Repository 'bcftools_plugin_counts'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_counts

Changeset 5:5bae20e2d7c8 (2017-04-13)
Previous changeset 4:902fd5bfb7f6 (2017-03-11) Next changeset 6:5ad5d4243987 (2017-12-12)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
modified:
bcftools_plugin_counts.xml
macros.xml
added:
test-data/csq.fa
test-data/csq.gff3
test-data/csq.vcf
test-data/mpileup.1.bam
test-data/mpileup.1.bam.bai
test-data/mpileup.2.bam
test-data/mpileup.2.bam.bai
test-data/mpileup.3.bam
test-data/mpileup.3.bam.bai
test-data/mpileup.3.cram
test-data/mpileup.4.bam
test-data/mpileup.ref.fa
test-data/mpileup.ref.fa.fai
test-data/mpileup.regions.bed
test-data/mpileup.regions.tab
test-data/roh.vcf
tool-data/fasta_indexes.loc.sample
tool_data_table_conf.xml.sample
b
diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 bcftools_plugin_counts.xml
--- a/bcftools_plugin_counts.xml Sat Mar 11 18:00:50 2017 -0500
+++ b/bcftools_plugin_counts.xml Thu Apr 13 17:46:36 2017 -0400
[
@@ -13,6 +13,8 @@
 @PREPARE_INPUT_FILE@
 #set $section = $sec_restrict
 @PREPARE_TARGETS_FILE@
+@PREPARE_REGIONS_FILE@
+
 bcftools plugin @EXECUTABLE@
 
 ## VCF input section
@@ -24,7 +26,7 @@
 
 ## Primary Input/Outputs
 @INPUT_FILE@ | tee counts_file.txt  
-&& sed 's/^.* \([a-zA-Z]*\):[ ]*\([0-9]*\)$/\1 \2/' counts_file.txt | python $transform > "$output_file"
+&& sed 's/^.* \([a-zA-Z]*\):[ ]*\([0-9]*\)$/\1 \2/' counts_file.txt | python $transform > '$output_file'
 ]]>
     </command>
     <configfiles>
b
diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 macros.xml
--- a/macros.xml Sat Mar 11 18:00:50 2017 -0500
+++ b/macros.xml Thu Apr 13 17:46:36 2017 -0400
[
@@ -1,5 +1,5 @@
 <macros>
-  <token name="@VERSION@">1.3.1</token>
+  <token name="@VERSION@">1.4.0</token>
   <xml name="stdio">
     <stdio>
       <exit_code range="1:" />
@@ -10,12 +10,14 @@
   </xml>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="1.3.1">bcftools</requirement>
-      <!-- conda dependency -->
-      <requirement type="package" version="1.3.2">htslib</requirement>
+      <requirement type="package" version="1.4">bcftools</requirement>
+      <requirement type="package" version="1.4">htslib</requirement>
       <yield />
     </requirements>
   </xml>
+  <xml name="samtools_requirement">
+      <requirement type="package" version="1.3.1">samtools</requirement>
+  </xml>
   <xml name="version_command">
     <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
   </xml>
@@ -245,7 +247,7 @@
   </xml>
   <token name="@OUTPUT_TYPE@">
 #if str($output_type) != "__none__":
-  --output-type "${output_type}"
+  --output-type '${output_type}'
 #end if
   </token>
 
@@ -279,14 +281,30 @@
         </when>
     </conditional>
   </xml>
+  <token name="@PREPARE_REGIONS_FILE@">
+<![CDATA[
+#set $regions_path = None
+#if 'regions' in $section
+  #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
+    #if $section.regions.regions_file.ext.startswith('bed'):
+      #set $regions_path = 'regions_file.bed'
+      ln -s '$section.regions.regions_file' $regions_path &&
+    #end if
+  #end if
+#end if
+]]>
+  </token>
   <token name="@REGIONS@">
 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
   --regions '$section.regions.regions'
 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
-  --regions-file '$section.regions.regions_file'
+  #if $regions_path is not None:
+    --regions-file '$regions_path'
+  #else:
+    --regions-file '$section.regions.regions_file'
+  #end if
 #end if
   </token>
-
   <xml name="macro_targets_file">
             <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
               <yield/>
@@ -356,11 +374,11 @@
 
   <xml name="macro_samples">
       <param name="samples" type="text" value="" label="Samples" optional="true"
-             help="(-s) comma separated list of samples to annotate (or exclude with &quot;^&quot; prefix)">
+             help="(-s) comma separated list of samples to annotate (or exclude)">
           <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
       </param>
       <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
-             help="inverts the query/filtering applied by Samples" />
+             help="inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
       <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
              help="(-S) file of samples to include" />
       <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"
b
diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/csq.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/csq.fa Thu Apr 13 17:46:36 2017 -0400
b
@@ -0,0 +1,34 @@
+>1
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+>2
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+>3
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
+
b
diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/csq.gff3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/csq.gff3 Thu Apr 13 17:46:36 2017 -0400
b
@@ -0,0 +1,40 @@
+##gff-version   3
+#! This file shows which fields are used and required by `bcftools +csq`. It is a trimmed version 
+#! of the GFF3 format, see an example of the full format here
+#!      ftp://ftp.ensembl.org/pub/grch37/release-84/gff3/homo_sapiens/
+#!
+###
+1 . gene 90 200 . + . ID=gene:ENSG00000000001;Name=XYZ;biotype=protein_coding
+1 . transcript 90 200 . + . ID=transcript:ENST00000000001;Parent=gene:ENSG00000000001;biotype=protein_coding
+1 . exon 90 110 . + . Parent=transcript:ENST00000000001
+1 . five_prime_UTR 90 98 . + . Parent=transcript:ENST00000000001
+1 . CDS 99 110 . + 1 Parent=transcript:ENST00000000001
+1 . exon 120 130 . + . Parent=transcript:ENST00000000001
+1 . CDS 120 130 . + 1 Parent=transcript:ENST00000000001
+1 . exon 140 150 . + . Parent=transcript:ENST00000000001
+1 . CDS 140 150 . + 2 Parent=transcript:ENST00000000001
+1 . exon 160 200 . + . Parent=transcript:ENST00000000001
+1 . CDS 160 171 . + 0 Parent=transcript:ENST00000000001
+1 . three_prime_UTR 172 200 . + . Parent=transcript:ENST00000000001
+2 . gene 80 200 . - . ID=gene:ENSG00000000002;Name=ABC;biotype=protein_coding
+2 . transcript 80 200 . - . ID=transcript:ENST00000000002;Parent=gene:ENSG00000000002;biotype=protein_coding
+2 . exon 80 110 . - . Parent=transcript:ENST00000000002
+2 . three_prime_UTR 80 98 . - . Parent=transcript:ENST00000000002
+2 . CDS 99 110 . - 0 Parent=transcript:ENST00000000002
+2 . exon 120 130 . - . Parent=transcript:ENST00000000002
+2 . CDS 120 130 . - 2 Parent=transcript:ENST00000000002
+2 . exon 140 150 . - . Parent=transcript:ENST00000000002
+2 . CDS 140 150 . - 1 Parent=transcript:ENST00000000002
+2 . exon 160 200 . - . Parent=transcript:ENST00000000002
+2 . CDS 160 171 . - 1 Parent=transcript:ENST00000000002
+2 . five_prime_UTR 172 200 . - . Parent=transcript:ENST00000000002
+3 . lincRNA_gene 20 50 . - . ID=gene:ENSG00000000004;Name=mir-007;biotype=lincRNA
+3 . lincRNA 20 50 . - . ID=transcript:ENSG00000000004;Parent=gene:ENSG00000000004;biotype=lincRNA
+3 . gene 100 200 . - . ID=gene:ENSG00000000003;Name=QWRTY;biotype=protein_coding
+3 . transcript 100 200 . - . ID=transcript:ENST00000000003;Parent=gene:ENSG00000000003;biotype=protein_coding
+3 . exon 100 110 . - . Parent=transcript:ENST00000000003
+3 . three_prime_UTR 100 105 . - . Parent=transcript:ENST00000000003
+3 . CDS 106 110 . - 0 Parent=transcript:ENST00000000003
+3 . exon 160 200 . - . Parent=transcript:ENST00000000003
+3 . CDS 160 171 . - 0 Parent=transcript:ENST00000000003
+3 . five_prime_UTR 172 200 . - . Parent=transcript:ENST00000000003
b
diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/csq.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/csq.vcf Thu Apr 13 17:46:36 2017 -0400
b
@@ -0,0 +1,40 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=EXP,Number=1,Type=String,Description="Expected consequence">
+##contig=<ID=1,length=2147483647>
+##contig=<ID=2,length=2147483647>
+##contig=<ID=3,length=2147483647>
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SmplAAA SmplBBB
+1 90 . C T . . EXP=5_prime_utr|XYZ|ENST00000000001|protein_coding GT 1|0 1|1
+1 102 . C T 1 . EXP=synonymous|XYZ|ENST00000000001|protein_coding|+|1Y|102C>T GT 1|0 1|0
+1 103 . G A 1 . EXP=missense|XYZ|ENST00000000001|protein_coding|+|2V>2I|103G>A GT 1|0 0|0
+1 103 . G C 1 . EXP=missense|XYZ|ENST00000000001|protein_coding|+|2V>2L|103G>C GT 0|0 1|0
+1 107 . G A 1 . EXP=missense|XYZ|ENST00000000001|protein_coding|+|3R>3Q|107G>A+108T>A GT 1|0 1|0
+1 108 . T A 1 . EXP=splice_region|XYZ|ENST00000000001|protein_coding,@107 GT 1|0 1|0
+1 121 . ACG A . . EXP=inframe_deletion|XYZ|ENST00000000001|protein_coding|+|5TY>5I|121ACG>A+124TA>T,splice_region|XYZ|ENST00000000001|protein_coding GT 1|0 1|0
+1 124 . TA T . . EXP=@121 GT 1|0 1|0
+1 128 . T C 1 . EXP=missense|XYZ|ENST00000000001|protein_coding|+|7V>6A|128T>C+129A>C,splice_region|XYZ|ENST00000000001|protein_coding GT 1|0 0/0
+1 129 . A C 1 . EXP=splice_region|XYZ|ENST00000000001|protein_coding,@128 GT 1|0 0/0
+1 140 . TA AACG . . EXP=inframe_insertion|XYZ|ENST00000000001|protein_coding|+|8LR>7QRR|140TA>AACG+142C>CC,splice_region|XYZ|ENST00000000001|protein_coding GT 1|0 0|0
+1 142 . C CC . . EXP=splice_region|XYZ|ENST00000000001|protein_coding,@140 GT 1|0 0|0
+1 145 . AC TA . . EXP=stop_gained|XYZ|ENST00000000001|protein_coding|+|10T>10*|145AC>TA GT 1|0 0|0
+1 160 . TA T . . EXP=*frameshift|XYZ|ENST00000000001|protein_coding|+|12YVRT>12SYV|160TA>T,splice_region|XYZ|ENST00000000001|protein_coding GT 1|0 0|0
+1 190 . C T . . EXP=3_prime_utr|XYZ|ENST00000000001|protein_coding GT 1|0 0|0
+2 97 . A C . . EXP=3_prime_utr|ABC|ENST00000000002|protein_coding GT 1|0 0|0
+2 105 . AC A . . EXP=@121 GT 1|0 0|0
+2 121 . AC A . . EXP=frameshift|ABC|ENST00000000002|protein_coding|-|11VVRTY>11*|105AC>A+121AC>A,splice_region|ABC|ENST00000000002|protein_coding GT 1|0 0|0
+2 126 . C CTT . . EXP=@127 GT 1|0 0|0
+2 127 . G GG . . EXP=inframe_insertion|ABC|ENST00000000002|protein_coding|-|9T>8TK|126C>CTT+127G>GG GT 1|0 0|0
+2 144 . TAC T . . EXP=@148 GT 1|0 0|0
+2 148 . TA T . . EXP=inframe_deletion|ABC|ENST00000000002|protein_coding|-|5YV>5T|144TAC>T+148TA>T,splice_region|ABC|ENST00000000002|protein_coding GT 1|0 0|0
+2 164 . T G . . EXP=missense|ABC|ENST00000000002|protein_coding|-|3T>3P|164T>G GT 1|0 0|0
+2 165 . A C . . EXP=synonymous|ABC|ENST00000000002|protein_coding|-|2R|165A>C GT 1|0 0|0
+2 169 . A G . . EXP=@170 GT 1|0 0|0
+2 170 . C T . . EXP=missense|ABC|ENST00000000002|protein_coding|-|1V>1T|169A>G+170C>T GT 1|0 0|0
+2 199 . G T . . EXP=5_prime_utr|ABC|ENST00000000002|protein_coding GT 1|0 0|0
+3 20 . T A . . EXP=non_coding|mir-007||lincRNA GT 1|0 0|0
+3 109 . ACGTACGT A 1 . EXP=splice_acceptor|QWRTY|ENST00000000003|protein_coding GT 1|0 0|0
+3 113 . A T . . EXP=splice_region|QWRTY|ENST00000000003|protein_coding GT 1|0 0|0
+3 120 . T A . . EXP=intron|QWRTY||protein_coding GT 1|0 0|0
+3 152 . T A . . EXP=splice_region|QWRTY|ENST00000000003|protein_coding GT 1|0 0|0
+3 159 . G A . . EXP=splice_donor|QWRTY|ENST00000000003|protein_coding GT 1|0 0|0
b
diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/mpileup.1.bam
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Binary file test-data/mpileup.1.bam has changed
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diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/mpileup.1.bam.bai
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diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/mpileup.2.bam
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Binary file test-data/mpileup.2.bam has changed
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diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/mpileup.2.bam.bai
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diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/mpileup.3.bam
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Binary file test-data/mpileup.3.bam has changed
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diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/mpileup.3.bam.bai
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Binary file test-data/mpileup.3.bam.bai has changed
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diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/mpileup.3.cram
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Binary file test-data/mpileup.3.cram has changed
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diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/mpileup.4.bam
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Binary file test-data/mpileup.4.bam has changed
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diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/mpileup.ref.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup.ref.fa Thu Apr 13 17:46:36 2017 -0400
b
@@ -0,0 +1,71 @@
+>17 17:1-4200
+AAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAA
+TGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGA
+GCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAA
+GACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACAC
+GCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACA
+GTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGA
+AAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATA
+AATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAG
+GAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATC
+ACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTG
+TGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACAT
+GCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGG
+CAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGA
+AAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATATTCTCTGTGTTGA
+TTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTAC
+CAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAG
+TGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCG
+CCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAA
+GAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGAC
+CAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGT
+TCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTC
+CCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGAC
+GCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCC
+CGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTA
+GGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGA
+GCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTT
+TGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCAGC
+CACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAG
+CGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCA
+CTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCC
+TGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGG
+TCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACA
+GTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGC
+CAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCAC
+GGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGC
+AGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGC
+ACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCG
+GCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAG
+CTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATC
+GTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAA
+AAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGG
+AGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCG
+CATCACTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTCTCAAAAAAGAAAGGAAGAA
+ATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGG
+CCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCT
+CTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTAT
+TTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGG
+ACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATG
+TGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCT
+TTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAG
+CAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTG
+CCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAG
+ACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGG
+GCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTA
+ATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCA
+GCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTG
+GCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGG
+GAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGT
+AAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCC
+TGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAACATATAT
+ATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTG
+TTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTAC
+ACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGC
+CTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCG
+TCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCAT
+GCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAT
+GGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACCCGCT
+ACACTCCTTCTTAGGGCTGATATTCCACGCACCCGCTACACTCCTTCTTAGGGCTGATAT
+TCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTT
+CTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCAC
b
diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/mpileup.ref.fa.fai
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup.ref.fa.fai Thu Apr 13 17:46:36 2017 -0400
b
@@ -0,0 +1,1 @@
+17 4200 14 60 61
b
diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/mpileup.regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup.regions.bed Thu Apr 13 17:46:36 2017 -0400
b
@@ -0,0 +1,1 @@
+17 99 110
b
diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/mpileup.regions.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mpileup.regions.tab Thu Apr 13 17:46:36 2017 -0400
b
@@ -0,0 +1,1 @@
+17 100 110
b
diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 test-data/roh.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/roh.vcf Thu Apr 13 17:46:36 2017 -0400
b
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b
diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 tool-data/fasta_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample Thu Apr 13 17:46:36 2017 -0400
b
@@ -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
b
diff -r 902fd5bfb7f6 -r 5bae20e2d7c8 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Apr 13 17:46:36 2017 -0400
b
@@ -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>