# HG changeset patch
# User iuc
# Date 1576621569 18000
# Node ID 606542a18f829a8a66eb9aa4f29315a8551a8f7e

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"

diff -r 000000000000 -r 606542a18f82 lofreq_alnqual.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lofreq_alnqual.xml	Tue Dec 17 17:26:09 2019 -0500
@@ -0,0 +1,98 @@
+<tool id="lofreq_alnqual" name="Add LoFreq alignment quality scores" version="@WRAPPER_VERSION@0">
+    <description>to aligned read SAM/BAM records</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @PREPARE_REF@
+        lofreq alnqual -b ${alnqual_choice.extended_baq} ${alnqual_choice.alnquals_to_use} $recompute_all '$reads' '$reference_fasta_fn' > '$output'
+    ]]></command>
+    <inputs>
+        <param type="data" name="reads" format="bam" label="Reads" />
+        <expand macro="reference_interface" />
+        <expand macro="handle_alnqual" mode="Add" />
+        <param argument="-r" name="recompute_all" type="boolean" truevalue="-r" falsevalue=""
+        label="Overwrite exisitng values with newly computed ones" />
+    </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" />
+            <conditional name="alnqual_choice">
+                <param name="alnquals_to_use" value="-B" />
+            </conditional>
+            <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" />
+            <conditional name="alnqual_choice">
+                <param name="alnquals_to_use" value="-A" />
+            </conditional>
+            <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" />
+            <conditional name="alnqual_choice">
+                <param name="extended_baq" value="false" />
+            </conditional>
+            <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
+aligned read records
+
+.. class:: infomark
+
+   **What it does**
+
+This tool can compute base- and/or indel-alignment quality scores for aligned
+reads in SAM/BAM format and store these scores under the custom tags ``lb``
+(for the base alignment qualities, ``ai`` (insertion alignment qualities) and
+``ad`` (deletion alignment qualities), which it will add to its output BAM.
+
+These tags and their scores can be reused by LoFreq call, which can
+incorporate them into its model for variant quality calculation.
+
+.. class:: warning
+
+   **Do not realign** your reads after adding alignment qualities to them since
+   the scores would not be updated in the process!
+
+Notes:
+
+- While LoFreq call can optionally calculate the exact same scores on the fly
+  if needed, having the scores added to the aligned read records is going to
+  save computation time with repeated variant calling from the same input data.
+
+- The base alignment quality scores have the same meaning as in samtools, but
+  are expressed as absolute scores, not as base quality offsets like with the
+  `BQ` tag generated by samtools.
+
+- `ai` and `ad` tags, if requested, will only be added to reads containing
+  insertions/deletions.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r 606542a18f82 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Dec 17 17:26:09 2019 -0500
@@ -0,0 +1,88 @@
+<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>
+            <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>
+    <xml name="handle_existing_alnqual">
+        <conditional name="alnqual_choice">
+            <param name="alnquals_to_use" type="select"
+            label="Use the following alignment quality scores">
+                <option value="">Base and indel alignment qualities (BAQ and IDAQ)</option>
+                <option value="-A">Only base alignment qualities (BAQ)</option>
+                <option value="-B">Only indel alignment qualities (IDAQ)</option>
+            </param>
+            <when value="-B">
+                <param name="extended_baq" type="hidden" value="" />
+            </when>
+            <when value="">
+                <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
+                label="If BAQ needs to be computed, calculate extended BAQ?" />
+            </when>
+            <when value="-A">
+                <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
+                label="If BAQ needs to be computed, calculate extended BAQ?" />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="handle_alnqual" token_mode="Use">
+        <conditional name="alnqual_choice">
+            <param name="alnquals_to_use" type="select"
+            label="@MODE@ the following alignment quality scores">
+                <option value="">Base and indel alignment qualities (BAQ and IDAQ)</option>
+                <option value="-A">Only base alignment qualities (BAQ)</option>
+                <option value="-B">Only indel alignment qualities (IDAQ)</option>
+            </param>
+            <when value="-B">
+                <param name="extended_baq" type="hidden" value="" />
+            </when>
+            <when value="">
+                <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
+                label="Use extended BAQ?" />
+            </when>
+            <when value="-A">
+                <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
+                label="Use extended BAQ?" />
+            </when>
+        </conditional>
+    </xml>
+</macros>
diff -r 000000000000 -r 606542a18f82 test-data/alnqual-out1.bam
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diff -r 000000000000 -r 606542a18f82 test-data/alnqual-out2.bam
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diff -r 000000000000 -r 606542a18f82 test-data/alnqual-out3.bam
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diff -r 000000000000 -r 606542a18f82 test-data/alnqual-out4.bam
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diff -r 000000000000 -r 606542a18f82 test-data/alnqual-out5.bam
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diff -r 000000000000 -r 606542a18f82 test-data/call-out1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/call-out1.vcf	Tue Dec 17 17:26:09 2019 -0500
@@ -0,0 +1,19 @@
+##fileformat=VCFv4.0
+##fileDate=20191125
+##source=lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic --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 606542a18f82 test-data/call-out2.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/call-out2.vcf	Tue Dec 17 17:26:09 2019 -0500
@@ -0,0 +1,27 @@
+##fileformat=VCFv4.0
+##fileDate=20191204
+##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmpjsbggC/job_working_directory/000/8/working/pp-tmp/lofreq2_call_parallelj9yxuugx/0.vcf.gz reads.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">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+pBR322	815	.	A	G	0	.	DP=665;AF=0.003008;SB=6;DP4=333,311,0,2
+pBR322	861	.	A	C	0	.	DP=946;AF=0.002114;SB=3;DP4=447,497,0,2
+pBR322	1001	.	A	C	0	.	DP=1797;AF=0.000556;SB=3;DP4=877,918,1,0
+pBR322	1013	.	C	G	0	.	DP=1773;AF=0.000564;SB=0;DP4=875,897,0,1
+pBR322	1068	.	T	G	0	.	DP=1774;AF=0.000564;SB=3;DP4=853,920,1,0
+pBR322	1084	.	G	T	0	.	DP=1789;AF=0.000559;SB=3;DP4=875,913,1,0
+pBR322	1113	.	T	A	0	.	DP=1784;AF=0.000561;SB=0;DP4=885,898,0,1
+pBR322	1134	.	C	T	49314	.	DP=1767;AF=1.000000;SB=0;DP4=0,0,910,857
+pBR322	1193	.	G	A	0	.	DP=1698;AF=0.000589;SB=3;DP4=865,832,0,1
+pBR322	1218	.	A	C	0	.	DP=1708;AF=0.000585;SB=3;DP4=875,831,0,1
+pBR322	1230	.	T	C	0	.	DP=1759;AF=0.000569;SB=3;DP4=907,850,0,1
+pBR322	1256	.	A	G	0	.	DP=1746;AF=0.000573;SB=0;DP4=902,842,1,0
+pBR322	1498	.	C	G	0	.	DP=1195;AF=0.000837;SB=3;DP4=588,606,1,0
+pBR322	1503	.	T	G	0	.	DP=1156;AF=0.000865;SB=3;DP4=563,592,1,0
+pBR322	1505	.	G	A	0	.	DP=1137;AF=0.000880;SB=0;DP4=560,576,0,1
diff -r 000000000000 -r 606542a18f82 test-data/indelqual-out1.bam
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diff -r 000000000000 -r 606542a18f82 test-data/indelqual-out2.bam
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diff -r 000000000000 -r 606542a18f82 test-data/indelqual-out3.bam
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diff -r 000000000000 -r 606542a18f82 test-data/lofreq-in1.bam
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diff -r 000000000000 -r 606542a18f82 test-data/pBR322.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pBR322.fa	Tue Dec 17 17:26:09 2019 -0500
@@ -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 606542a18f82 test-data/viterbi-out1.bam
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diff -r 000000000000 -r 606542a18f82 test-data/viterbi-out2.bam
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diff -r 000000000000 -r 606542a18f82 tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Tue Dec 17 17:26:09 2019 -0500
@@ -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 606542a18f82 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Dec 17 17:26:09 2019 -0500
@@ -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>