 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
| author | iuc |
|---|---|
| date | Wed, 30 May 2018 15:36:59 -0400 |
| parents | |
| children | a17c446c53b5 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/presto_assemblepairs.xml Wed May 30 15:36:59 2018 -0400 @@ -0,0 +1,186 @@ +<tool id="presto_assemblepairs" name="pRESTO AssemblePairs" version="@PRESTO_VERSION@"> + <description>Assembles paired-end reads into a single sequence.</description> + + <macros> + <import>presto_macros.xml</import> + <xml name="align-params"> + <param argument="--alpha" type="float" value="1e-05" label="Alpha" help="Significance threshold for de-novo assembly."/> + <param argument="--maxerror" type="float" value="0.3" label="Max Error" help="Maximum error rate for de novo assembly."/> + <param argument="--minlen" type="integer" value="8" label="Minimum Length" help="Minimum sequence length to scan for overlap."/> + <param argument="--maxlen" type="integer" value="1000" label="Maximum Length" help="Maximum sequence length to scan for overlap."/> + <param argument="--scanrev" type="boolean" value="false" truevalue="--scanrev" falsevalue="" label="Scan past the end of the tail sequence in de novo assembly to allow the head sequence to overhang the end of the tail sequence."/> + </xml> + + <xml name="reference-params"> + <param argument="-r" type="data" format="fasta" label="Reference sequence FASTA file."/> + <param argument="--minident" type="float" value="0.5" label="Minimum Identity" help="Minimum identical fraction between assembled sequence and reference."/> + <param argument="--evalue" type="float" value="1e-05" label="E-Value" help="Minimum E-value for reference alignment for both the read sequences."/> + <param argument="--maxhits" type="integer" value="100" label="Max Hits" help="Maximum number of hits in the reference sequence to examine per assembled sequence."/> + <param argument="--fill" type="boolean" value="false" truevalue="--fill" falsevalue="" label="Fill With Reference" help="For read pairs with a gap between them, fill with reference sequence instead of Ns."/> + <param argument="--aligner" type="select" value="blastn" label="Aligner" help="Aligner to use to align reads to reference."> + <option value="blastn">Blast</option> + <option value="usearch">USearch</option> + </param> + </xml> + </macros> + + <expand macro="requirements"/> + + <version_command>AssemblePairs.py --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$r1_in' r1.fastq && + ln -s '$r2_in' r2.fastq && + #if $varExists('cc.r') + ln -s '$cc.r' reference.fasta && + #end if + AssemblePairs.py $cc.command + --nproc "\${GALAXY_SLOTS:-1}" + -1 r1.fastq + -2 r2.fastq + --coord $coord + #if $rc + --rc '$rc' + #end if + #if $r1_annotations + --1f $r1_annotations + #end if + #if $r2_annotations + --2f $r2_annotations + #end if + + #if $cc.command == "join" + --gap '$cc.gap' + #end if + + #if $cc.command == "align" or $cc.command == "sequential" + --alpha '$cc.alpha' + --maxerror '$cc.maxerror' + --minlen '$cc.minlen' + --maxlen '$cc.maxlen' + $cc.scanrev + #end if + + #if $cc.command == "reference" or $cc.command == "sequential" + -r reference.fasta + --minident '$cc.minident' + --evalue '$cc.evalue' + --maxhits '$cc.maxhits' + --aligner '$cc.aligner' + $cc.fill + #end if + + --outdir=. + --outname=tmp + #if $capture_log + --log '$log_out' + #end if + ]]></command> + <inputs> + <param argument="-1" name="r1_in" type="data" format="fastq" label="Read 1 FASTQ file"/> + <param argument="-2" name="r2_in" type="data" format="fastq" label="Read 2 FASTQ file"/> + <param argument="--rc" type="select" label="Reverse Complement" value="" help="Reverse complement neither, R1, R2 or both reads before assembly."> + <option value="">Neither</option> + <option value="head">Read 1 Only</option> + <option value="tail">Read 2 Only</option> + <option value="both">R1 and R2</option> + </param> + <param argument="--1f" name="r1_annotations" type="text" optional="true" label="R1 Fields To Copy" help="Annotation fields to copy from R1 into the output."> + <expand macro="text-regex-validator"/> + </param> + <param argument="--2f" name="r2_annotations" type="text" optional="true" label="R2 Fields To Copy" help="Annotation fields to copy from R2 into the output."> + <expand macro="text-regex-validator"/> + </param> + + <conditional name="cc"> + <param name="command" type="select" label="Command" value="sequential"> + <option value="align">Assemble pairs by aligning ends (align)</option> + <option value="join">Assemble pairs by concatenating ends (join)</option> + <option value="reference">Assemble pairs by aligning reads against a reference (reference)</option> + <option value="sequential">Attempt assembly via alignment, then reference guided assembly (sequential)</option> + </param> + <when value="align"> + <expand macro="align-params"/> + </when> + <when value="join"> + <param argument="--gap" type="integer" value="0" label="Gap Size" help="Number of N characters to place between joined Ns."/> + </when> + <when value="reference"> + <expand macro="reference-params"/> + </when> + <when value="sequential"> + <expand macro="align-params"/> + <expand macro="reference-params"/> + </when> + </conditional> + + <expand macro="presto-coord-param"/> + <expand macro="presto-log-param"/> + </inputs> + + <outputs> + <data name="fastq_out" format="fastq" from_work_dir="tmp_assemble-pass.fastq"/> + <expand macro="presto-log-output"/> + </outputs> + + <tests> + <test> + <param name="command" value="join"/> + <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/> + <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/> + <param name="coord" value="presto"/> + <param name="rc" value="tail"/> + <param name="r1_annotations" value="CONSCOUNT"/> + <param name="r2_annotations" value="PRCONS CONSCOUNT"/> + <param name="gap" value="10"/> + <output name="fastq_out" file="presto_assemblepairs_test_join_out.fastq" sort="true"/> + </test> + + <test> + <param name="command" value="align"/> + <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/> + <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/> + <param name="coord" value="presto"/> + <param name="rc" value="tail"/> + <param name="r1_annotations" value="CONSCOUNT"/> + <param name="r2_annotations" value="PRCONS CONSCOUNT"/> + <param name="scanrev" value="true"/> + <output name="fastq_out" file="presto_assemblepairs_test_align_out.fastq" sort="true"/> + </test> + + <test> + <param name="command" value="reference"/> + <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/> + <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/> + <param name="coord" value="presto"/> + <param name="rc" value="tail"/> + <param name="r1_annotations" value="CONSCOUNT"/> + <param name="r2_annotations" value="PRCONS CONSCOUNT"/> + <param name="r" value="reference_repertoire.fasta"/> + <param name="aligner" value="blastn"/> + <output name="fastq_out" file="presto_assemblepairs_test_reference_out.fastq" sort="true"/> + </test> + + <test> + <param name="command" value="sequential"/> + <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/> + <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/> + <param name="coord" value="presto"/> + <param name="rc" value="tail"/> + <param name="r1_annotations" value="CONSCOUNT"/> + <param name="r2_annotations" value="PRCONS CONSCOUNT"/> + <param name="scanrev" value="true"/> + <param name="r" value="reference_repertoire.fasta"/> + <param name="aligner" value="blastn"/> + <output name="fastq_out" file="presto_assemblepairs_test_sequential_out.fastq" sort="true"/> + </test> + </tests> + + <help><![CDATA[ +Assembles paired-end reads into a single sequence. + +See the `pRESTO online help <@PRESTO_URL_BASE@/AssemblePairs.html>`_ for more information. + +@HELP_NOTE@ + ]]></help> + <expand macro="citations" /> +</tool>