# HG changeset patch
# User iuc
# Date 1725040430 0
# Node ID 3a213e01bc7fc43f27f4a1b35b0517098397c5f4

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet commit 09ce055ec6cd95f6999cc680a707418cee25d42a

diff -r 000000000000 -r 3a213e01bc7f chainnet.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chainnet.xml	Fri Aug 30 17:53:50 2024 +0000
@@ -0,0 +1,146 @@
+<tool id="ucsc_chainnet" name="chainNet" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
+    <description>
+        make alignment nets out of alignment chains
+    </description>
+    <macros>
+        <token name="@TOOL_VERSION@">469</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">ucsc-chainnet</requirement>
+    </requirements>
+    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    chainNet
+        '$in_chain'
+        #if str( $target_reference_index_source.target_reference_index_source_selector ) == "history":
+            '${target_reference_index_source.in_tar_ref_index}'
+        #else:
+            '$target_reference_index_source.tar_ref_index_file.fields.path'
+        #end if
+        #if str( $query_reference_index_source.query_reference_index_source_selector ) == "history":
+            '${query_reference_index_source.in_que_ref_index}'
+        #else:
+            '$query_reference_index_source.que_ref_index_file.fields.path'
+        #end if
+        '$targetNet'
+        '$queryNet'
+        #if str($minSpace)
+            -minSpace=$minSpace
+        #end if
+        #if str($minFill)
+            -minFill=$minFill
+        #end if
+        #if str($minScore)
+            -minScore=$minScore
+        #end if
+        $inclHap
+        #if str($verbose)
+            -verbose=$verbose
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="in_chain" format="chain" type="data" label="Chain dataset" help="Select chain dataset" />
+
+        <conditional name="target_reference_index_source">
+            <param name="target_reference_index_source_selector" type="select" label="Choose the source for the target reference genome index">
+                <option value="cached">Built-in</option>
+                <option value="history">From history</option>
+            </param>
+            <when value="cached">
+                <param name="tar_ref_index_file" type="select" label="Using reference genome index">
+                  <options from_data_table="fasta_indexes" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="in_tar_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for target sequence. Typically a '.fai' file." />
+            </when>
+        </conditional>
+
+        <conditional name="query_reference_index_source">
+            <param name="query_reference_index_source_selector" type="select" label="Choose the source for the query reference genome index">
+                <option value="cached">Built-in</option>
+                <option value="history">From history</option>
+            </param>
+            <when value="cached">
+                <param name="que_ref_index_file" type="select" label="Using reference genome index">
+                  <options from_data_table="fasta_indexes" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="in_que_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for query sequence. Typically a '.fai' file." />
+            </when>
+        </conditional>
+
+        <param argument="-minSpace" type="integer" optional="true" min="0" label="Minimum gap size to fill" help="default 25" />
+        <param argument="-minFill" type="integer" optional="true" min="0" label="Minimum fill to record" help="default half of minSpace" />
+        <param argument="-minScore" type="integer" optional="true" label="Minimum chain score to consider" help="default 2000" />
+        <param argument="-inclHap" type="boolean" optional="true" truevalue="-inclHap" falsevalue="" label="Include query sequences name in the form *_hap*|*_alt*. Normally these are excluded from nets as being haplotype pseudochromosomes." />
+        <param argument="-verbose" type="integer" optional="true" label="Verbosity" help="default 1" />
+
+    </inputs>
+    <outputs>
+        <data name="targetNet" format="ucsc.net" label="${tool.name} on ${on_string}: target.net"/>
+        <data name="queryNet" format="ucsc.net" label="${tool.name} on ${on_string}: query.net" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="in_chain" value="input.chain" />
+            <conditional name="target_reference_index_source">
+                <param name="target_reference_index_source_selector" value="history" />
+                <param name="in_tar_ref_index" value="hg38.chr20.chunk.fasta.fai"/>
+            </conditional>
+            <conditional name="query_reference_index_source">
+                <param name="query_reference_index_source_selector" value="history" />
+                <param name="in_que_ref_index" value="mm39.chr2.chunk.fasta.fai"/>
+            </conditional>
+            <output name="targetNet" file="target.net"/>
+            <output name="queryNet" file="query.net"/>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="in_chain" value="input.chain" />
+            <conditional name="target_reference_index_source">
+                <param name="target_reference_index_source_selector" value="cached" />
+                <param name="tar_ref_index_file" value="hg38.chr20.chunk"/>
+            </conditional>
+            <conditional name="query_reference_index_source">
+                <param name="query_reference_index_source_selector" value="cached" />
+                <param name="que_ref_index_file" value="mm39.chr2.chunk"/>
+            </conditional>
+            <output name="targetNet" file="target.net"/>
+            <output name="queryNet" file="query.net"/>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="in_chain" value="input.chain" />
+            <param name="minScore" value="1200" />
+            <conditional name="target_reference_index_source">
+                <param name="target_reference_index_source_selector" value="cached" />
+                <param name="tar_ref_index_file" value="hg38.chr20.chunk"/>
+            </conditional>
+            <conditional name="query_reference_index_source">
+                <param name="query_reference_index_source_selector" value="history" />
+                <param name="in_que_ref_index" value="mm39.chr2.chunk.fasta.fai"/>
+            </conditional>
+            <output name="targetNet" file="target.1200.net"/>
+            <output name="queryNet" file="query.1200.net"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`chainNet`_ is a tool that makes alignment nets out of `alignment chains`_.
+It outputs two files in the `ucsc.net`_ format -- one for the target sequence and one for the query sequence.
+
+For implementation details see ChainNet's `source code`_.
+
+.. _chainNet: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
+.. _ucsc.net: https://genome.ucsc.edu/goldenPath/help/net.html
+.. _alignment chains: https://genome.ucsc.edu/goldenPath/help/chain.html
+.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/chainNet/chainNet.c
+    ]]>    </help>
+    <citations>
+        <citation type="doi">10.1093/bib/bbs038</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 3a213e01bc7f test-data/fasta_indexes.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc	Fri Aug 30 17:53:50 2024 +0000
@@ -0,0 +1,2 @@
+hg38.chr20.chunk	hg38	hg38.chr20.chunk	${__HERE__}/hg38.chr20.chunk.fasta.fai
+mm39.chr2.chunk	mm39	mm39.chr2.chunk	${__HERE__}/mm39.chr2.chunk.fasta.fai
diff -r 000000000000 -r 3a213e01bc7f test-data/hg38.chr20.chunk.fasta.fai
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hg38.chr20.chunk.fasta.fai	Fri Aug 30 17:53:50 2024 +0000
@@ -0,0 +1,1 @@
+hg38.chr20:10004760-11615810	1611050	30	1611050	1611051
diff -r 000000000000 -r 3a213e01bc7f test-data/input.chain
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.chain	Fri Aug 30 17:53:50 2024 +0000
@@ -0,0 +1,159 @@
+##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+##gapPenalties=axtChain O=400 E=30
+chain 64329 hg38.chr20:10004760-11615810 1611050 + 879848 882025 mm39.chr2:136351215-137822786 1471571 - 648557 650527 2
+24	0	1
+52	12	0
+46	0	6
+24	1	0
+63	0	1
+6	0	9
+78	14	0
+25	0	4
+14	4	0
+4	19	0
+12	9	0
+43	77	0
+19	2	0
+37	2	0
+61	1	0
+16	0	4
+74	0	7
+51	1	0
+30	17	0
+18	1	0
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+8	0	14
+8	0	3
+88	5	0
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+5	0	1
+6	0	7
+21	0	1
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+64	10	0
+46	2	0
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+5	3	0
+28	2	0
+34	1	0
+24	0	2
+39	1	0
+29	3	0
+68	17	0
+4	0	3
+29
+
+chain 13332 hg38.chr20:10004760-11615810 1611050 + 266744 267005 mm39.chr2:136351215-137822786 1471571 - 1226958 1227276 3
+17	0	14
+111	2	0
+42	3	0
+39	0	47
+31	0	1
+16
+
+chain 9256 hg38.chr20:10004760-11615810 1611050 + 288278 288554 mm39.chr2:136351215-137822786 1471571 + 260289 260601 4
+34	8	0
+38	0	2
+9	0	17
+11	0	24
+15	0	1
+161
+
+chain 8091 hg38.chr20:10004760-11615810 1611050 + 288114 288275 mm39.chr2:136351215-137822786 1471571 + 260754 260915 5
+161
+
+chain 6961 hg38.chr20:10004760-11615810 1611050 + 84589 84726 mm39.chr2:136351215-137822786 1471571 + 87751 87887 6
+83	1	0
+53
+
+chain 6916 hg38.chr20:10004760-11615810 1611050 + 87669 87836 mm39.chr2:136351215-137822786 1471571 + 87101 87269 7
+58	0	1
+109
+
+chain 5978 hg38.chr20:10004760-11615810 1611050 + 600994 601124 mm39.chr2:136351215-137822786 1471571 + 546215 546345 8
+130
+
+chain 5958 hg38.chr20:10004760-11615810 1611050 + 288132 288220 mm39.chr2:136351215-137822786 1471571 + 258580 258668 9
+88
+
+chain 5873 hg38.chr20:10004760-11615810 1611050 + 796556 796658 mm39.chr2:136351215-137822786 1471571 + 722616 722717 10
+31	1	0
+70
+
+chain 5421 hg38.chr20:10004760-11615810 1611050 + 890884 891032 mm39.chr2:136351215-137822786 1471571 - 646945 647095 11
+25	0	2
+123
+
+chain 4864 hg38.chr20:10004760-11615810 1611050 + 1425778 1425898 mm39.chr2:136351215-137822786 1471571 + 1342678 1342798 12
+120
+
+chain 4568 hg38.chr20:10004760-11615810 1611050 + 49202 49378 mm39.chr2:136351215-137822786 1471571 + 42266 42438 13
+99	4	0
+73
+
+chain 3681 hg38.chr20:10004760-11615810 1611050 + 640387 640507 mm39.chr2:136351215-137822786 1471571 + 579921 580041 14
+120
+
+chain 2152 hg38.chr20:10004760-11615810 1611050 + 148667 148736 mm39.chr2:136351215-137822786 1471571 + 158262 158331 15
+10	1	0
+38	0	1
+20
+
+chain 1838 hg38.chr20:10004760-11615810 1611050 + 469454 469477 mm39.chr2:136351215-137822786 1471571 + 409807 409830 16
+23
+
+chain 1399 hg38.chr20:10004760-11615810 1611050 + 796671 796752 mm39.chr2:136351215-137822786 1471571 + 722717 722799 17
+30	5	0
+8	3	0
+27	0	9
+8
+
+chain 1336 hg38.chr20:10004760-11615810 1611050 + 195854 195904 mm39.chr2:136351215-137822786 1471571 + 189780 189830 18
+50
+
+chain 1280 hg38.chr20:10004760-11615810 1611050 + 398052 398107 mm39.chr2:136351215-137822786 1471571 + 364812 364861 19
+11	1	0
+7	0	1
+15	6	0
+15
+
+chain 1248 hg38.chr20:10004760-11615810 1611050 + 195952 195990 mm39.chr2:136351215-137822786 1471571 + 189050 189087 20
+22	2	0
+5	0	1
+9
+
+chain 1208 hg38.chr20:10004760-11615810 1611050 + 1121156 1121254 mm39.chr2:136351215-137822786 1471571 + 1062631 1062720 21
+9	0	1
+12	7	0
+12	4	0
+13	0	1
+41
+
+chain 1201 hg38.chr20:10004760-11615810 1611050 + 580524 580629 mm39.chr2:136351215-137822786 1471571 + 516292 516362 22
+14	3	0
+16	19	0
+19	13	0
+21
+
+chain 1170 hg38.chr20:10004760-11615810 1611050 + 806859 806881 mm39.chr2:136351215-137822786 1471571 + 737566 737588 23
+22
+
+chain 1030 hg38.chr20:10004760-11615810 1611050 + 1532147 1532161 mm39.chr2:136351215-137822786 1471571 + 1423235 1423249 24
+14
+
+chain 1012 hg38.chr20:10004760-11615810 1611050 + 361832 361870 mm39.chr2:136351215-137822786 1471571 + 345076 345108 25
+20	6	0
+12
diff -r 000000000000 -r 3a213e01bc7f test-data/mm39.chr2.chunk.fasta.fai
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm39.chr2.chunk.fasta.fai	Fri Aug 30 17:53:50 2024 +0000
@@ -0,0 +1,1 @@
+mm39.chr2:136351215-137822786	1471571	31	1471571	1471572
diff -r 000000000000 -r 3a213e01bc7f test-data/query.1200.net
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/query.1200.net	Fri Aug 30 17:53:50 2024 +0000
@@ -0,0 +1,25 @@
+##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+##gapPenalties=axtChain O=400 E=30
+net mm39.chr2:136351215-137822786 1471571
+ fill 42266 172 hg38.chr20:10004760-11615810 + 49202 176 id 13 score 4568 ali 172
+ fill 87101 168 hg38.chr20:10004760-11615810 + 87669 167 id 7 score 6916 ali 167
+ fill 87751 136 hg38.chr20:10004760-11615810 + 84589 137 id 6 score 6961 ali 136
+ fill 158262 69 hg38.chr20:10004760-11615810 + 148667 69 id 15 score 2152 ali 68
+ fill 189050 37 hg38.chr20:10004760-11615810 + 195952 38 id 20 score 1248 ali 36
+ fill 189780 50 hg38.chr20:10004760-11615810 + 195854 50 id 18 score 1336 ali 50
+ fill 244295 318 hg38.chr20:10004760-11615810 - 266744 261 id 3 score 13332 ali 256
+  gap 244343 47 hg38.chr20:10004760-11615810 - 266919 70
+ fill 258580 88 hg38.chr20:10004760-11615810 + 288132 88 id 9 score 5958 ali 88
+ fill 260289 312 hg38.chr20:10004760-11615810 + 288278 276 id 4 score 9256 ali 268
+ fill 260754 161 hg38.chr20:10004760-11615810 + 288114 161 id 5 score 8091 ali 161
+ fill 364812 49 hg38.chr20:10004760-11615810 + 398052 55 id 19 score 1280 ali 48
+ fill 409807 23 hg38.chr20:10004760-11615810 + 469454 23 id 16 score 1838 ali 23
+ fill 516292 70 hg38.chr20:10004760-11615810 + 580524 105 id 22 score 1201 ali 70
+ fill 546215 130 hg38.chr20:10004760-11615810 + 600994 130 id 8 score 5978 ali 130
+ fill 579921 120 hg38.chr20:10004760-11615810 + 640387 120 id 14 score 3681 ali 120
+ fill 722616 101 hg38.chr20:10004760-11615810 + 796556 102 id 10 score 5873 ali 101
+ fill 722717 82 hg38.chr20:10004760-11615810 + 796671 81 id 17 score 1399 ali 73
+ fill 821044 1970 hg38.chr20:10004760-11615810 - 879848 2177 id 2 score 64329 ali 1889
+ fill 824476 150 hg38.chr20:10004760-11615810 - 890884 148 id 11 score 5421 ali 148
+ fill 1062631 89 hg38.chr20:10004760-11615810 + 1121156 98 id 21 score 1208 ali 87
+ fill 1342678 120 hg38.chr20:10004760-11615810 + 1425778 120 id 12 score 4864 ali 120
diff -r 000000000000 -r 3a213e01bc7f test-data/query.net
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/query.net	Fri Aug 30 17:53:50 2024 +0000
@@ -0,0 +1,18 @@
+##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+##gapPenalties=axtChain O=400 E=30
+net mm39.chr2:136351215-137822786 1471571
+ fill 42266 172 hg38.chr20:10004760-11615810 + 49202 176 id 13 score 4568 ali 172
+ fill 87101 168 hg38.chr20:10004760-11615810 + 87669 167 id 7 score 6916 ali 167
+ fill 87751 136 hg38.chr20:10004760-11615810 + 84589 137 id 6 score 6961 ali 136
+ fill 158262 69 hg38.chr20:10004760-11615810 + 148667 69 id 15 score 2152 ali 68
+ fill 244295 318 hg38.chr20:10004760-11615810 - 266744 261 id 3 score 13332 ali 256
+  gap 244343 47 hg38.chr20:10004760-11615810 - 266919 70
+ fill 258580 88 hg38.chr20:10004760-11615810 + 288132 88 id 9 score 5958 ali 88
+ fill 260289 312 hg38.chr20:10004760-11615810 + 288278 276 id 4 score 9256 ali 268
+ fill 260754 161 hg38.chr20:10004760-11615810 + 288114 161 id 5 score 8091 ali 161
+ fill 546215 130 hg38.chr20:10004760-11615810 + 600994 130 id 8 score 5978 ali 130
+ fill 579921 120 hg38.chr20:10004760-11615810 + 640387 120 id 14 score 3681 ali 120
+ fill 722616 101 hg38.chr20:10004760-11615810 + 796556 102 id 10 score 5873 ali 101
+ fill 821044 1970 hg38.chr20:10004760-11615810 - 879848 2177 id 2 score 64329 ali 1889
+ fill 824476 150 hg38.chr20:10004760-11615810 - 890884 148 id 11 score 5421 ali 148
+ fill 1342678 120 hg38.chr20:10004760-11615810 + 1425778 120 id 12 score 4864 ali 120
diff -r 000000000000 -r 3a213e01bc7f test-data/target.1200.net
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/target.1200.net	Fri Aug 30 17:53:50 2024 +0000
@@ -0,0 +1,25 @@
+##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+##gapPenalties=axtChain O=400 E=30
+net hg38.chr20:10004760-11615810 1611050
+ fill 49202 176 mm39.chr2:136351215-137822786 + 42266 172 id 13 score 4568 ali 172
+ fill 84589 137 mm39.chr2:136351215-137822786 + 87751 136 id 6 score 6961 ali 136
+ fill 87669 167 mm39.chr2:136351215-137822786 + 87101 168 id 7 score 6916 ali 167
+ fill 148667 69 mm39.chr2:136351215-137822786 + 158262 69 id 15 score 2152 ali 68
+ fill 195854 50 mm39.chr2:136351215-137822786 + 189780 50 id 18 score 1336 ali 50
+ fill 195952 38 mm39.chr2:136351215-137822786 + 189050 37 id 20 score 1248 ali 36
+ fill 266744 261 mm39.chr2:136351215-137822786 - 244295 318 id 3 score 13332 ali 256
+ fill 288114 161 mm39.chr2:136351215-137822786 + 260754 161 id 5 score 8091 ali 161
+ fill 288278 276 mm39.chr2:136351215-137822786 + 260289 312 id 4 score 9256 ali 268
+ fill 398052 55 mm39.chr2:136351215-137822786 + 364812 49 id 19 score 1280 ali 48
+ fill 469454 23 mm39.chr2:136351215-137822786 + 409807 23 id 16 score 1838 ali 23
+ fill 580524 105 mm39.chr2:136351215-137822786 + 516292 70 id 22 score 1201 ali 70
+ fill 600994 130 mm39.chr2:136351215-137822786 + 546215 130 id 8 score 5978 ali 130
+ fill 640387 120 mm39.chr2:136351215-137822786 + 579921 120 id 14 score 3681 ali 120
+ fill 796556 102 mm39.chr2:136351215-137822786 + 722616 101 id 10 score 5873 ali 101
+ fill 796671 81 mm39.chr2:136351215-137822786 + 722717 82 id 17 score 1399 ali 73
+ fill 879848 2177 mm39.chr2:136351215-137822786 - 821044 1970 id 2 score 64329 ali 1889
+  gap 880298 77 mm39.chr2:136351215-137822786 - 822602 0
+  gap 881628 27 mm39.chr2:136351215-137822786 - 821380 0
+ fill 890884 148 mm39.chr2:136351215-137822786 - 824476 150 id 11 score 5421 ali 148
+ fill 1121156 98 mm39.chr2:136351215-137822786 + 1062631 89 id 21 score 1208 ali 87
+ fill 1425778 120 mm39.chr2:136351215-137822786 + 1342678 120 id 12 score 4864 ali 120
diff -r 000000000000 -r 3a213e01bc7f test-data/target.net
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/target.net	Fri Aug 30 17:53:50 2024 +0000
@@ -0,0 +1,18 @@
+##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+##gapPenalties=axtChain O=400 E=30
+net hg38.chr20:10004760-11615810 1611050
+ fill 49202 176 mm39.chr2:136351215-137822786 + 42266 172 id 13 score 4568 ali 172
+ fill 84589 137 mm39.chr2:136351215-137822786 + 87751 136 id 6 score 6961 ali 136
+ fill 87669 167 mm39.chr2:136351215-137822786 + 87101 168 id 7 score 6916 ali 167
+ fill 148667 69 mm39.chr2:136351215-137822786 + 158262 69 id 15 score 2152 ali 68
+ fill 266744 261 mm39.chr2:136351215-137822786 - 244295 318 id 3 score 13332 ali 256
+ fill 288114 161 mm39.chr2:136351215-137822786 + 260754 161 id 5 score 8091 ali 161
+ fill 288278 276 mm39.chr2:136351215-137822786 + 260289 312 id 4 score 9256 ali 268
+ fill 600994 130 mm39.chr2:136351215-137822786 + 546215 130 id 8 score 5978 ali 130
+ fill 640387 120 mm39.chr2:136351215-137822786 + 579921 120 id 14 score 3681 ali 120
+ fill 796556 102 mm39.chr2:136351215-137822786 + 722616 101 id 10 score 5873 ali 101
+ fill 879848 2177 mm39.chr2:136351215-137822786 - 821044 1970 id 2 score 64329 ali 1889
+  gap 880298 77 mm39.chr2:136351215-137822786 - 822602 0
+  gap 881628 27 mm39.chr2:136351215-137822786 - 821380 0
+ fill 890884 148 mm39.chr2:136351215-137822786 - 824476 150 id 11 score 5421 ali 148
+ fill 1425778 120 mm39.chr2:136351215-137822786 + 1342678 120 id 12 score 4864 ali 120
diff -r 000000000000 -r 3a213e01bc7f tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Fri Aug 30 17:53:50 2024 +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.fai
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fai
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fai
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fai
\ No newline at end of file
diff -r 000000000000 -r 3a213e01bc7f tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Aug 30 17:53:50 2024 +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>
\ No newline at end of file
diff -r 000000000000 -r 3a213e01bc7f tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Aug 30 17:53:50 2024 +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="${__HERE__}/test-data/fasta_indexes.loc" />
+    </table>
+</tables>
\ No newline at end of file