# HG changeset patch
# User veg
# Date 1479320363 18000
# Node ID 9ba5e79006b8a36efa9a4eba5e7d2ea7dad9fa7e

Uploaded

diff -r 000000000000 -r 9ba5e79006b8 bioext/.shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bioext/.shed.yml	Wed Nov 16 13:19:23 2016 -0500
@@ -0,0 +1,10 @@
+name: bioext
+owner: veg
+description: A few handy bioinformatics tools not already within BioPython
+long_description: |
+  Long description goes here.
+remote_repository_url: https://github.com/davebx/bioext-gx/
+homepage_url: https://pypi.python.org/pypi/biopython-extensions/
+type: unrestricted
+categories:
+ - Next Gen Mappers
diff -r 000000000000 -r 9ba5e79006b8 bioext/bioext_bealign.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bioext/bioext_bealign.xml	Wed Nov 16 13:19:23 2016 -0500
@@ -0,0 +1,118 @@
+<?xml version="1.0"?>
+<tool id="bioext_bealign" version="0.18" name="bealign">
+  <description>align sequences to a reference using a codon alignment algorithm</description>
+  <requirements>
+    <requirement type="package" version="1.11.2">numpy</requirement>
+    <requirement type="package" version="1.68">biopython</requirement>
+    <requirement type="package" version="0.18.5">biopython-extensions</requirement>
+    <requirement type="package" version="3.5">python</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:"/>
+  </stdio>
+  <version_command>bealign --version</version_command>
+  <command><![CDATA[
+        bealign
+            #if str($reference.input_alignment) == "history":
+                --reference "$reference.history_reference"
+            #else:
+                --reference "$reference.internal_reference"
+            #end if
+            "$input_fasta" "$output_alignments"
+    ]]></command>
+  <inputs>
+    <param name="input_fasta" label="Input FASTA" type="data" format="fasta"/>
+    <conditional name="reference">
+      <param label="Input alignment" name="input_alignment" type="select">
+        <option value="history">Use a FASTA file from the history</option>
+        <option value="builtin">Use a built-in reference</option>
+      </param>
+      <when value="history">
+        <param format="fasta" label="Select the reference genome" name="history_reference" type="data"/>
+      </when>
+      <when value="builtin">
+        <param name="internal_reference" type="select">
+          <option value="HXB2_tat">HXB2_tat</option>
+          <option value="HXB2_nef">HXB2_nef</option>
+          <option value="HXB2_vpu">HXB2_vpu</option>
+          <option value="HXB2_vif">HXB2_vif</option>
+          <option value="HXB2_env">HXB2_env</option>
+          <option value="HXB2_vpr">HXB2_vpr</option>
+          <option value="HXB2_rev">HXB2_rev</option>
+          <option value="HXB2_pol">HXB2_pol</option>
+          <option value="HXB2_prrt">HXB2_prrt</option>
+          <option value="NL4-3_prrt">NL4-3_prrt</option>
+          <option value="HXB2_rt">HXB2_rt</option>
+          <option value="HXB2_gag">HXB2_gag</option>
+          <option value="HXB2_pr">HXB2_pr</option>
+          <option value="HXB2_int">HXB2_int</option>
+        </param>
+      </when>
+    </conditional>
+    <conditional name="options">
+      <param label="Additional options" name="advanced" type="select">
+        <option value="defaults">Use defaults</option>
+        <option value="advanced">Specify additional parameters</option>
+      </param>
+      <when value="defaults"/>
+      <when value="advanced">
+        <param label="Alphabet" name="alphabet" type="select">
+          <option value="codon">codon</option>
+          <option value="dna">dna</option>
+          <option value="amino">amino</option>
+        </param>
+        <param label="Score matrix" name="score" type="select">
+          <option value="BLOSUM62">BLOSUM62</option>
+          <option value="PAM250">PAM250</option>
+          <option value="DNA80">DNA80</option>
+          <option value="HIV_BETWEEN_F">HIV_BETWEEN_F</option>
+          <option value="DNA70">DNA70</option>
+          <option value="DNA88">DNA88</option>
+          <option value="PAM200">PAM200</option>
+          <option value="DNA95">DNA95</option>
+          <option value="DNA65">DNA65</option>
+        </param>
+        <param name="reverse_complement" type="boolean" truevalue="--reverse-complement" falsevalue="" label="Also align the reverse complement of each query sequence"/>
+        <param name="keep_reference" type="boolean" truevalue="--keep-reference" falsevalue="" label="Include the reference sequence as the first one in the resulting BAM file"/>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="bam" name="output_alignments"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="history_reference" value="bealign-in-ref-1.fa"/>
+      <param name="input_fasta" value="bealign-in1.fa"/>
+      <output file="bealign-out1.bam" ftype="bam" name="output_alignments"/>
+    </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]
+]]></help>
+</tool>
diff -r 000000000000 -r 9ba5e79006b8 bioext/test-data/bealign-in-ref-1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bioext/test-data/bealign-in-ref-1.fa	Wed Nov 16 13:19:23 2016 -0500
@@ -0,0 +1,22 @@
+>CUSTOM_JP_REFERENCE
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diff -r 000000000000 -r 9ba5e79006b8 bioext/test-data/bealign-in1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bioext/test-data/bealign-in1.fa	Wed Nov 16 13:19:23 2016 -0500
@@ -0,0 +1,130 @@
+>Z|JP|K03455|2036
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+atacaggagttgagagaacatctactgaaatggggatttaccacaccagataaaaaa
+>Z|JP|K03455|2036|DUPLICATE 2
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+cagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccaga
+aaaagacagctggactgtcaatgacatacagaagttagtggggaaattgaattgggcaagtcagatttacccagggatta
+aagtaaggcaattatgtaaactccttagaggaaccaaagcactaacagaagtaataccactaacagaagaagcagagcta
+gaactggcagaaaacagagagattctaaaagaaccagtacatggagtgtattatgacccatcaaaagacttaatagcaga
+aatacagaagcaggggcaaggccaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaaatatg
+caagaatgaggggtgcccacactaatgatgtaaaacaattaacagaggcagtgcaaaaaataaccacagaaagcatagta
+atatggggaaagactcctaaatttaaactgcccatacaaaaggaaacatgggaaacatggtggacagagtattggcaagc
+cacctggattcctgagtgggagtttgttaatacccctcccttagtgaaattatggtaccagttagagaaagaacccatag
+taggagcagaaaccttc
diff -r 000000000000 -r 9ba5e79006b8 bioext/test-data/bealign-out1.bam
Binary file bioext/test-data/bealign-out1.bam has changed