# HG changeset patch
# User dave
# Date 1574868333 0
# Node ID b37a6b94e9fe3deb31ed3ccc5fb3893fe38c0fb4

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

diff -r 000000000000 -r b37a6b94e9fe lofreq_call.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lofreq_call.xml	Wed Nov 27 15:25:33 2019 +0000
@@ -0,0 +1,200 @@
+<tool id="lofreq_call" name="Call variants" version="@WRAPPER_VERSION@0">
+    <description>with LoFreq</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ## prepare reference genome and mapped reads input
+        @PREPARE_REF@
+        ln -s '$reads' reads.bam &&
+        ln -s -f '${reads.metadata.bam_index}' reads.bam.bai &&
+
+        ## call variants with lofreq
+
+        ## make lofreq stick to tool contract by
+        ## generating tmp output inside job working dir
+        mkdir pp-tmp &&
+        export TMPDIR=pp-tmp &&
+
+        lofreq call-parallel
+
+        --ref '$reference_fasta_fn' --out variants.vcf --pp-threads \${GALAXY_SLOTS:-1}
+
+        #if $advanced_options.option_selector == 'yes'
+            #if $advanced_options.regions.bed
+                --bed '$advanced_options.regions.bed'
+            #end if
+            #if $advanced_options.source_qual.ign_vcf
+                --ign-vcf '$advanced_options.source_qual.ign_vcf'
+            #end if
+            #if $advanced_options.regions.region
+                --region $advanced_options.regions.region
+            #end if
+            #if $advanced_options.pval.bonf
+                --bonf $advanced_options.pval.bonf
+            #else
+                --bonf dynamic
+            #end if
+            --min-bq $advanced_options.bc_quals.min_bq
+            --min-alt-bq $advanced_options.bc_quals.min_alt_bq
+            --def-alt-bq $advanced_options.bc_quals.def_alt_bq
+            --min-jq $advanced_options.bc_quals.min_jq
+            --min-alt-jq $advanced_options.bc_quals.min_alt_jq
+            --def-alt-jq $advanced_options.bc_quals.def_alt_jq
+            --min-mq $advanced_options.map_quals.min_mq
+            --max-mq $advanced_options.map_quals.max_mq
+            --def-nm-q $advanced_options.source_qual.def_nm_q
+            --sig $advanced_options.pval.sig
+            --min-cov $advanced_options.misc.min_cov
+            --max-depth $advanced_options.misc.max_depth
+            $advanced_options.align_quals.no_baq
+            $advanced_options.align_quals.no_idaq
+            $advanced_options.align_quals.del_baq
+            $advanced_options.align_quals.no_ext_baq
+            $advanced_options.map_quals.no_mq
+            $advanced_options.indels.call_indels
+            $advanced_options.indels.only_indels
+            $advanced_options.source_qual.src_qual
+            $advanced_options.misc.use_orphan
+            $advanced_options.misc.plp_summary_only
+            $advanced_options.misc.no_default_filter
+        #end if
+
+        reads.bam 2>&1
+
+        ## in case of errors add the log files produced
+        ## by the parallel workers to stderr
+        || (tool_exit_code=\$? && cat pp-tmp/lofreq2_call_parallel*/*.log 1>&2 && exit \$tool_exit_code)
+    ]]></command>
+    <inputs>
+        <param type="data" name="reads" format="bam" label="Input reads in BAM format" />
+        <expand macro="reference_interface" />
+        <conditional name="advanced_options">
+            <param name="option_selector" type="select" label="Advanced options">
+                <option value="no" selected="true">Use defaults</option>
+                <option value="yes">Specify parameters</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <section name="regions" title="Regions" expanded="false">
+                    <param argument="--bed" type="data" format="bed" optional="true" label="BED file with regions to examine" />
+                    <param argument="--region" type="text" label="Limit calls to this region" />
+                </section>
+                <section name="bc_quals" title="Base-calling quality" expanded="false">
+                    <param name="min_bq" argument="--min-bq" type="integer" value="6" label="Mimimum baseQ" />
+                    <param name="min_alt_bq" argument="--min-alt-bq" type="integer" value="6" label="Mimimum baseQ for alternate bases" />
+                    <param name="def_alt_bq" argument="--def-alt-bq" type="integer" value="0" label="Overwrite baseQs of alternate bases with this value" />
+                    <param name="min_jq" argument="--min-jq" type="integer" value="0" label="Minimum joinedQ" />
+                    <param name="min_alt_jq" argument="--min-alt-jq" type="integer" value="0" label="Minimum joinedQ for alternate bases" />
+                    <param name="def_alt_jq" argument="--def-alt-jq" type="integer" value="0" label="Overwrite joinedQs of alternate bases with this value" />
+                </section>
+                <section name="align_quals" title="Base alignment quality" expanded="false">
+                    <param name="no_baq" argument="--no-baq" type="boolean" truevalue="--no-baq" falsevalue="" label="Disable use of base-alignment quality" />
+                    <param name="no_idaq" argument="--no-idaq" type="boolean" truevalue="--no-idaq" falsevalue="" label="Don't use IDAQ values" />
+                    <param name="del_baq" argument="--del-baq" type="boolean" truevalue="--del-baq" falsevalue="" label="Delete pre-existing BAQ values" help="Computes BAQ values regardless of their presence in the input BAM" />
+                    <param name="no_ext_baq" argument="--no-ext-baq" type="boolean" truevalue="--no-ext-baq" falsevalue="" label="Do not use external BAQ" help="Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)" />
+                </section>
+                <section name="map_quals" title="Mapping quality" expanded="false">
+                    <param name="min_mq" argument="--min-mq" type="integer" value="0" label="Minimum mapping quality" />
+                    <param name="max_mq" argument="--max-mq" type="integer" value="255" label="Maximum mapping quality" />
+                    <param name="no_mq" argument="--no-mq" type="boolean" truevalue="--src-qua" falsevalue="" label="Don't merge mapping quality" />
+                </section>
+                <section name="indels" title="Indels" expanded="false">
+                    <param name="call_indels" argument="--call-indels" type="boolean" truevalue="--call-indels" falsevalue="" label="Enable indel calls" help="Note: This adds a preprocessing step to include indel alignment qualities" />
+                    <param name="only_indels" argument="--only-indels" type="boolean" truevalue="--only-indels" falsevalue="" label="Only call indels; no SNVs" />
+                </section>
+                <section name="source_qual" title="Source quality" expanded="false">
+                    <param name="ign_vcf" argument="--ign-vcf" type="data" format="vcf" optional="true" label="Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas" />
+                    <param name="src_qual" argument="--src-qual" type="boolean" truevalue="--src-qua" falsevalue="" label="Enable computation of source quality" />
+                    <param name="def_nm_q" argument="--def-nm-q" type="integer" value="-1" label="Replace non-match base qualities with this value" />
+                </section>
+                <section name="pval" title="P-values" expanded="false">
+                    <param argument="--sig" type="float" value="0.01" label="P-Value cutoff" />
+                    <param argument="--bonf" type="integer" optional="true" label="Bonferroni factor" help="Leave unset to increase the factor per performed test or specify a factor here" />
+                </section>
+                <section name="misc" title="Other options" expanded="false">
+                    <param name="min_cov" argument="--min-cov" type="integer" value="1" label="Test only positions having at least this coverage" />
+                    <param name="max_depth" argument="--max-depth" type="integer" value="1000000" label="Cap coverage at this depth" />
+                    <param name="use_orphan" argument="--use-orphan" type="boolean" truevalue="--use-orphan" falsevalue="" label="Count anomalous read pairs" />
+                    <param name="plp_summary_only" argument="--plp-summary-only" type="boolean" truevalue="--plp-summary-only" falsevalue="" label="No variant calling, just output pileup summary per column" />
+                    <param name="no_default_filter" argument="--no-default-filter" type="boolean" truevalue="--no-default-filter" falsevalue="" label="Don't run default 'lofreq filter' automatically after calling variants" />
+                </section>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="variants" from_work_dir="variants.vcf" format="vcf" />
+    </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="variants" file="call-out1.vcf" lines_diff="4" />
+        </test>
+    </tests>
+    <help><![CDATA[
+lofreq call: call variants from BAM file
+
+Usage: lofreq call [options] in.bam
+
+Options:
+
+- Reference:
+    -f | --ref FILE              Indexed reference fasta file (gzip supported) [null]
+
+- Output:
+    -o | --out FILE              Vcf output file [- = stdout]
+
+- Regions:
+    -r | --region STR            Limit calls to this region (chrom:start-end) [null]
+    -l | --bed FILE              List of positions (chr pos) or regions (BED) [null]
+
+- Base-call quality:
+    -q | --min-bq INT            Skip any base with baseQ smaller than INT [6]
+    -Q | --min-alt-bq INT        Skip alternate bases with baseQ smaller than INT [6]
+    -R | --def-alt-bq INT        Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep) [0]
+    -j | --min-jq INT            Skip any base with joinedQ smaller than INT [0]
+    -J | --min-alt-jq INT        Skip alternate bases with joinedQ smaller than INT [0]
+    -K | --def-alt-jq INT        Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep) [0]
+
+- Base-alignment (BAQ) and indel-aligment (IDAQ) qualities:
+    -B | --no-baq                Disable use of base-alignment quality (BAQ)
+    -A | --no-idaq               Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging)
+    -D | --del-baq               Delete pre-existing BAQ values, i.e. compute even if already present in BAM
+    -e | --no-ext-baq            Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)
+
+- Mapping quality:
+    -m | --min-mq INT            Skip reads with mapping quality smaller than INT [0]
+    -M | --max-mq INT            Cap mapping quality at INT [255]
+    -N | --no-mq                 Don't merge mapping quality in LoFreq's model
+
+- Indels:
+    --call-indels           Enable indel calls (note: preprocess your file to include indel alignment qualities!)
+    --only-indels           Only call indels; no SNVs
+
+- Source quality:
+    -s | --src-qual              Enable computation of source quality
+    -S | --ign-vcf FILE          Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas
+    -T | --def-nm-q INT          If >= 0, then replace non-match base qualities with this default value [-1]
+
+- P-values:
+    -a | --sig                   P-Value cutoff / significance level [0.010000]
+    -b | --bonf                  Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']
+
+- Misc.:
+    -C | --min-cov INT           Test only positions having at least this coverage [1]
+                                (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)
+    -d | --max-depth INT         Cap coverage at this depth [1000000]
+         --illumina-1.3          Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded
+         --use-orphan            Count anomalous read pairs (i.e. where mate is not aligned properly)
+         --plp-summary-only      No variant calling. Just output pileup summary per column
+         --no-default-filter     Don't run default 'lofreq filter' automatically after calling variants
+         --force-overwrite       Overwrite any existing output
+         --verbose               Be verbose
+         --debug                 Enable debugging
+
+]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r b37a6b94e9fe macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Nov 27 15:25:33 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 b37a6b94e9fe test-data/alnqual-out1.bam
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diff -r 000000000000 -r b37a6b94e9fe test-data/alnqual-out4.bam
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diff -r 000000000000 -r b37a6b94e9fe test-data/alnqual-out5.bam
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diff -r 000000000000 -r b37a6b94e9fe test-data/call-out1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/call-out1.vcf	Wed Nov 27 15:25:33 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 b37a6b94e9fe test-data/indelqual-out1.bam
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diff -r 000000000000 -r b37a6b94e9fe test-data/indelqual-out2.bam
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diff -r 000000000000 -r b37a6b94e9fe test-data/indelqual-out3.bam
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diff -r 000000000000 -r b37a6b94e9fe test-data/lofreq-in1.bam
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diff -r 000000000000 -r b37a6b94e9fe test-data/pBR322.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pBR322.fa	Wed Nov 27 15:25:33 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 b37a6b94e9fe test-data/viterbi-out1.bam
Binary file test-data/viterbi-out1.bam has changed
diff -r 000000000000 -r b37a6b94e9fe test-data/viterbi-out2.bam
Binary file test-data/viterbi-out2.bam has changed
diff -r 000000000000 -r b37a6b94e9fe 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 15:25:33 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 b37a6b94e9fe 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 15:25:33 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>