Mercurial > repos > iuc > bioext_bealign
diff bealign.xml @ 0:2064a7540ecd draft
planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
| author | iuc |
|---|---|
| date | Wed, 16 May 2018 17:33:45 -0400 |
| parents | |
| children | e44c8819b04f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bealign.xml Wed May 16 17:33:45 2018 -0400 @@ -0,0 +1,117 @@ +<?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[ + 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>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>