# HG changeset patch
# User dave
# Date 1574868284 0
# Node ID d1b53ef02092f5d2dfdc6a21b314e9ae14f26910

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"

diff -r 000000000000 -r d1b53ef02092 lofreq_alnqual.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lofreq_alnqual.xml	Wed Nov 27 15:24:44 2019 +0000
@@ -0,0 +1,78 @@
+<tool id="lofreq_alnqual" name="Add BAQ and IDAQ" version="@WRAPPER_VERSION@0">
+    <description>to BAM with LoFreq</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @PREPARE_REF@
+        lofreq alnqual -b $extended $no_baq $no_idaq $recompute_all '$reads' '$reference_fasta_fn' > '$output'
+    ]]></command>
+    <inputs>
+        <param type="data" name="reads" format="bam" />
+        <expand macro="reference_interface" />
+        <param name="extended" argument="-e" type="boolean" truevalue="-e" falsevalue="" label="Use default instead of extended BAQ" help="Extended BAQ gives better sensitivity with lower specificity" />
+        <param name="no_baq" argument="-B" type="boolean" truevalue="-B" falsevalue="" label="Skip base alignment quality calculation" />
+        <param name="no_idaq" argument="-A" type="boolean" truevalue="-A" falsevalue="" label="Skip indel alignment quality calculation" />
+        <param name="recompute_all" argument="-r" type="boolean" truevalue="-r" falsevalue="" label="Overwrite existing values with computed values" />
+    </inputs>
+    <outputs>
+        <data name="output" format="bam" label="${tool.name} to ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <output name="output" file="alnqual-out1.bam" />
+        </test>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <param name="no_baq" value="true" />
+            <output name="output" file="alnqual-out2.bam" />
+        </test>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <param name="no_idaq" value="true" />
+            <output name="output" file="alnqual-out3.bam" />
+        </test>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <param name="extended" value="true" />
+            <output name="output" file="alnqual-out4.bam" />
+        </test>
+        <test>
+            <param name="reads" ftype="bam" value="lofreq-in1.bam" />
+            <param name="ref_selector" value="history" />
+            <param name="ref" ftype="fasta" value="pBR322.fa" />
+            <param name="recompute" value="true" />
+            <output name="output" file="alnqual-out5.bam" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        lofreq alnqual: add base- and indel-alignment qualities (BAQ, IDAQ) to BAM file
+
+Usage:   lofreq alnqual [options] <aln.bam> <ref.fasta>
+Options:
+         -b       BAM output (instead of SAM)
+         -u       Uncompressed BAM output (for piping)
+         -S       The input is SAM with header
+         -e       Use default instead of extended BAQ (the latter gives better sensitivity but lower specificity)
+         -B       Don't compute base alignment qualities
+         -A       Don't compute indel alignment qualities
+         -r       Recompute i.e. overwrite existing values
+- Output BAM will be written to stdout.
+- Only reads containing indels will contain indel-alignment qualities (tags: ai and ad).
+- Do not change the alignmnent after running this, i.e. use this as last postprocessing step!
+- This program is based on samtools. BAQ was introduced by Heng Li PMID:21320865
+
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file
diff -r 000000000000 -r d1b53ef02092 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Nov 27 15:24:44 2019 +0000
@@ -0,0 +1,47 @@
+<macros>
+    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token>
+    <token name="@TOOL_VERSION@">2.1.3.1</token>
+    <xml name="requirements">
+        <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">lofreq</requirement>
+        <requirement type="package" version="1.9">samtools</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/nar/gks918</citation>
+            <yield />
+        </citations>
+    </xml>
+    <token name="@PREPARE_REF@"><![CDATA[
+        #if str($reference_source.ref_selector) == 'history':
+            #set $reference_fasta_fn = 'reference.fa'
+            ln -s '$reference_source.ref' $reference_fasta_fn &&
+            lofreq faidx $reference_fasta_fn 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&
+        #else
+            #set $reference_fasta_fn = str($reference_source.ref.fields.path)
+        #end if
+    ]]></token>
+    <xml name="reference_interface">
+        <conditional name="reference_source">
+            <param name="ref_selector" type="select"
+            label="Choose the source for the reference genome">
+                <option value="cached">Locally cached</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param argument="--ref" type="select"
+                label="Reference genome">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" column="dbkey" key="dbkey" ref="reads" />
+                        <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param argument="--ref" type="data" format="fasta" label="Reference" help="Reference sequence" />
+            </when>
+        </conditional>
+    </xml>
+</macros>
diff -r 000000000000 -r d1b53ef02092 test-data/alnqual-out1.bam
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diff -r 000000000000 -r d1b53ef02092 test-data/alnqual-out2.bam
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diff -r 000000000000 -r d1b53ef02092 test-data/alnqual-out3.bam
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diff -r 000000000000 -r d1b53ef02092 test-data/alnqual-out4.bam
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diff -r 000000000000 -r d1b53ef02092 test-data/alnqual-out5.bam
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diff -r 000000000000 -r d1b53ef02092 test-data/call-out1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/call-out1.vcf	Wed Nov 27 15:24:44 2019 +0000
@@ -0,0 +1,19 @@
+##fileformat=VCFv4.0
+##fileDate=20191125
+##source=lofreq call --ref reference.fa --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallel3mrmthi_/0.vcf.gz alignments.bam 
+##reference=reference.fa
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
+##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
+##FILTER=<ID=min_snvqual_38,Description="Minimum SNV Quality (Phred) 38">
+##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
+##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10">
+##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
+##FILTER=<ID=min_snvqual_38,Description="Minimum SNV Quality (Phred) 38">
+##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+pBR322	1134	.	C	T	49314	PASS	DP=1767;AF=1.000000;SB=0;DP4=0,0,910,857
diff -r 000000000000 -r d1b53ef02092 test-data/indelqual-out1.bam
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diff -r 000000000000 -r d1b53ef02092 test-data/indelqual-out2.bam
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diff -r 000000000000 -r d1b53ef02092 test-data/indelqual-out3.bam
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diff -r 000000000000 -r d1b53ef02092 test-data/lofreq-in1.bam
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diff -r 000000000000 -r d1b53ef02092 test-data/pBR322.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pBR322.fa	Wed Nov 27 15:24:44 2019 +0000
@@ -0,0 +1,74 @@
+>pBR322
+TTCTCATGTTTGACAGCTTATCATCGATAAGCTTTAATGCGGTAGTTTATCACAGTTAAA
+TTGCTAACGCAGTCAGGCACCGTGTATGAAATCTAACAATGCGCTCATCGTCATCCTCGG
+CACCGTCACCCTGGATGCTGTAGGCATAGGCTTGGTTATGCCGGTACTGCCGGGCCTCTT
+GCGGGATATCGTCCATTCCGACAGCATCGCCAGTCACTATGGCGTGCTGCTAGCGCTATA
+TGCGTTGATGCAATTTCTATGCGCACCCGTTCTCGGAGCACTGTCCGACCGCTTTGGCCG
+CCGCCCAGTCCTGCTCGCTTCGCTACTTGGAGCCACTATCGACTACGCGATCATGGCGAC
+CACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCAC
+AGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCA
+CTTCGGGCTCATGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGG
+ACTGTTGGGCGCCATCTCCTTGCATGCACCATTCCTTGCGGCGGCGGTGCTCAACGGCCT
+CAACCTACTACTGGGCTGCTTCCTAATGCAGGAGTCGCATAAGGGAGAGCGTCGACCGAT
+GCCCTTGAGAGCCTTCAACCCAGTCAGCTCCTTCCGGTGGGCGCGGGGCATGACTATCGT
+CGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGCCGGCAGCGCT
+CTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCT
+TGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAA
+ACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGT
+CTTGCTGGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTC
+CGGCGGCATCGGGATGCCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGATGACGACCA
+TCAGGGACAGCTTCAAGGATCGCTCGCGGCTCTTACCAGCCTAACTTCGATCACTGGACC
+GCTGATCGTCACGGCGATTTATGCCGCCTCGGCGAGCACATGGAACGGGTTGGCATGGAT
+TGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGCGTCGCGGTGCATGGAGCCG
+GGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGGATTCACCACTCCAAGA
+ATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGGCAGAAC
+ATATCCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGG
+TCCTGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGCTAGGCTGGCGG
+GGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCGAGCGAACGTGAAGCGACTGC
+TGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTTCCGTGTTTCG
+TAAAGTCTGGAAACGCGGAAGTCAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCA
+GGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTGGCATTGA
+CCCTGAGTGATTTTTCTCTGGTCCCGCCGCATCCATACCGCCAGTTGTTTACCCTCACAA
+CGTTCCAGTAACCGGGCATGTTCATCATCAGTAACCCGTATCGTGAGCATCCTCTCTCGT
+TTCATCGGTATCATTACCCCCATGAACAGAAATCCCCCTTACACGGAGGCATCAGTGACC
+AAACAGGAAAAAACCGCCCTTAACATGGCCCGCTTTATCAGAAGCCAGACATTAACGCTT
+CTGGAGAAACTCAACGAGCTGGACGCGGATGAACAGGCAGACATCTGTGAATCGCTTCAC
+GACCACGCTGATGAGCTTTACCGCAGCTGCCTCGCGCGTTTCGGTGATGACGGTGAAAAC
+CTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGC
+AGACAAGCCCGTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCGCAGCCATGACC
+CAGTCACGTAGCGATAGCGGAGTGTATACTGGCTTAACTATGCGGCATCAGAGCAGATTG
+TACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACC
+GCATCAGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGC
+GGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATA
+ACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCG
+CGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCT
+CAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAA
+GCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTC
+TCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGT
+AGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCG
+CCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGG
+CAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCT
+TGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGC
+TGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCG
+CTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTC
+AAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTT
+AAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAA
+AATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAAT
+GCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCT
+GACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTG
+CAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAG
+CCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTA
+ATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTG
+CCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCG
+GTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCT
+CCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTA
+TGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTG
+GTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCC
+CGGCGTCAACACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTG
+GAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGA
+TGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTG
+GGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAAT
+GTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTC
+TCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCA
+CATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCT
+ATAAAAATAGGCGTATCACGAGGCCCTTTCGTCTTCAAGAA
\ No newline at end of file
diff -r 000000000000 -r d1b53ef02092 test-data/viterbi-out1.bam
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diff -r 000000000000 -r d1b53ef02092 test-data/viterbi-out2.bam
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diff -r 000000000000 -r d1b53ef02092 tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Wed Nov 27 15:24:44 2019 +0000
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 000000000000 -r d1b53ef02092 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Nov 27 15:24:44 2019 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of SAMTools indexes for FASTA files -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>