# HG changeset patch
# User iuc
# Date 1648839771 0
# Node ID 07e8b80f278c356cddee2622b1075f36a2da647e
# Parent  841fb4dc3ab365b126cda259a94a5686a876cdf9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"

diff -r 841fb4dc3ab3 -r 07e8b80f278c bedToBam.xml
--- a/bedToBam.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/bedToBam.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,7 @@
 bedtools bedtobam
 $bed12
 -mapq $mapq
--g @GENOME_FILE@
+@GENOME_FILE@
 -i '$input'
 > '$output'
     ]]></command>
diff -r 841fb4dc3ab3 -r 07e8b80f278c bedpeToBam.xml
--- a/bedpeToBam.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/bedpeToBam.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
@@ -13,7 +13,7 @@
 bedtools bedpetobam
 -mapq $mapq
 -i '$input'
--g @GENOME_FILE@
+@GENOME_FILE@
 > '$output'
     ]]></command>
     <inputs>
diff -r 841fb4dc3ab3 -r 07e8b80f278c closestBed.xml
--- a/closestBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/closestBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -149,6 +149,13 @@
             <param name="k" value="3" />
             <output name="output" file="closestBed_result6.bed" ftype="bed" />
         </test>
+        <test>
+            <param name="inputA" value="closestBedA.bed" ftype="bed" />
+            <param name="source" value="data_table" />
+            <param name="inputB" value="testid" />
+            <param name="k" value="3" />
+            <output name="output" file="closestBed_result6.bed" ftype="bed" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
diff -r 841fb4dc3ab3 -r 07e8b80f278c complementBed.xml
--- a/complementBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/complementBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>Extract intervals not represented by an interval file</description>
     <macros>
         <import>macros.xml</import>
@@ -9,7 +9,7 @@
     <command><![CDATA[
 complementBed
 -i '$input'
--g @GENOME_FILE@
+@GENOME_FILE@
 > '$output'
     ]]></command>
     <inputs>
diff -r 841fb4dc3ab3 -r 07e8b80f278c fisherBed.xml
--- a/fisherBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/fisherBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>calculate Fisher statistic between two feature files</description>
     <macros>
         <import>macros.xml</import>
@@ -13,7 +13,7 @@
 -a '$inputA'
 -b '$inputB'
 @OVERLAP@
--g @GENOME_FILE@
+@GENOME_FILE@
 $reciprocal
 $m
 > '$output'
diff -r 841fb4dc3ab3 -r 07e8b80f278c flankBed.xml
--- a/flankBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/flankBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>create new intervals from the flanks of existing intervals</description>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,7 @@
 flankBed
 $pct
 $strand
--g @GENOME_FILE@
+@GENOME_FILE@
 -i '$input'
 
 #if $addition.addition_select == 'b':
diff -r 841fb4dc3ab3 -r 07e8b80f278c getfastaBed.xml
--- a/getfastaBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/getfastaBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -91,6 +91,15 @@
             <param name="nameOnly" value="True" />
             <output name="output" file="getfastaBed_result4.bed" ftype="fasta" />
         </test>
+        <test>
+            <param name="input" value="nucBed2.bed" ftype="bed" />
+            <param name="fasta_source_selector" value="preloaded"/>
+            <param name="fasta_id" value="testid" />
+            <param name="tab" value="False" />
+            <param name="split" value="False" />
+            <param name="nameOnly" value="True" />
+            <output name="output" file="getfastaBed_result4.bed" ftype="fasta" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
diff -r 841fb4dc3ab3 -r 07e8b80f278c intersectBed.xml
--- a/intersectBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/intersectBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>find overlapping intervals in various ways</description>
     <macros>
         <import>macros.xml</import>
@@ -51,6 +51,7 @@
 $header
 $modes
 @SORTED@
+@GENOME_FILE@
 $bed
 $count
 > '${output}'
@@ -117,6 +118,7 @@
             label="When using BAM input, write output as BED instead of BAM." />
         <!-- -sorted -g  -->
         <expand macro="sorted" />
+        <expand macro="input_conditional_genome_file" optional="true" help="Only applies when used with -sorted option."/>
         <expand macro="print_header" />
     </inputs>
     <outputs>
@@ -151,7 +153,7 @@
                 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-wa,-wb" />
-            <param name="sorted" value="-sorted" />
+            <param name="sorted" value="true" />
             <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" />
         </test>
         <test>
@@ -163,7 +165,7 @@
                 <param name="names" value="yes" />
             </conditional>
             <param name="overlap_mode" value="-wa,-wb" />
-            <param name="sorted" value="-sorted" />
+            <param name="sorted" value="true" />
             <output name="output" file="intersect-multiple-wa-wb-wnames.bed" ftype="bed" />
         </test>
         <test>
@@ -173,7 +175,7 @@
                 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
             </conditional>
             <param name="invert" value="-v" />
-            <param name="sorted" value="-sorted" />
+            <param name="sorted" value="true" />
             <output name="output" file="intersect-multiple-invert.bed" ftype="bed" />
         </test>
         <test>
@@ -187,7 +189,7 @@
                 <param name="fraction_select" value="specify"/>
                 <param name="overlap" value="1.0" />
             </conditional>
-            <param name="sorted" value="-sorted" />
+            <param name="sorted" value="true" />
             <output name="output" file="intersect-multiple-fracA.bed" ftype="bed" />
         </test>
         <test>
diff -r 841fb4dc3ab3 -r 07e8b80f278c macros.xml
--- a/macros.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/macros.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -67,48 +67,29 @@
             label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
             help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
     </xml>
-    <xml name="input_conditional_genome_file">
+    <xml name="input_conditional_genome_file" token_optional="false" token_help="">
         <conditional name="genome_file_opts">
-            <param name="genome_file_opts_selector" type="select" label="Genome file">
+            <param name="genome_file_opts_selector" type="select" label="Genome file" help="@HELP@">
                 <option value="loc" selected="true">Locally installed Genome file</option>
                 <option value="hist">Genome file from your history</option>
             </param>
             <when value="loc">
-                <param name="genome" type="select" multiple="false" label="Genome file">
+                <param name="genome" type="select" optional="@OPTIONAL@" multiple="false" label="Genome file">
                     <options from_data_table="__dbkeys__" />
                 </param>
             </when>
             <when value="hist">
-                <param name="genome" type="data" format="tabular" label="Genome file" />
+                <param name="genome" type="data" optional="@OPTIONAL@" format="tabular" label="Genome file" />
             </when>
         </conditional>
     </xml>
-    <xml name="input_optional_genome_file">
-        <conditional name="genome">
-            <param name="genome_choose" argument="-g" type="select"
-                label="Specify a genome file that defines the expected chromosome order in the input files." >
-                <option value="" selected="true">No</option>
-                <option value="-g">Yes</option>
-            </param>
-            <when value="-g">
-                <expand macro="input_conditional_genome_file" />
-            </when>
-            <when value="" />
-        </conditional>
-    </xml>
     <token name="@GENOME_FILE@">
-#if $genome_file_opts.genome_file_opts_selector == "loc":
-    '$genome_file_opts.genome.fields.len_path'
-#elif $genome_file_opts.genome_file_opts_selector == "hist":
-    '$genome_file_opts.genome'
-#end if
-    </token>
-    <token name="@GENOME_FILE_MAPBED@">
-#if $genome.genome_choose == "-g":
-    #if $genome.genome_file_opts.genome_file_opts_selector == "loc":
-        -g '$genome.genome_file_opts.genome.fields.len_path'
-    #elif $genome.genome_file_opts.genome_file_opts_selector == "hist":
-        -g '$genome.genome_file_opts.genome'
+#if $genome_file_opts.genome
+    -g 
+    #if $genome_file_opts.genome_file_opts_selector == "loc":
+        '$genome_file_opts.genome.fields.len_path'
+    #elif $genome_file_opts.genome_file_opts_selector == "hist":
+        '$genome_file_opts.genome'
     #end if
 #end if
     </token>
diff -r 841fb4dc3ab3 -r 07e8b80f278c mapBed.xml
--- a/mapBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/mapBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2" profile="@PROFILE@">
+<tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.3" profile="@PROFILE@">
     <description>apply a function to a column for each overlapping interval</description>
     <macros>
         <import>macros.xml</import>
@@ -19,7 +19,7 @@
 $reciprocal
 $split
 $header
-@GENOME_FILE_MAPBED@
+@GENOME_FILE@
 > '${output}'
     ]]></command>
     <inputs>
@@ -36,7 +36,7 @@
         </expand>
         <expand macro="split" />
         <expand macro="print_header" />
-        <expand macro="input_optional_genome_file" />
+        <expand macro="input_conditional_genome_file" optional="true"/>
     </inputs>
     <outputs>
         <data name="output" format_source="inputA" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
@@ -88,9 +88,24 @@
                 <param name="operation" value="collapse" />
             </repeat>
             <param name="strand" value="-s" />
-            <param name="genome_choose" value="-g" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9.len" ftype="bed" />
+            <conditional name="genome_file_opts">
+                <param name="genome_file_opts_selector" value="hist" />
+                <param name="genome" value="mm9.len" ftype="bed" />
+            </conditional>
+            <output name="output" file="mapBed_result5.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="mapBed3.bed" ftype="bed" />
+            <param name="inputB" value="mapBed4.bed" ftype="bed" />
+            <repeat name="c_and_o_argument_repeat">
+                <param name="col" value="5" />
+                <param name="operation" value="collapse" />
+            </repeat>
+            <param name="strand" value="-s" />
+            <conditional name="genome_file_opts">
+                <param name="genome_file_opts_selector" value="loc" />
+                <param name="genome" value="mm9"/>
+            </conditional>
             <output name="output" file="mapBed_result5.bed" ftype="bed" />
         </test>
     </tests>
diff -r 841fb4dc3ab3 -r 07e8b80f278c randomBed.xml
--- a/randomBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/randomBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>generate random intervals in a genome</description>
     <macros>
         <import>macros.xml</import>
@@ -8,7 +8,7 @@
     <expand macro="stdio" />
     <command><![CDATA[
 bedtools random
--g @GENOME_FILE@
+@GENOME_FILE@
 -l $length
 -n $intervals
 #if str($seed.seed_choose) == "True":
diff -r 841fb4dc3ab3 -r 07e8b80f278c shuffleBed.xml
--- a/shuffleBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/shuffleBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>randomly redistrubute intervals in a genome</description>
     <macros>
         <import>macros.xml</import>
@@ -8,7 +8,7 @@
     <expand macro="stdio" />
     <command><![CDATA[
 bedtools shuffle
--g @GENOME_FILE@
+@GENOME_FILE@
 -i '$inputA'
 $bedpe
 #if str($seed.seed_choose) == "True":
diff -r 841fb4dc3ab3 -r 07e8b80f278c slopBed.xml
--- a/slopBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/slopBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>adjust the size of intervals</description>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,7 @@
 bedtools slop
 $pct
 $strand
--g @GENOME_FILE@
+@GENOME_FILE@
 -i '$inputA'
 #if $addition.addition_select == 'b':
     -b $addition.b
diff -r 841fb4dc3ab3 -r 07e8b80f278c sortBed.xml
--- a/sortBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/sortBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>order the intervals</description>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,7 @@
 sortBed
 -i '$input'
 $option
-@GENOME_FILE_MAPBED@
+@GENOME_FILE@
 > '$output'
     ]]></command>
     <inputs>
@@ -25,7 +25,7 @@
             <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
             <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
         </param>
-        <expand macro="input_optional_genome_file" />
+        <expand macro="input_conditional_genome_file" help="Sort according to the chromosomes declared in a genome file" />
     </inputs>
     <outputs>
         <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/>
@@ -44,9 +44,10 @@
         <test>
             <param name="input" value="sortBed2.bed" ftype="bed" />
             <param name="option" value="" />
-            <param name="genome_choose" value="-g" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9.len" ftype="bed" />
+            <conditional name="genome_file_opts">
+                <param name="genome_file_opts_selector" value="hist" />
+                <param name="genome" value="mm9.len" ftype="bed" />
+            </conditional>
             <output name="output" file="sortBed_result3.bed" ftype="bed" />
         </test>
     </tests>
diff -r 841fb4dc3ab3 -r 07e8b80f278c test-data/all_gff.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_gff.loc	Fri Apr 01 19:02:51 2022 +0000
@@ -0,0 +1,15 @@
+#This file lists the locations and dbkeys of all the GFF files
+#This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_gff.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/annotation/apiMel3/apiMel3.gff
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/annotation/hg19/hg19canon.gff
+#hg19full	hg19	Human (Homo sapiens): hg19 Representative transcripts	/path/to/annotation/hg19/hg19_representative_tx.gff
+#
+#Your all_gff.loc file should contain an entry for each different annotation.
+#So there can be multiple gff files for each build, such as with hg19 above.
+testid	testdbkey	testdisplay	${__HERE__}/a.bed
diff -r 841fb4dc3ab3 -r 07e8b80f278c test-data/dbkeys.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbkeys.loc	Fri Apr 01 19:02:51 2022 +0000
@@ -0,0 +1,14 @@
+#This file lists the locations and dbkeys of all the genome files
+#See here for details: http://bedtools.readthedocs.io/en/latest/content/general-usage.html#genome-file-format
+#You can add elements to this data table using the data_manager_fetch_genome_dbkeys_all_fasta data manager.
+#Alternatively, index files created using samtools faidx (http://www.htslib.org/doc/faidx.html) contain 3 extra columns, but work fine.
+#This file has the format (white space characters are TAB characters):
+#
+#<dbkey>	<display_name>	<file_path>
+#
+#So, dbkeys.loc could look something like this:
+#
+#apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.len
+#hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.len
+#
+mm9	Mus Musculus	${__HERE__}/mm9.len
\ No newline at end of file
diff -r 841fb4dc3ab3 -r 07e8b80f278c test-data/fasta_indexes.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc	Fri Apr 01 19:02:51 2022 +0000
@@ -0,0 +1,30 @@
+#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
+testid	testdbkey	testdisplay	${__HERE__}/nucBed1.fasta
\ No newline at end of file
diff -r 841fb4dc3ab3 -r 07e8b80f278c test-data/nucBed1.fasta.fai
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nucBed1.fasta.fai	Fri Apr 01 19:02:51 2022 +0000
@@ -0,0 +1,1 @@
+chr1	359	18	80	81
diff -r 841fb4dc3ab3 -r 07e8b80f278c test-data/sortBed_result2.bed
--- a/test-data/sortBed_result2.bed	Wed Jan 12 19:22:14 2022 +0000
+++ b/test-data/sortBed_result2.bed	Fri Apr 01 19:02:51 2022 +0000
@@ -1,3 +1,3 @@
 chr1	800	1000
+chr2	1	10
 chr10	80	180
-chr2	1	10
diff -r 841fb4dc3ab3 -r 07e8b80f278c tool-data/all_fasta.loc.sample
--- a/tool-data/all_fasta.loc.sample	Wed Jan 12 19:22:14 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-#This file lists the locations and dbkeys of all the fasta files
-#under the "genome" directory (a directory that contains a directory
-#for each build). The script extract_fasta.py will generate the file
-#all_fasta.loc. This file has the format (white space characters are
-#TAB characters):
-#
-#<unique_build_id>	<dbkey>	<display_name>	<file_path>
-#
-#So, all_fasta.loc could look something like this:
-#
-#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
-#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
-#
-#Your all_fasta.loc file should contain an entry for each individual
-#fasta file. So there will be multiple fasta files for each build,
-#such as with hg19 above.
-#
diff -r 841fb4dc3ab3 -r 07e8b80f278c tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed Jan 12 19:22:14 2022 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Apr 01 19:02:51 2022 +0000
@@ -1,9 +1,4 @@
 <tables>
-    <!-- Locations of all fasta files under genome directory -->
-    <table name="all_fasta" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/all_fasta.loc" />
-    </table>
     <!-- Locations of all sam indexes under genome directory -->
     <table name="fasta_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
diff -r 841fb4dc3ab3 -r 07e8b80f278c tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Apr 01 19:02:51 2022 +0000
@@ -0,0 +1,17 @@
+<tables>
+    <!-- Locations of all sam indexes under genome directory -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/fasta_indexes.loc" />
+    </table>
+    <!-- Locations of all gff files with annotations of genome builds -->
+    <table name="all_gff" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_gff.loc" />
+    </table>
+    <!-- Locations of dbkeys and len files under genome directory -->
+    <table name="__dbkeys__" comment_char="#">
+        <columns>value, name, len_path</columns>
+        <file path="${__HERE__}/test-data/dbkeys.loc" />
+    </table>
+</tables>