Mercurial > repos > iuc > length_and_gc_content

changeset 1:f088370d2a3c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 0a56599c36b4968095ec5a3cb589f94fb139466c
author iuc
date Sun, 28 Jan 2018 04:04:58 -0500
parents 2ca1baabdae0
children e3ba567abdf5
files all_fasta.loc.sample get_length_and_gc_content.r get_length_and_gc_content.xml test-data/cached_locally/all_fasta.loc test-data/cached_locally/gene_sets.loc test-data/cached_locally/ref.fasta test-data/cached_locally/ref.gtf test-data/gene_length.tab tool-data/all_fasta.loc.sample tool-data/gene_sets.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 12 files changed, 199 insertions(+), 1012 deletions(-) [+]
line wrap: on
line diff
--- a/all_fasta.loc.sample	Thu Nov 17 16:41:06 2016 -0500
+++ /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.
-#
--- a/get_length_and_gc_content.r	Thu Nov 17 16:41:06 2016 -0500
+++ b/get_length_and_gc_content.r	Sun Jan 28 04:04:58 2018 -0500
@@ -15,9 +15,9 @@
 
 option_list <- list(
     make_option(c("-g","--gtf"), type="character", help="Input GTF file with gene / exon information."),
-    make_option(c("-f","--fasta"), type="character", default=FALSE, help="Fasta file that corresponds to the supplied GTF."),
-    make_option(c("-l","--length"), type="character", default=FALSE, help="Output file with gene name and length."),
-    make_option(c("-gc","--gc_content"), type="character", default=FALSE, help="Output file with gene name and GC content.")
+    make_option(c("-f","--fasta"), type="character", default=FALSE, help="FASTA file that corresponds to the supplied GTF."),
+    make_option(c("-l","--length"), type="character", default=FALSE, help="Output file with Gene ID and length."),
+    make_option(c("-gc","--gc_content"), type="character", default=FALSE, help="Output file with Gene ID and GC content.")
   )
 
 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
--- a/get_length_and_gc_content.xml	Thu Nov 17 16:41:06 2016 -0500
+++ b/get_length_and_gc_content.xml	Sun Jan 28 04:04:58 2018 -0500
@@ -1,10 +1,10 @@
-<tool id="length_and_gc_content" name="Gene length and gc content" version="0.1.0">
-    <description>from GTF file</description>
+<tool id="length_and_gc_content" name="Gene length and GC content" version="0.1.1">
+    <description>from GTF and FASTA file</description>
     <requirements>
         <requirement type="package" version="1.3.2">r-optparse</requirement>
-        <requirement type="package" version="1.4.1">r-reshape2</requirement>
-        <requirement type="package" version="1.9.6">r-data.table</requirement>
-        <requirement type="package" version="1.34.1">bioconductor-rtracklayer</requirement>
+        <requirement type="package" version="1.4.2">r-reshape2</requirement>
+        <requirement type="package" version="1.10.4">r-data.table</requirement>
+        <requirement type="package" version="1.34.2">bioconductor-rtracklayer</requirement>
     </requirements>
     <stdio>
         <regex match="Execution halted"
@@ -20,70 +20,165 @@
                level="fatal"
                description="An undefined error occured, please check your input carefully and contact your administrator." />
     </stdio>
+    <version_command><![CDATA[
+        echo $(R --version | grep version | grep -v GNU)", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", reshape2 version" $(R --vanilla --slave -e "library(reshape2); cat(sessionInfo()\$otherPkgs\$reshape2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rtracklayer version" $(R --vanilla --slave -e "library(rtracklayer); cat(sessionInfo()\$otherPkgs\$rtracklayer\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", data.table version" $(R --vanilla --slave -e "library(data.table); cat(sessionInfo()\$otherPkgs\$data.table\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+    ]]></version_command>
     <command><![CDATA[
-        Rscript '$__tool_directory__'/get_length_and_gc_content.r --gtf '$gtf'
-        #if $fastaSource.genomeSource == 'indexed':
-            --fasta '$fastaSource.fasta_pre_installed.fields.path'
-        #else:
-            --fasta '$fastaSource.fasta_history'
-        #end if
-        --length '$length'
-        --gc_content '$gc_content'
+
+## Get GTF
+
+#if $gtf_file.gtfSource == 'cached':
+    ln -s '$gtf_file.gtf_pre_installed.fields.path' gtf
+#else:
+    ln -s '$gtf_file.gtf_history' gtf
+#end if
+
+&&
+
+## Get FASTA
+
+#if $fasta_file.fastaSource == 'indexed':
+    ln -s '$fasta_file.fasta_pre_installed.fields.path' fasta
+#else:
+    ln -s '$fasta_file.fasta_history' fasta
+#end if
+
+&&
+
+Rscript '$__tool_directory__/get_length_and_gc_content.r'
+
+--gtf gtf
+--fasta fasta
+
+#if $length_out:
+    --length '$length'
+#end if
+
+#if $gc_out:
+    --gc_content '$gc_content'
+#end if
+
     ]]></command>
+
     <inputs>
-        <param name="gtf" type="data" format="gtf" help="The GTF must match the FASTA file" label="GTF file for length and GC calculation"/>
-        <conditional name="fastaSource">
-            <param help="choose history if you don't see the correct genome fasta" label="Select a reference fasta from your history or use a built-in fasta?" name="genomeSource" type="select">
-                <option value="indexed">Use a built-in fasta</option>
-                <option value="history">Use fasta from history</option>
+        <conditional name="gtf_file">
+            <param name="gtfSource" type="select" label="Select a built-in GTF file or one from your history"  help="Choose history if you don't see the correct GTF" >
+                <option value="cached" selected="true">Use a built-in GTF</option>
+                <option value="history">Use a GTF from history</option>
+            </param>
+            <when value="cached">
+                <param name="gtf_pre_installed" type="select" label="Select a GTF file" help="Select the GTF from a list of pre-installed files">
+                    <options from_data_table="gene_sets">
+                        <filter type="sort_by" column="1" />
+                    </options>
+                    <validator type="no_options" message="No annotations are available."/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="gtf_history" type="data" format="gtf" label="Select a GTF file" help="Make sure that the GTF corresponds to the same genome as the FASTA"/>
+            </when>
+        </conditional>
+
+        <conditional name="fasta_file">
+            <param name="fastaSource" type="select" label="Select a built-in FASTA or one from your history" help="Choose history if you don't see the correct FASTA. The FASTA must be the same genome version as the GTF.">
+                <option value="indexed" selected="true">Use a built-in FASTA </option>
+                <option value="history">Use a FASTA from history</option>
             </param>
             <when value="indexed">
-                <param name="fasta_pre_installed" type="select" help="Select the fasta file from a list of pre-installed genomes" label="Select a fasta sequence">
+                <param name="fasta_pre_installed" type="select" help="Select the FASTA file from a list of pre-installed genomes" label="Select a FASTA file">
                     <options from_data_table="all_fasta">
-                        <filter type="data_meta" key="dbkey" ref="gtf" column="0"/>
+                        <filter type="sort_by" column="2" />
                     </options>
                     <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                 </param>
             </when>
-        <when value="history">
-            <param name="fasta_history" type="data" format="fasta" label="Select a fasta file that matches the supplied GTF file">
-                <options>
-                    <filter type="data_meta" key="dbkey" ref="gtf"/>
-                </options>
-                <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
-            </param>
-        </when>
+            <when value="history">
+                <param name="fasta_history" type="data" format="fasta" label="Select a FASTA file that matches the supplied GTF file" />
+            </when>
         </conditional>
+
+
+        <param name="length_out" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Output length file?" help="Default: Yes" />
+        <param name="gc_out" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Output GC content file?" help="Default: Yes" />
+
     </inputs>
+
     <outputs>
-        <data name="length" format="tabular" label="gene length">
+        <data name="length" format="tabular" label="Gene length">
+            <filter>length_out is True</filter>
             <actions>
-                <action name="column_names" type="metadata" default="gene,length" />
+                <action name="column_names" type="metadata" default="GeneID,Length" />
             </actions>
         </data>
-        <data name="gc_content" format="tabular" label="gene gc content">
+        <data name="gc_content" format="tabular" label="Gene GC content">
+            <filter>gc_out is True</filter>
              <actions>
-                <action name="column_names" type="metadata" default="gene,gc_content" />
+                <action name="column_names" type="metadata" default="GeneID,GC_content" />
             </actions>
         </data>
     </outputs>
+
     <tests>
-        <test>
-            <param name="gtf" value="in.gtf" ftype="gtf"></param>
-            <param name="fastaSource|genomeSource" value="history"></param>
-            <param name="fastaSource|fasta_history" value="in.fasta" ftype="fasta"></param>
-            <output name="length" file="length.tab"></output>
-            <output name="gc_content" file="gc.tab"></output>
+        <!-- Ensure length and GC files are output -->
+        <test expect_num_outputs="2">
+            <param name="gtfSource" value="history" />
+            <param name="gtf_history" ftype="gtf" value="in.gtf" />
+            <param name="fastaSource" value="history" />
+            <param name="fasta_history" ftype="fasta" value="in.fasta" />
+            <output name="length" file="length.tab" />
+            <output name="gc_content" file="gc.tab" />
+        </test>
+        <!-- Ensure built-in fasta and gtf work -->
+        <test expect_num_outputs="2">
+            <param name="gtfSource" value="cached" />
+            <param name="fastaSource" value="indexed" />
+            <output name="length" file="length.tab" />
+            <output name="gc_content" file="gc.tab" />
+        </test>
+        <!-- Ensure optional gc content works  -->
+        <test expect_num_outputs="1">
+            <param name="gtfSource" value="cached" />
+            <param name="fastaSource" value="indexed" />
+            <param name="gc_out" value="False" />
+            <output name="length" file="length.tab" />
+        </test>
+        <!-- Ensure optional length works -->
+        <test expect_num_outputs="1">
+            <param name="gtfSource" value="cached" />
+            <param name="fastaSource" value="indexed" />
+            <param name="length_out" value="False" />
+            <output name="gc_content" file="gc.tab" />
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
+
+**What it does**
+
+.. class:: infomark
 
-        **What it does**
+This tool calculates the length and GC content for the genes in a GTF file. It requires a FASTA file that is the same genome version as the GTF.
+
+-----
+
+**Inputs**
+
+- a GTF file
+- a FASTA file
 
-        Returns a tabular file with gene id and length and a tabular file with gene id and GC content, based on a supplied GTF and a FASTA file.
+-----
+
+**Outputs**
+
+- a tabular file with Gene ID and length
+- a tabular file with Gene ID and GC content
 
+-----
 
-        </help>
+**More Information**
+
+To calculate gene length, this tool counts the number of bases in all exons of a gene, after merging any overlapping exons from different transcripts.
+
+    ]]></help>
     <citations>
     </citations>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/all_fasta.loc	Sun Jan 28 04:04:58 2018 -0500
@@ -0,0 +1,1 @@
+hg38	hg38	Human (hg38)	${__HERE__}/ref.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/gene_sets.loc	Sun Jan 28 04:04:58 2018 -0500
@@ -0,0 +1,1 @@
+hg38	hg38	hg38GTF	${__HERE__}/ref.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/ref.fasta	Sun Jan 28 04:04:58 2018 -0500
@@ -0,0 +1,2 @@
+>1
+AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAAAAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAATTTTT
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/ref.gtf	Sun Jan 28 04:04:58 2018 -0500
@@ -0,0 +1,6 @@
+1	ensembl_havana	gene	1	103	.	+	.	gene_id "ENSG00000162526"; gene_version "4"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1";
+1	ensembl_havana	transcript	1	103	.	+	.	gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	exon	1	103	.	+	.	gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; exon_id "ENSE00002319515"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	CDS	1	100	.	+	0	gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; protein_id "ENSP00000334393"; protein_version "3"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	start_codon	1	3	.	+	0	gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	stop_codon	101	103	.	+	0	gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA";
--- a/test-data/gene_length.tab	Thu Nov 17 16:41:06 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,948 +0,0 @@
-ENSG00000003096	6983
-ENSG00000004534	7302
-ENSG00000006327	1848
-ENSG00000006831	5878
-ENSG00000006837	3057
-ENSG00000007392	6176
-ENSG00000008735	5901
-ENSG00000009844	7262
-ENSG00000010322	9161
-ENSG00000010932	3602
-ENSG00000011638	2558
-ENSG00000012983	7620
-ENSG00000013275	2387
-ENSG00000014216	7553
-ENSG00000018408	8413
-ENSG00000018607	1774
-ENSG00000018699	3185
-ENSG00000022556	6313
-ENSG00000023041	3748
-ENSG00000023330	2536
-ENSG00000023697	2844
-ENSG00000023892	2545
-ENSG00000027697	2571
-ENSG00000029363	9297
-ENSG00000032389	5775
-ENSG00000033050	4448
-ENSG00000035403	9992
-ENSG00000042445	4005
-ENSG00000049541	2211
-ENSG00000057608	4033
-ENSG00000057935	10580
-ENSG00000059122	8419
-ENSG00000059588	7743
-ENSG00000063015	5115
-ENSG00000063322	3835
-ENSG00000064545	3281
-ENSG00000065000	8601
-ENSG00000065060	9908
-ENSG00000066739	14778
-ENSG00000066923	8583
-ENSG00000068028	3683
-ENSG00000068650	13733
-ENSG00000069712	4556
-ENSG00000070495	5969
-ENSG00000070610	4803
-ENSG00000070961	9493
-ENSG00000071889	5098
-ENSG00000072071	8487
-ENSG00000072121	15706
-ENSG00000072134	8517
-ENSG00000072864	5525
-ENSG00000072958	14371
-ENSG00000073614	12106
-ENSG00000074054	11052
-ENSG00000074071	1097
-ENSG00000074211	9198
-ENSG00000074319	3839
-ENSG00000074621	9084
-ENSG00000075399	3428
-ENSG00000076356	13781
-ENSG00000079215	6265
-ENSG00000079246	5463
-ENSG00000079785	3833
-ENSG00000079974	5870
-ENSG00000080603	13674
-ENSG00000080815	9947
-ENSG00000081087	5325
-ENSG00000082068	7039
-ENSG00000083535	4253
-ENSG00000083544	6814
-ENSG00000083720	4194
-ENSG00000084073	3572
-ENSG00000085365	5106
-ENSG00000085377	3762
-ENSG00000085982	9352
-ENSG00000085999	3212
-ENSG00000086205	3824
-ENSG00000086289	2864
-ENSG00000087586	2928
-ENSG00000088340	9067
-ENSG00000088448	4563
-ENSG00000089009	4447
-ENSG00000090020	5974
-ENSG00000090273	2856
-ENSG00000090402	6138
-ENSG00000091140	5299
-ENSG00000092068	5991
-ENSG00000092098	4982
-ENSG00000092208	2532
-ENSG00000092445	10945
-ENSG00000099139	12705
-ENSG00000099910	4646
-ENSG00000100014	7324
-ENSG00000100027	4713
-ENSG00000100038	6641
-ENSG00000100106	12238
-ENSG00000100191	2030
-ENSG00000100292	2405
-ENSG00000100336	4377
-ENSG00000100354	19998
-ENSG00000100441	8015
-ENSG00000100478	7223
-ENSG00000100526	1836
-ENSG00000100577	8477
-ENSG00000100852	10888
-ENSG00000101247	7217
-ENSG00000101294	10000
-ENSG00000101473	4213
-ENSG00000102030	4742
-ENSG00000102349	9022
-ENSG00000102606	11768
-ENSG00000102804	8586
-ENSG00000102901	5539
-ENSG00000103035	2740
-ENSG00000103121	12781
-ENSG00000103932	7046
-ENSG00000104325	3507
-ENSG00000104331	7594
-ENSG00000104368	6618
-ENSG00000104450	5055
-ENSG00000105173	2550
-ENSG00000105220	9112
-ENSG00000105223	5184
-ENSG00000105325	5802
-ENSG00000105355	2813
-ENSG00000105438	2251
-ENSG00000105519	4428
-ENSG00000105568	7437
-ENSG00000105879	5481
-ENSG00000106012	9240
-ENSG00000106305	1838
-ENSG00000106683	6902
-ENSG00000106771	9484
-ENSG00000106789	5717
-ENSG00000106803	1190
-ENSG00000106868	4183
-ENSG00000106948	10601
-ENSG00000107295	2682
-ENSG00000107833	928
-ENSG00000108055	4275
-ENSG00000108091	7345
-ENSG00000108306	11038
-ENSG00000108591	7411
-ENSG00000108666	5740
-ENSG00000108848	8151
-ENSG00000108947	3222
-ENSG00000108953	3847
-ENSG00000108960	3177
-ENSG00000109079	3889
-ENSG00000109171	6524
-ENSG00000109610	2128
-ENSG00000109680	3434
-ENSG00000109771	7360
-ENSG00000109787	6297
-ENSG00000109920	7596
-ENSG00000109929	5566
-ENSG00000110002	6403
-ENSG00000110092	4830
-ENSG00000110906	9865
-ENSG00000111247	2558
-ENSG00000111249	7648
-ENSG00000111331	8251
-ENSG00000111652	3113
-ENSG00000111707	5731
-ENSG00000111860	9462
-ENSG00000111877	12496
-ENSG00000112062	6860
-ENSG00000112306	767
-ENSG00000112312	2476
-ENSG00000112365	5519
-ENSG00000112406	5614
-ENSG00000112531	17368
-ENSG00000112874	4304
-ENSG00000113048	6511
-ENSG00000113328	3096
-ENSG00000113621	5265
-ENSG00000113649	8714
-ENSG00000113812	4066
-ENSG00000113916	5938
-ENSG00000114026	8733
-ENSG00000114120	9277
-ENSG00000114315	2062
-ENSG00000114416	12054
-ENSG00000114735	19425
-ENSG00000114999	15732
-ENSG00000115107	4562
-ENSG00000115221	6357
-ENSG00000115464	18125
-ENSG00000115841	5999
-ENSG00000116127	14054
-ENSG00000116171	8305
-ENSG00000116209	9149
-ENSG00000116455	2805
-ENSG00000116580	11967
-ENSG00000116604	6400
-ENSG00000116685	3281
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-ENSG00000239926	747
-ENSG00000240005	589
-ENSG00000240392	575
-ENSG00000240418	893
-ENSG00000240540	1183
-ENSG00000240821	579
-ENSG00000241258	3540
-ENSG00000241370	1606
-ENSG00000241494	438
-ENSG00000241680	375
-ENSG00000241697	2611
-ENSG00000241772	1051
-ENSG00000241923	622
-ENSG00000242061	438
-ENSG00000242140	231
-ENSG00000242349	1427
-ENSG00000242600	2616
-ENSG00000242612	4046
-ENSG00000242858	602
-ENSG00000243122	413
-ENSG00000243396	402
-ENSG00000243701	4206
-ENSG00000243779	321
-ENSG00000244171	1291
-ENSG00000244270	403
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Sun Jan 28 04:04:58 2018 -0500
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the genome and transcriptome fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build. 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:
+#
+#apiMel4.5	apiMel4.5	Honeybee (Apis mellifera): apiMel4.5	/path/to/genome/apiMel4.5/apiMel4.5.fa
+#hg38canon	hg38	Human (Homo sapiens): hg38 Canonical	/path/to/genome/hg38/hg38canon.fa
+#hg38full	hg38	Human (Homo sapiens): hg38 Full	/path/to/genome/hg38/hg38full.fa
+#hg38full.90	hg38    Human (Homo sapiens): hg38 Full Trans v90	/path/to/genome/hg38/hg38fulltrans.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 hg38 above.
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gene_sets.loc.sample	Sun Jan 28 04:04:58 2018 -0500
@@ -0,0 +1,15 @@
+# This is a sample file distributed with featureCounts that enables it and other# tools to use gene/exon annotations in the GFF/GTF format.
+# 
+# The gene_sets.loc file syntax is:
+#<unique_build_id>	<dbkey>	<display_name>	<path>
+# 
+# Please ensure that the above fields are tab separated.
+# 
+# In case you have TWO or MORE providers PER dbkey, the one mentioned
+# first in the file, should have the "default" priority.
+#
+#Example:
+#
+#Homo_sapiens.GRCh38.90	hg38	GRCh38 (hg38) annotation from Ensembl, release 90	/depot/data2/galaxy/hg38/gene_sets/Homo_sapiens.GRCh38.90.gtf
+#Homo_sapiens.GRCh37.87	hg19	GRCh37 (hg19) annotation from Ensembl, release 87	/depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.87.gtf
+
--- a/tool_data_table_conf.xml.sample	Thu Nov 17 16:41:06 2016 -0500
+++ b/tool_data_table_conf.xml.sample	Sun Jan 28 04:04:58 2018 -0500
@@ -1,7 +1,12 @@
 <tables>
     <!-- Locations of all fasta files under genome directory -->
-    <table name="all_fasta" comment_char="#">
+    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/all_fasta.loc" />
     </table>
+    <!-- Locations of all gtf files with annotations of genome builds -->
+    <table name="gene_sets" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/gene_sets.loc" />
+    </table>	
 </tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Sun Jan 28 04:04:58 2018 -0500
@@ -0,0 +1,10 @@
+<tables>
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/cached_locally/all_fasta.loc" />
+    </table>
+    <table name="gene_sets" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/cached_locally/gene_sets.loc" />
+    </table>
+</tables>
\ No newline at end of file