Mercurial > repos > iuc > bbtools_callvariants

changeset 0:18b91d72794b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
author iuc
date Tue, 05 Oct 2021 20:05:50 +0000
parents
children b955346ef41e
files callvariants.xml macros.xml test-data/13-1941-6_S4_L001_R1_600000.fastq.gz test-data/13-1941-6_S4_L001_R2_600000.fastq.gz test-data/NC_002945v4.fasta test-data/cv_input.bam test-data/cv_output.gff test-data/cv_output.txt test-data/cv_output.vcf test-data/cv_qualityhist_output.tabular test-data/cv_scorehist_output.tabular test-data/cv_zygosityhist_output.tabular test-data/fasta_indexes.loc test-data/output1.bam test-data/output2.bam test-data/output3.bam tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 19 files changed, 502 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/callvariants.xml	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,110 @@
+<tool id="bbtools_callvariants" name="BBTools: call variants" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>in aligned Bam files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import os
+
+#if str($ref_source_cond.ref_source) == 'cached'
+    #set ref = str($ref_source_cond.reference.fields.path)
+#else:
+    #set ref = $ref_source_cond.reference
+#end if
+
+## callvariants uses the file extension to determine the input format.
+#set input_name = str($os.path.basename($input.file_name)) + '.bam'
+ln -s '${input}' '${input_name}' &&
+
+callvariants.sh in='${input_name}' threads=\${GALAXY_SLOTS:-4} ref='${ref}' ploidy=$ploidy
+#if $output_variant_score_hist:
+    shist='$output_scorehist'
+#end if
+#if $output_zygosity_hist:
+    zhist='$output_zygosityhist'
+#end if
+#if $output_quality_hist:
+    qhist='$output_qualityhist'
+#end if
+#if str($output_format) == 'vcf':
+    vcf='out.vcf' && mv 'out.vcf' '$output'
+#elif str($output_format) == 'gff':
+    outgff='out.gff' && mv 'out.gff' '$output'
+#else:
+    out='output.txt' && mv 'output.txt' '$output'
+#end if
+]]></command>
+    <inputs>
+        <param name="input" type="data" format="bam" label="Bam file" help="Bam files produced by BBMap are recommended"/>
+        <expand macro="reference_source_cond"/>
+        <param name="ploidy" type="integer" value="1" min="1" label="Ploidy" help="See help section below"/>
+        <param name="output_format" type="select" label="Select output format">
+            <option value="vcf" selected="true">vcf</option>
+            <option value="gff">gff</option>
+            <option value="txt">txt</option>
+        </param>
+        <param name="output_variant_score_hist" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output variant score histogram?"/>
+        <param name="output_zygosity_hist" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output zygosity histogram?"/>
+        <param name="output_quality_hist" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output quality histogram?"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="vcf">
+            <change_format>
+                <when input="output_format" value="gff" format="gff"/>
+                <when input="output_format" value="txt" format="txt"/>
+            </change_format>
+        </data>
+        <data name="output_scorehist" format="tabular" label="${tool.name} on ${on_string} (scorehist)">
+            <filter>output_variant_score_hist</filter>
+        </data>
+        <data name="output_zygosityhist" format="tabular" label="${tool.name} on ${on_string} (zygosityhist)">
+            <filter>output_zygosity_hist</filter>
+        </data>
+        <data name="output_qualityhist" format="tabular" label="${tool.name} on ${on_string} (qualityhist)">
+            <filter>output_quality_hist</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="4">
+            <param name="input" value="cv_input.bam" ftype="bam"/>
+            <param name="ploidy" value="2"/>
+            <param name="output_variant_score_hist" value="yes"/>
+            <param name="output_zygosity_hist" value="yes"/>
+            <param name="output_quality_hist" value="yes"/>
+            <output name="output" file="cv_output.vcf" ftype="vcf" compare="contains"/>
+            <output name="output_scorehist" file="cv_scorehist_output.tabular" ftype="tabular" compare="contains"/>
+            <output name="output_zygosityhist" file="cv_zygosityhist_output.tabular" ftype="tabular" compare="contains"/>
+            <output name="output_qualityhist" file="cv_qualityhist_output.tabular" ftype="tabular" compare="contains"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="cv_input.bam" ftype="bam"/>
+            <param name="ploidy" value="2"/>
+            <param name="output_format" value="gff"/>
+            <output name="output" file="cv_output.gff" ftype="gff" compare="contains"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="cv_input.bam" ftype="bam"/>
+            <param name="ploidy" value="2"/>
+            <param name="output_format" value="txt"/>
+            <output name="output" file="cv_output.txt" ftype="txt" compare="contains"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+CallVariants is a high-speed, multithreaded variant caller that accepts bam files, and output VCF files.  It is capable
+of indel realignment, multi-sample variant-calling, and processing samples with arbitrary ploidy.
+
+BBMap is the recommended mapping program for CallVariants, but output from any aligner is acceptable.  Reads can be
+realigned with the "realign" flag.  This is slower, but is highly recommended if the input is from any mapping tool
+other than BBMap. Output from BBMap should not be realigned.
+
+**Options**
+
+ * **Ploidy** - Arbitrary ploidy is supported - the default is 1 which works for haploid organisms.  Allele fractions lower than those expected for the ploidy (for example, anything below 0.5 for a diploid, or 0.25 for a tetraploid) will incur a score penalty. When calling variants on non-haploid organisms, it is crucial to set the ploidy.
+
+    </help>
+    <expand macro="citations"/>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,63 @@
+<macros>
+    <token name="@WRAPPER_VERSION@">1.0.0</token>
+    <token name="@VERSION_SUFFIX@">1.0.0</token>
+    <token name="@PROFILE@">20.09</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="38.92">bbmap</requirement>
+        </requirements>
+    </xml>
+    <macro name="dbKeyActionsBBMap">
+        <expand macro="dbKeyActions">
+            <option type="from_data_table" name="fasta_indexes" column="1" offset="0">
+                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                <filter type="param_value" ref="ref_source_cond.reference" column="1"/>
+            </option>
+        </expand>
+    </macro>
+    <macro name="dbKeyActions">
+        <actions>
+            <conditional name="ref_source_cond.ref_source">
+                <when value="cached">
+                    <action type="metadata" name="dbkey">
+                        <yield/>
+                    </action>
+                </when>
+                <when value="history">
+                    <action type="metadata" name="dbkey">
+                        <option type="from_param" name="ref_source_cond.reference" param_attribute="dbkey"/>
+                    </action>
+                </when>
+            </conditional>
+        </actions>
+    </macro>
+    <macro name="reference_source_cond">
+        <conditional name="ref_source_cond">
+            <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
+                <option value="cached" selected="True">Use a cached reference</option>
+                <option value="history">Use a reference from the history</option>
+            </param>
+            <when value="cached">
+                <param name="reference" type="select" label="Using reference genome">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="A built-in reference genome is not available"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="reference" type="data" format="fasta" label="Using reference genome">
+                    <validator type="no_options" message="The current history does not include a fasta dataset"/>
+                </param>
+            </when>
+        </conditional>
+    </macro>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">
+                https://doi.org/10.1371/journal.pone.0185056
+            </citation>
+        </citations>
+    </xml>
+</macros>
+
Binary file test-data/13-1941-6_S4_L001_R1_600000.fastq.gz has changed
Binary file test-data/13-1941-6_S4_L001_R2_600000.fastq.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_002945v4.fasta	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,101 @@
+>NC_002945.4 Mycobacterium bovis AF2122/97 genome assembly, chromosome: Mycobacterium_bovis_AF2122/97
+TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACC
+CTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAGCAAAGGGCTTG
+GCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTTGCTCTGTTATCCGTGCCGAGCAGCTTTGTC
+CAAAACGAAATCGAGCGCCATCTGCGGGCCCCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGA
+TCCAACTCGGGGTCCGCATCGCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGA
+AAATCCTGCTACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG
+GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCGCAATACCGATTCCGCTACCGCTG
+GCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGCGCCTCCAACCGGTTCGCGCA
+CGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCTTACAACCCCCTGTTCATCTGGGGCGAGTCC
+GGTCTCGGCAAGACACACCTGCTACACGCGGCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGG
+TCAAATATGTCTCCACCGAGGAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGC
+ATTCAAACGCAGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG
+GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATCGTCATCTCAT
+CTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACCCGCTTTGAGTGGGGGCTGAT
+CACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCCATCTTGCGCAAGAAAGCACAGATGGAACGG
+CTCGCGATCCCCGACGATGTCCTCGAACTCATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGG
+GCGCGCTGATCCGGGTCACCGCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGAT
+TGTGCTTCGCGATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC
+GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTGGCCCAGTCAC
+GACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCCAAAATCGGCCAAGCGTTCGG
+CCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATCCTGTCCGAGATGGCCGAGCGCCGTGAGGTC
+TTTGATCACGTCAAAGAACTCACCACTCGCATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCC
+GACAACGTTCTTAAAAAAACTTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCT
+GTGCACAAACCGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG
+ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACCTGCACCAAGA
+CCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCTTCGTCGTTTGTTCTTGGAAA
+GACAGCGCTGGGGATCGTTCGCTGGATACCACCCGCATAACTGGCTCGTCGCGGTGGGTCAGAGGTCAAT
+GATGAACTTTCAAGTTGACGTGAGAAGCTCTACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGG
+GTCACGCGTCATGGGCGTTCGTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTC
+ATCGTGAGGTGAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT
+TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGCCCGCGGTGCC
+GGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTTCCGGATTCGACTACGAGGTT
+TCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTGGAAGCGTTTTAGTTTCTGGCCGATTGTTGT
+CCGATATTACCCGGGCGTTGCCTAACAAGCCCGTAGGCGTTCATGTCGAAGGTAACCGGGTCGCATTGAC
+CTGCGGTAACGCCAGGTTTTCGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCG
+GAAGAGACCGGATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC
+GGGACGACACGCTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGGTTTTGGCCGC
+TACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGTCGCCAGATATCGAAGCGGCT
+GTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAGCGGGCATCGGCGGCTCTGACGTTCGTTTGT
+CGTTGGGTACTGGGCCGGGGGTGGGCAAGGATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCAC
+CACGCGACTTCTTGATGCCGAGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCC
+ACCATGGACGTGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG
+TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGACGAGCCGAGGA
+AGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACCCAACCTATCTAACGGACGGT
+TTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTACGACTGCGGGTAAGCCTGCCTTGCTACGTC
+CGGTGTCCGGGGACGATCGCCCTGTGGCGGGTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGA
+CTATGTCTATCTGTTGATGCCGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCG
+TCATTTGGGGCTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT
+TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACGACGTTAGGTT
+CGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGTGCGGTGATCTCCACGATCGT
+GGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATCGCCACGGGGCGAGTCAACAAAGCGCGATTG
+AATCGATCATCGGTCCGAAGTACACGTGATGTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGG
+ATCTGGGGTTGGTTCGTGGGGATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAG
+GCCTGCGATCGCTGCGGTACGAGCCGAATATGAGAGGGTGGTGCGCCAGCGGACGGCGTTATTGAAGTCC
+GTACCTGGAGCACGGTATCGGGGTGACCGGGGTGTGTTTGACACTCTTGAGGTATGGGACAGTCGTTTGG
+CGGAGCACGGGGCTGAACTGGTGGCCGCCCGCATCGATTTGGTCAACCAGTTGGCACCGGAAGTGAAGAA
+GGCATACCAGCTGTTGGCGCCGGAATCGCGATCGGCGTCTATCGGTTATCGGGCCAGCATGGATGTAACC
+GGTCCCAGCGAGCAGTCAGATACCGATCGGCAATTGTTAGCAGCTCGGCTGTTGGCGGCGCTGGCGGCCC
+GTCGGGATGCCGAACTCGAGCGTGGGGTTTGTCTAGTTGGTCCGCACCGTGACGACCTAATACTGCGACT
+AGGCGATCAACCCGCGAAAGGATTTGCTAGCCATGGGGAGGCGTGGTCGTTGGCGGTGGCACTGCGGTTG
+GCGGCCTATCAACTGTTACGCGTTGATGGTGGTGAGCCGGTGTTGTTGCTCGACGACGTGTTCGCCGAAC
+TGGATGTCATGCGCCGTCGAGCGTTGGCGACGGCGGCCGAGTCCGCCGAACAGGTGTTGGTGACTGCCGC
+GGTGCTCGAGGATATTCCCGCCGGCTGGGACGCCAGGCGGGTGCACATCGATGTGCGTGCCGATGACACC
+GGATCGATGTCGGTGGTTCTGCCATGACGGGTTCTGTTGACCGGCCCGACCAGAATCGCGGTGAGCGATT
+AATGAAGTCACCAGGGTTGGATTTGGTCAGGCGCACCCTGGACGAAGCTCGTGCTGCTGCCCGCGCGCGC
+GGACAAGACGCCGGTCGAGGGCGGGTCGCTTCCGTTGCGTCGGGTCGGGTGGCCGGACGGCGACGAAGCT
+GGTCGGGTCCGGGGCCCGACATTCGTGATCCACAACCGCTGGGTAAGGCCGCTCGTGAGCTGGCAAAGAA
+ACGCGGCTGGTCGGTGCGGGTCGCCGAGGGTATGGTGCTCGGCCAGTGGTCTGCGGTGGTCGGCCACCAG
+ATCGCCGAACATGCACGCCCGACTGCGCTAAACGACGGGGTGTTGAGCGTGATTGCGGAGTCGACGGCGT
+GGGCGACGCAGTTGAGGATCATGCAGGCCCAGCTTCTGGCCAAGATCGCCGCAGCGGTTGGCAACGATGT
+GGTGCGATCGCTAAAGATCACCGGGCCGGCGGCACCATCGTGGCGCAAGGGGCCTCGCCATATTGCCGGT
+AGGGGTCCGCGCGACACCTACGGATAACACGTCGATCGGCCCAGAACAAGGCGCTCCGGTCCCGGCCTGA
+GAGCCTCGAGGACGAAGCGGATCCGTATGCCGGACGTCGGGACGCACCAGGAAGAAAGATGTCCGACGCA
+CGGCGCGGTTAGATGGGTAAAAACGAGGCCAGAAGATCGGCCCTGGCGCCCGATCACGGTACAGTGGTGT
+GCGACCCCCTGCGGCGACTCAACCGCATGCACGCAACCCCTGAGGAGAGTATTCGGATCGTGGCTGCCCA
+GAAAAAGAAGGCCCAAGACGAATACGGCGCTGCGTCTATCACCATTCTCGAAGGGCTGGAGGCCGTCCGC
+AAACGTCCCGGCATGTACATTGGCTCGACCGGTGAGCGCGGTTTACACCATCTCATTTGGGAGGTGGTCG
+ACAACGCGGTCGACGAGGCGATGGCCGGTTATGCAACCACAGTGAACGTAGTGCTGCTTGAGGATGGCGG
+TGTCGAGGTCGCCGACGACGGCCGCGGCATTCCGGTCGCCACCCACGCCTCCGGCATACCGACCGTCGAC
+GTGGTGATGACACAACTACATGCCGGCGGCAAGTTCGACTCGGACGCGTATGCGATATCTGGTGGTCTGC
+ACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCGGCTCGAAGTCGAGATCAAGCGCGACGGGTA
+CGAGTGGTCTCAGGTTTATGAGAAGTCGGAACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACG
+GGGTCAACGGTACGGTTCTGGGCCGACCCCGCTGTTTTCGAAACCACGGAATACGACTTCGAAACCGTCG
+CCCGCCGGCTGCAAGAGATGGCGTTCCTCAACAAGGGGCTGACCATCAACCTGACCGACGAGAGGGTGAC
+CCAAGACGAGGTCGTCGACGAAGTGGTCAGCGACGTCGCCGAGGCGCCGAAGTCGGCAAGTGAACGCGCA
+GCCGAATCCACTGCACCGCACAAAGTTAAGAGCCGCACCTTTCACTATCCGGGTGGCCTGGTGGACTTCG
+TGAAACACATCAACCGCACCAAGAACGCGATTCATAGCAGCATCGTGGACTTTTCCGGCAAGGGCACCGG
+GCACGAGGTGGAGATCGCGATGCAATGGAACGCCGGGTATTCGGAGTCGGTGCACACCTTCGCCAACACC
+ATCAACACCCACGAGGGCGGCACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGT
+ACGCCAAGGACCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT
+GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAAGTTGGGCAAC
+ACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAATGAACAGCTGACCCACTGGTTTGAAGCCAACCCCA
+CCGACTCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGCGCAAGCCCGTATCGCGGCACGTAAGGCACG
+AGAGTTGGTGCGGCGTAAGAGCGCCACCGACATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCC
+ACGGATCCGCGCAAGTCCGAACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTC
+GCGATTCGATGTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA
+CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCACGACGAGTTC
+GATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGATGTTGACGGCCAACATATTT
+CCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCCGCTCATCGAGAACGGGCATGTGTTTTTGGC
+ACAACCGCCGCTGTACAAACTCAAGTGGCAGCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGC
Binary file test-data/cv_input.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_output.gff	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,18 @@
+##gff-version
+#BBMapVersion
+#ploidy	2
+#rarity	1.00000
+#minAlleleFraction	0.1000
+#reads	2207
+#pairedReads	0
+#properlyPairedReads	0
+#readLengthAvg
+#properPairRate	0.0000
+#totalQualityAvg
+#mapqAvg
+#reference
+#seqid	source	type	start	end	score	strand	phase	attributes
+NC_002945.4	.	sequence_variant_obs	976327	976327
+NC_002945.4	.	sequence_variant_obs	1501932	1501932
+NC_002945.4	.	sequence_variant_obs	3380579	3380579
+NC_002945.4	.	sequence_variant_obs	3646293	3646293
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_output.txt	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,18 @@
+#fileformat
+#BBMapVersion
+#ploidy	2
+#rarity	1.00000
+#minAlleleFraction	0.1000
+#reads	2207
+#pairedReads	0
+#properlyPairedReads	0
+#readLengthAvg
+#properPairRate
+#totalQualityAvg
+#mapqAvg
+#reference
+#scaf	start	stop	type	call	r1p	r1m	r2p	r2m	paired	lengthSum	mapq	mapqMax	baseq	baseqMax	edist	edistMax	id	idMax	cov	minusCov	nearbyVarCount	flagged	contigEndDist	phredScore	readCount	alleleFraction	revisedAF	strandRatio	baseqAvg	mapqAvg	edistAvg	identityAvg	edistScore	identityScore	qualityScore	pairedScore	biasScore	coverageScore	homopolymerScore	score
+0	976326	976327	SUB	T
+0	1501931	1501932	SUB	C
+0	3380578	3380579	SUB	G
+0	3646292	3646293	SUB	A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_output.vcf	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,60 @@
+##fileformat=VCFv4.2
+##BBMapVersion=
+##ploidy=2
+##rarity=1.00000
+##minallelefraction=0.10000
+##reads=2207
+##pairedReads=0
+##properlyPairedReads=0
+##readLengthAvg=
+##properPairRate=0.00000
+##totalQualityAvg=
+##mapqAvg=43.348
+##reference=
+##contig=<ID=NC_002945.4,length=7000>
+##FILTER=<ID=FAIL,Description="Fail">
+##FILTER=<ID=PASS,Description="Pass">
+##INFO=<ID=SN,Number=1,Type=Integer,Description="Scaffold Number">
+##INFO=<ID=STA,Number=1,Type=Integer,Description="Start">
+##INFO=<ID=STO,Number=1,Type=Integer,Description="Stop">
+##INFO=<ID=TYP,Number=1,Type=String,Description="Type">
+##INFO=<ID=R1P,Number=1,Type=Integer,Description="Read1 Plus Count">
+##INFO=<ID=R1M,Number=1,Type=Integer,Description="Read1 Minus Count">
+##INFO=<ID=R2P,Number=1,Type=Integer,Description="Read2 Plus Count">
+##INFO=<ID=R2M,Number=1,Type=Integer,Description="Read2 Minus Count">
+##INFO=<ID=AD,Number=1,Type=Integer,Description="Allele Depth">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=MCOV,Number=1,Type=Integer,Description="Minus Coverage">
+##INFO=<ID=PPC,Number=1,Type=Integer,Description="Paired Count">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Fraction">
+##INFO=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction">
+##INFO=<ID=LS,Number=1,Type=Integer,Description="Length Sum">
+##INFO=<ID=MQS,Number=1,Type=Integer,Description="MAPQ Sum">
+##INFO=<ID=MQM,Number=1,Type=Integer,Description="MAPQ Max">
+##INFO=<ID=BQS,Number=1,Type=Integer,Description="Base Quality Sum">
+##INFO=<ID=BQM,Number=1,Type=Integer,Description="Base Quality Max">
+##INFO=<ID=EDS,Number=1,Type=Integer,Description="End Distance Sum">
+##INFO=<ID=EDM,Number=1,Type=Integer,Description="End Distance Max">
+##INFO=<ID=IDS,Number=1,Type=Integer,Description="Identity Sum">
+##INFO=<ID=IDM,Number=1,Type=Integer,Description="Identity Max">
+##INFO=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count">
+##INFO=<ID=FLG,Number=1,Type=Integer,Description="Flagged">
+##INFO=<ID=CED,Number=1,Type=Integer,Description="Contig End Distance">
+##INFO=<ID=HMP,Number=1,Type=Integer,Description="Homopolymer Count">
+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Ref+, Ref-, Alt+, Alt-">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele Depth">
+##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele Fraction">
+##FORMAT=<ID=RAF,Number=1,Type=Float,Description="Revised Allele Fraction">
+##FORMAT=<ID=NVC,Number=1,Type=Integer,Description="Nearby Variation Count">
+##FORMAT=<ID=FLG,Number=1,Type=Integer,Description="Flagged">
+##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
+##FORMAT=<ID=SC,Number=1,Type=Float,Description="Score">
+##FORMAT=<ID=PF,Number=1,Type=String,Description="Pass Filter">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	
+NC_002945.4	976327	.	N	T	22.21	PASS	SN=0;STA=976326;STO=976327;TYP=SUB;R1P=2;R1M=0;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=77;MQM=40;BQS=48;BQM=24;EDS=111;EDM=65;IDS=1930;IDM=972;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:22.21:PASS
+NC_002945.4	1501932	.	N	C	27.20	PASS	SN=0;STA=1501931;STO=1501932;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=292;MQS=88;MQM=44;BQS=64;BQM=39;EDS=74;EDM=38;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:27.20:PASS
+NC_002945.4	3380579	.	N	G	27.85	PASS	SN=0;STA=3380578;STO=3380579;TYP=SUB;R1P=0;R1M=2;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=289;MQS=87;MQM=44;BQS=75;BQM=38;EDS=105;EDM=63;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=0.9980	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:0.9980:27.85:PASS
+NC_002945.4	3646293	.	N	A	23.34	PASS	SN=0;STA=3646292;STO=3646293;TYP=SUB;R1P=1;R1M=1;R2P=0;R2M=0;AD=2;DP=2;MCOV=-1;PPC=0;AF=1.0000;RAF=1.0000;LS=291;MQS=86;MQM=44;BQS=76;BQM=38;EDS=44;EDM=31;IDS=1986;IDM=993;NVC=0;FLG=0;CED=0;HMP=0;SB=1.0000	GT:DP:AD:AF:RAF:NVC:FLG:SB:SC:PF	1/1:2:2:1.0000:1.0000:0:0:1.0000:23.34:PASS
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_qualityhist_output.tabular	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,46 @@
+#BaseQualityHist
+#Vars
+#Mean
+#Median
+#Mode
+#Quality	AvgCount	MaxCount
+0	0	0
+1	0	0
+2	0	0
+3	0	0
+4	0	0
+5	0	0
+6	0	0
+7	0	0
+8	0	0
+9	0	0
+10	0	0
+11	0	0
+12	0	0
+13	0	0
+14	0	0
+15	0	0
+16	0	0
+17	0	0
+18	0	0
+19	0	0
+20	0	0
+21	0	0
+22	0	0
+23	0	0
+24	1	1
+25	0	0
+26	0	0
+27	0	0
+28	0	0
+29	0	0
+30	0	0
+31	0	0
+32	1	0
+33	0	0
+34	0	0
+35	0	0
+36	0	0
+37	1	0
+38	1	2
+39	0	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_scorehist_output.tabular	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,34 @@
+#ScoreHist
+#Vars
+#Mean
+#Median
+#Mode
+#Quality	Count
+0	0
+1	0
+2	0
+3	0
+4	0
+5	0
+6	0
+7	0
+8	0
+9	0
+10	0
+11	0
+12	0
+13	0
+14	0
+15	0
+16	0
+17	0
+18	0
+19	0
+20	0
+21	0
+22	1
+23	1
+24	0
+25	0
+26	0
+27	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cv_zygosityhist_output.tabular	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,8 @@
+#ZygoHist
+#Vars
+#Mean
+#HomozygousFraction
+#Zygosity	Count
+0	0
+1	0
+2	4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,1 @@
+89	89	Mycobacterium_AF2122	${__HERE__}/NC_002945v4.fasta
Binary file test-data/output1.bam has changed
Binary file test-data/output2.bam has changed
Binary file test-data/output3.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Tue Oct 05 20:05:50 2021 +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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,6 @@
+<tables>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/fasta_indexes.loc" />
+    </table>
+</tables>