Mercurial > repos > rdvelazquez > bioext_bealign
changeset 2:85d823cf0872 draft
planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'9b6c45716dc6760ae1a91530c0c12860b8d50088\n'-dirty
| author | rdvelazquez |
|---|---|
| date | Fri, 22 Mar 2019 11:42:49 -0400 |
| parents | d91cbcdac691 |
| children | f7866771310a |
| files | bealign.xml test-data/bealign-out1.bam test-data/bealign-out2.bam test-data/bealign-out3.bam |
| diffstat | 4 files changed, 105 insertions(+), 124 deletions(-) [+] |
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--- a/bealign.xml Thu Apr 19 12:10:57 2018 -0400 +++ b/bealign.xml Fri Mar 22 11:42:49 2019 -0400 @@ -1,134 +1,115 @@ <?xml version="1.0"?> <tool id="bioext_bealign" name="Align sequences" version="@VERSION@.0"> - <description>to a reference using a codon alignment algorithm</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <version_command>bealign --version</version_command> - <command detect_errors="exit_code"> - <![CDATA[ + <description>to a reference using a codon alignment + algorithm</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <version_command>bealign --version</version_command> + <command detect_errors="exit_code"><![CDATA[ bealign --reference '$select_reference.reference' --alphabet $advanced.alphabet #if $advanced.expected_identity: --expected-identity $advanced.expected_identity #end if --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference - #if $advanced.discard: - $advanced.discard $advanced.discarded_reads - #end if - $input $output - ]]> - </command> - <inputs> - <param name="input" type="data" format="fasta" label="Input reads" /> - <conditional name="select_reference"> - <param name="reference_type" type="select"> - <option value="preset">Select preset</option> - <option value="dataset">Use a history dataset</option> - </param> - <when value="preset"> - <param argument="--reference" type="select"> - <option value="HXB2_tat">HXB2 tat</option> - <option value="HXB2_gag">HXB2 gag</option> - <option value="HXB2_pol">HXB2 polymerase</option> - <option value="HXB2_int">HXB2 integrase</option> - <option value="HXB2_vif">HXB2 vif</option> - <option value="HXB2_pr">HXB2 protease</option> - <option value="HXB2_vpr">HXB2 vpr</option> - <option value="NL4-3_prrt">NL4-3 protease and reverse transcriptase</option> - <option value="HXB2_nef">HXB2 nef</option> - <option value="HXB2_env">HXB2 envelope</option> - <option value="HXB2_rt">HXB2 reverse transcriptase</option> - <option value="HXB2_prrt">HXB2 protease and reverse transcriptase</option> - <option value="HXB2_rev">HXB2 rev</option> - <option value="HXB2_vpu">HXB2 vpu</option> - </param> - </when> - <when value="dataset"> - <param argument="--reference" type="data" format="fasta" label="Reference sequences" /> - </when> - </conditional> - <section name="advanced" title="Advanced options" expanded="False"> - <param name="expected_identity" argument="--expected-identity" type="float" min="0" max="1" optional="True" label="Discard sequences that are insufficiently identical to the reference" /> - <param argument="--alphabet" type="select" label="Alphabet to use for alignment"> - <option value="codon" selected="True">Codon</option> - <option value="dna">DNA</option> - <option value="amino">Amino acids</option> - </param> - <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix"> - <option value="BLOSUM62" selected="True">Blocks substitution</option> - <option value="DNA65">DNA, 65% expected identity</option> - <option value="DNA70">DNA, 70% expected identity</option> - <option value="DNA88">DNA, 88% expected identity</option> - <option value="DNA80">DNA, 80% expected identity</option> - <option value="DNA95">DNA, 95% expected identity</option> - <option value="PAM200">PAM 200 substitution</option> - <option value="PAM250">PAM 250 substitution</option> - <option value="HIV_BETWEEN_F">HIV between+F</option> - </param> - <param argument="--discard" type="boolean" checked="False" truevalue="--discard" falsevalue="" label="Output discarded sequences to a separate dataset" /> - <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference" /> - <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM" /> - </section> - </inputs> - <outputs> - <data name="output" format="bam"/> - <data name="discarded_reads" format="fasta"> - <filter>discard</filter> - </data> - </outputs> - <tests> - <test> - <param name="input" ftype="fasta" value="bealign-in1.fa" /> - <param name="reference_type" value="dataset" /> - <param name="score_matrix" value="HIV_BETWEEN_F" /> - <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa" /> - <output name="output" file="bealign-out1.bam" /> - </test> - <test> - <param name="input" ftype="fasta" value="bealign-in2.fa" /> - <param name="reference_type" value="dataset" /> - <param name="score_matrix" value="BLOSUM62" /> - <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" /> - <output name="output" file="bealign-out2.bam" /> - </test> - <test> - <param name="input" ftype="fasta" value="bealign-in2.fa" /> - <param name="reference_type" value="dataset" /> - <param name="expected_identity" value="0.9" /> - <param name="score_matrix" value="BLOSUM62" /> - <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" /> - <output name="output" file="bealign-out3.bam" /> - </test> - </tests> - <help> - <![CDATA[ - -r REFERENCE, --reference REFERENCE - REFERENCE FASTA file or {HXB2_tat, HXB2_nef, HXB2_vpu, - HXB2_vif, HXB2_env, HXB2_vpr, HXB2_rev, HXB2_pol, - HXB2_prrt, NL4-3_prrt, HXB2_rt, HXB2_gag, HXB2_pr, - HXB2_int} - -e EXPECTED_IDENTITY, --expected-identity EXPECTED_IDENTITY - discard sequences that are insufficiently identical to - the reference - -a ALPHABET, --alphabet ALPHABET - perform an alignment using one of {amino, dna, codon} - [default=codon] - -m SCOREMATRIX, --score-matrix SCOREMATRIX - parameterize using one of {PAM250, DNA80, - HIV_BETWEEN_F, BLOSUM62, DNA70, DNA88, PAM200, DNA95, - DNA65} [default=BLOSUM62] - -D DISCARD, --discard DISCARD - discarded sequences are sent to DISCARD - -R, --reverse-complement - also align the reverse complement of each query - sequence, returning it if the alignment is superior - -S, --no-sort do NOT sort the resulting BAM file [the default is to - sort] - -q, --quiet do not print status update messages - -v, --version print version information and exit - -K, --keep-reference include the reference sequence as the first one in the - resulting BAM file [the default is to strip it] + '$input' '$output' + ]]></command> + <inputs> + <param name="input" type="data" format="fasta" label="Input reads"/> + <conditional name="select_reference"> + <param name="reference_type" type="select"> + <option value="preset">Select preset</option> + <option value="dataset">Use a history dataset</option> + </param> + <when value="preset"> + <param argument="--reference" type="select"> + <option value="HXB2_tat">HXB2 tat</option> + <option value="HXB2_gag">HXB2 gag</option> + <option value="HXB2_pol">HXB2 polymerase</option> + <option value="HXB2_int">HXB2 integrase</option> + <option value="HXB2_vif">HXB2 vif</option> + <option value="HXB2_pr">HXB2 protease</option> + <option value="HXB2_vpr">HXB2 vpr</option> + <option value="NL4-3_prrt">NL4-3 protease and reverse + transcriptase</option> + <option value="HXB2_nef">HXB2 nef</option> + <option value="HXB2_env">HXB2 envelope</option> + <option value="HXB2_rt">HXB2 reverse + transcriptase</option> + <option value="HXB2_prrt">HXB2 protease and reverse + transcriptase</option> + <option value="HXB2_rev">HXB2 rev</option> + <option value="HXB2_vpu">HXB2 vpu</option> + </param> + </when> + <when value="dataset"> + <param argument="--reference" type="data" format="fasta" label="Reference sequences"/> + </when> + </conditional> + <section name="advanced" title="Advanced options" expanded="False"> + <param name="expected_identity" argument="--expected-identity" type="float" min="0" max="1" optional="True" label="Discard sequences that are insufficiently identical to the reference"/> + <param argument="--alphabet" type="select" label="Alphabet to use for alignment"> + <option value="codon" selected="True">Codon</option> + <option value="dna">DNA</option> + <option value="amino">Amino acids</option> + </param> + <param name="score_matrix" argument="--score-matrix" type="select" label="Parametrize using score matrix"> + <option value="BLOSUM62" selected="True">Blocks + substitution</option> + <option value="DNA65">DNA, 65% expected identity</option> + <option value="DNA70">DNA, 70% expected identity</option> + <option value="DNA88">DNA, 88% expected identity</option> + <option value="DNA80">DNA, 80% expected identity</option> + <option value="DNA95">DNA, 95% expected identity</option> + <option value="PAM200">PAM 200 substitution</option> + <option value="PAM250">PAM 250 substitution</option> + <option value="HIV_BETWEEN_F">HIV between+F</option> + </param> + <param name="reverse_complement" argument="--reverse-complement" type="boolean" checked="False" truevalue="--reverse-complement" falsevalue="" label="Also try to align against reverse complement of reference"/> + <param name="keep_reference" argument="--keep-reference" type="boolean" checked="False" truevalue="--keep-reference" falsevalue="" label="Include reference as first sequence in aligned BAM"/> + </section> + </inputs> + <outputs> + <data name="output" format="bam"/> + <data name="discarded_reads" format="fasta"> + <filter>advanced['discard']</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" ftype="fasta" value="bealign-in1.fa"/> + <param name="reference_type" value="dataset"/> + <param name="score_matrix" value="HIV_BETWEEN_F"/> + <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa"/> + <output name="output" file="bealign-out1.bam"/> + </test> + <test> + <param name="input" ftype="fasta" value="bealign-in2.fa"/> + <param name="reference_type" value="dataset"/> + <param name="score_matrix" value="BLOSUM62"/> + <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa"/> + <output name="output" file="bealign-out2.bam"/> + </test> + <test> + <param name="input" ftype="fasta" value="bealign-in2.fa"/> + <param name="reference_type" value="dataset"/> + <param name="expected_identity" value="0.9"/> + <param name="score_matrix" value="BLOSUM62"/> + <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa"/> + <output name="output" file="bealign-out3.bam"/> + </test> + </tests> + <help><![CDATA[ +bealign +------- + +Align sequences to a reference using a codon alignment algorithm. + +NOTES +----- + +Reference can be one of the presets or a custom history reference. ]]></help> <expand macro="citations"/> </tool>