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changeset 0:2defe48e4c7a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
author iuc
date Thu, 02 Aug 2018 09:57:30 -0400
parents
children 8cffbd184762
files jcvi_gff_stats.xml macros.xml test-data/all.pdf test-data/all_fasta.loc test-data/annot.gff3 test-data/genome.fasta test-data/summary.txt tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 10 files changed, 428 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jcvi_gff_stats.xml	Thu Aug 02 09:57:30 2018 -0400
@@ -0,0 +1,91 @@
+<?xml version="1.0"?>
+<tool id="jcvi_gff_stats" name="Genome annotation statistics" profile="16.04" version="@VERSION@">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command><![CDATA[
+
+        ln -s '${gff}' 'input.gff'
+
+        &&
+
+        python -m jcvi.annotation.stats genestats 'input.gff' > '${summary}'
+
+        &&
+
+        #if str($ref_genome.genome_type_select) == "indexed":
+            python -m jcvi.annotation.stats summary 'input.gff' '${ref_genome.genome.fields.path}' 2>&1 | tail -n +3 >> '${summary}'
+        #else
+            python -m jcvi.annotation.stats summary 'input.gff' '${ref_genome.genome}' 2>&1 | tail -n +3 >> '${summary}'
+        #end if
+
+        &&
+
+        python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '${summary}'
+
+        &&
+
+        python -m jcvi.annotation.stats histogram 'input.gff'
+
+        &&
+
+        pdfunite *.input.pdf '${graphs}'
+    ]]></command>
+    <inputs>
+        <param name="gff" type="data" format="gff" label="Annotation to analyse"/>
+        <conditional name="ref_genome">
+            <param label="Reference genome" name="genome_type_select" type="select">
+                <option selected="True" value="indexed">Use a built-in genome</option>
+                <option value="history">Use a genome from history</option>
+            </param>
+            <when value="indexed">
+                <param
+                  help="If your genome of interest is not listed, contact the Galaxy server administrators"
+                  label="Select a reference genome"
+                  name="genome"
+                  type="select"
+                  >
+                    <options from_data_table="all_fasta">
+                        <filter column="2" type="sort_by" />
+                        <validator message="No genomes are available" type="no_options" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                  <param name="genome" type="data" format="fasta" label="Corresponding genome sequence"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="summary" label="${tool.name} on ${on_string}: summary"/>
+        <data format="pdf" name="graphs" label="${tool.name} on ${on_string}: gene length"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="gff" value="annot.gff3"/>
+            <conditional name="ref_genome">
+                <param name="genome_type_select" value="history"/>
+                <param name="genome" value="genome.fasta"/>
+            </conditional>
+            <output name="summary" file="summary.txt"/>
+            <output name="graphs" file="all.pdf" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="gff" value="annot.gff3"/>
+            <conditional name="ref_genome">
+                <param name="genome_type_select" value="indexed"/>
+                <param name="genome" value="merlin"/>
+            </conditional>
+            <output name="summary" file="summary.txt"/>
+            <output name="graphs" file="all.pdf" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Based on JCVI Python utility libraries on genome assembly, annotation and comparative genomics.
+
+        .. _JCVI Python utilities: https://github.com/tanghaibao/jcvi
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Aug 02 09:57:30 2018 -0400
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">jcvi</requirement>
+            <requirement type="package" version="0.67.0">poppler</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <token name="@VERSION@">0.8.4</token>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.5281/zenodo.31631</citation>
+        </citations>
+    </xml>
+
+</macros>
Binary file test-data/all.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Thu Aug 02 09:57:30 2018 -0400
@@ -0,0 +1,19 @@
+#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.
+#
+merlin	merlin	Merlin	${__HERE__}/genome.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annot.gff3	Thu Aug 02 09:57:30 2018 -0400
@@ -0,0 +1,41 @@
+##gff-version 3
+HS08198	maker	gene	352	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0
+HS08198	maker	mRNA	352	1848	2869	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS08198-exonerate_est2genome-gene-0.0;Name=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=70|1|1|1|0|0|7|0|192
+HS08198	maker	exon	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	421	582	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	812	894	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1053	1123	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1208	1315	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:13;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1587	1688	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:14;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	exon	1772	1848	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:exon:15;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	five_prime_UTR	352	397	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	five_prime_UTR	421	444	.	+	.	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	445	582	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	812	894	.	+	0	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1053	1123	.	+	1	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1208	1315	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1587	1688	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+HS08198	maker	CDS	1772	1848	.	+	2	ID=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS08198-exonerate_est2genome-gene-0.0-mRNA-1
+###
+HS04636	maker	gene	1813	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0
+HS04636	maker	mRNA	1813	6903	8728	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0;Name=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1;_AED=0.00;_eAED=0.00;_QI=49|1|1|1|0|0|9|0|572
+HS04636	maker	exon	1813	1934	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:0;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	2055	2198	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:1;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	2852	2995	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:2;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	3426	3607	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:3;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	4340	4423	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:4;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	4543	4789	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:5;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	5072	5358	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:6;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	5860	6007	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:7;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	exon	6494	6903	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:exon:8;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	five_prime_UTR	1813	1861	.	+	.	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	1862	1934	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	2055	2198	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	2852	2995	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	3426	3607	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	4340	4423	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	4543	4789	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	5072	5358	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	5860	6007	.	+	0	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+HS04636	maker	CDS	6494	6903	.	+	2	ID=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1:cds;Parent=maker-HS04636-exonerate_est2genome-gene-0.0-mRNA-1
+###
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fasta	Thu Aug 02 09:57:30 2018 -0400
@@ -0,0 +1,200 @@
+>HS04636
+gagctcacattaactatttacagggtaactgcttaggaccagtattatgaggagaattta
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+aagcatgactgataaaatagctatcttttgatactgacaaggaagaaaacagaaatgaag
+gaatagcaaattttaaaaattgcattccagttgcttgaaagcttgtgatcagatgcaata
+aatgtttttattatttattttgtgcaaataggagagactattaagattgtgattgaagat
+tatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
+aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactgg
+catccccttctgcctgacacctttcaaattcatgaccagaaatacaactatcaacagttt
+atctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcacc
+aggcaaattgctggcagggtaagcattattattgaaaaccaaaacaaaagactagtcagt
+aactttagaatttctgccacggaaattatttttcttaaacttactaaaagagtagttagt
+tatattgctagtaaaattattttattgatataagaagcctaactttgtttgaaaagtcta
+aacttttagtctagtctacagttgtcagacaaatagcaaattgtacccctaccttaaaaa
+tattttcaaaaagtatctataatcttataggaataaatattttaggcttgaatactagtg
+ttatttttgaaatgtaaaaaggcaaattagttctaggctggtgtcccattgaattttaag
+cagagctcctgttgaaatgtaggtaagcatctttccagcaaataaaaattgtctccgctg
+ggagtttcagttttacctgatttgtacctaaggcaagctgaatacaaacagtaaatatgc
+ctaaaattcttgttttacaactaattttactttccacaggttgctggtggtaggaatgtt
+ccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaatac
+cagtcttttaatgagtaccgcaaacgctttatgctgaagccctatgaatcatttgaagaa
+cttacaggtaagaaacagtttctaaacttcttcgttttttgtttgtttgtttgtttttgt
+tgtttttggttttcttttcgagatggagccgccctctgtcacccaggctggagtgcagtg
+gcgccatctcggctcactgcaacctccgcctcctgggttcaagcaattctcctgcctcaa
+cttcctgagtagctgggactacaggctcacgtcgcacgcatggataattttttgtatttt
+cagtatagacggggtttcaccgtgttagccaggctggtctcaaactcctgacctagtgat
+ccgccggcttcggcctcccgaagtgctgggattacaggcgtgagccaccgcgcctggccc
+ctaaacttcttaaaagaatcaggggtcaaatggaaacagagaagttggcagcaaattgag
+caaaagaatcaaactgttttttattttgtgaagtttgacattggttgtatctctgtcttc
+atcgccttcacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacatc
+gatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatcttt
+ggtgaaaccatggtagaagttggagcaccattctccttgaaaggacttatgggtaatgtt
+atatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatc
+atcaacactgcctcaattcagtctctcatctgcaataacgtgaagggctgtccctttact
+tcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaagttcttcc
+cgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactg
+tagaagtctaatgatcatatttatttatttatatgaaccatgtctattaatttaattatt
+taataatatttatattaaactccttatgttacttaacatcttctgtaacagaagtcagta
+ctcctgttgcggagaaaggagtcatacttgtgaagacttttatgtcactactctaaagat
+tttgctgttgctgttaagtttggaaaacagtttttattctgttttataaaccagagagaa
+atgagttttgacgtctttttacttgaatttcaacttatattataagaacgaaagtaaaga
+tgtttgaatacttaaacactatcacaagatggcaaaatgctgaaagtttttacactgtcg
+atgtttccaatgcatcttccatgatgcattagaagtaactaatgtttgaaattttaaagt
+acttttggttatttttctgtcatcaaacaaaaacaggtatcagtgcattattaaatgaat
+atttaaattagacattaccagtaatttcatgtctactttttaaaatcagcaatgaaacaa
+taatttgaaatttctaaattcatagggtagaatcacctgtaaaagcttgtttgatttctt
+aaagttattaaacttgtacatataccaaaaagaagctgtcttggatttaaatctgtaaaa
+tcagatgaaattttactacaattgcttgttaaaatattttataagtgatgttcctttttc
+accaagagtataaacctttttagtgtgactgttaaaacttccttttaaatcaaaatgcca
+aatttattaaggtggtggagccactgcagtgttatctcaaaataagaatattttgttgag
+atattccagaatttgtttatatggctggtaacatgtaaaatctatatcagcaaaagggtc
+tacctttaaaataagcaataacaaagaagaaaaccaaattattgttcaaatttaggttta
+aacttttgaagcaaacttttttttatccttgtgcactgcaggcctggtactcagattttg
+ctatgaggttaatgaagtaccaagctgtgcttgaataacgatatgttttctcagattttc
+tgttgtacagtttaatttagcagtccatatcacattgcaaaagtagcaatgacctcataa
+aatacctcttcaaaatgcttaaattcatttcacacattaattttatctcagtcttgaagc
+caattcagtaggtgcattggaatcaagcctggctacctgcatgctgttccttttcttttc
+ttcttttagccattttgctaagagacacagtcttctcatcacttcgtttctcctattttg
+ttttactagttttaagatcagagttcactttctttggactctgcctatattttcttacct
+gaacttttgcaagttttcaggtaaacctcagctcaggactgctatttagctcctcttaag
+aagattaaaagagaaaaaaaaaggcccttttaaaaatagtatacacttattttaagtgaa
+aagcagagaattttatttatagctaattttagctatctgtaaccaagatggatgcaaaga
+ggctagtgcctcagagagaactgtacggggtttgtgactggaaaaagttacgttcccatt
+ctaattaatgccctttcttatttaaaaacaaaaccaaatgatatctaagtagttctcagc
+aataataataatgacgataatacttcttttccacatctcattgtcactgacatttaatgg
+tactgtatattacttaatttattgaagattattatttatgtcttattaggacactatggt
+tataaactgtgtttaagcctacaatcattgatttttttttgttatgtcacaatcagtata
+ttttctttggggttacctctctgaatattatgtaaacaatccaaagaaatgattgtatta
+agatttgtgaataaatttttagaaatctgattggcatattgagatatttaaggttgaatg
+tttgtccttaggataggcctatgtgctagcccacaaagaatattgtctcattagcctgaa
+tgtgccataagactgaccttttaaaatgttttgagggatctgtggatgcttcgttaattt
+gttcagccacaatttattgagaaaatattctgtgtcaagcactgtgggttttaatatttt
+taaatcaaacgctgattacagataatagtatttatataaataattgaaaaaaattttctt
+ttgggaagagggagaaaatgaaataaatatcattaaagataactcaggagaatcttcttt
+acaattttacgtttagaatgtttaaggttaagaaagaaatagtcaatatgcttgtataaa
+acactgttcactgttttttttaaaaaaaaaacttgatttgttattaacattgatctgctg
+acaaaacctgggaatttgggttgtgtatgcgaatgtttcagtgcctcagacaaatgtgta
+tttaacttatgtaaaagataagtctggaaataaatgtctgtttatttttgtactatttaa
+aaaaaaaaaaaaaaatcgatgtcgactcgagtc
+>HS08198
+agcgggcggcggtcgtgggcggggttgcaggcgaggctcaacgaacgctggtctgaccgt
+cggcgctccctgttgccgggccctgagcaagtggcttcatgaaccccgtgacgttggcca
+tggagataagaccactgggtgatggtttaaggaagataacgtgtaaagggctaaggactg
+tcggtggaaatcaggggtgcaggagaaatggataaacagccagaggtcaactcggacttt
+gtacataggacatggtgccaggccctgccaggaagtgcagatcgaagctaggctcacgag
+gaggctggaggtggggggtggggaggcaacggatggacatggacttcctgggctgggctc
+tgtgacagcagagtagactctgtcctgggacttggtggtgctacccttggcctcccacag
+tcctgccaccctgctgccgccaccatgctgccccctgggactgcgaccctcttgactctg
+ctcctggcagctggctcgctgggccagaagcctcagaggccacgccggcccgcatccccc
+atcagcaccatccagcccaaggccaattttgatgcgcagcaggtagaagttggggggggt
+agagggaggcaggtagaagttgtgggaggggtagagggagacaggtagaagttgttgcgg
+gggagagggaagcaggtgaagttgtggggggtgtagagggaagcaggtgaggggccctcc
+cacagtgccctcgagttctcccatggtctgcccccagtttgcagggacctggctccttgt
+ggctgtgggctccgcttgccgtttcctgcaggagcagggccaccgggccgaggccaccac
+actgcatgtggctccccagggcacagccatggctgtcagtaccttccgaaagctgtgagt
+cccagagcagccctgcaccctaaccccaaccctcctctcagcccccggacttcagccctg
+ctctggcccctgaccccaccccggctgtggcctggactaggattcctggttggggtctcc
+cagcctgtggtgcctcctccccgcccccccagggatgggatctgctggcaggtgcgccag
+ctctatggagacacaggggtcctcggccgcttcctgcttcaaggtgaggcaggggctgca
+ggtcatgtgggtgggggatgacgcagccactgtggctctctgacatggctactgtggctc
+tgcccagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccag
+agtttcgctgtcctgtacctggagcgggcggggcagctgtcagtgaagctctacggtatg
+tgggggccagcctctgtgaccaggcaggcgctcaagctctgcacactcactgggccaccc
+cgaggggctgggtgagccatggggacacacttcctttctcccatcctgatcctcctgcta
+agcaggggcccagggagtagtgacagacaggcctggtgtgggagcagggaggagggcccc
+gaggggcaggggacacacagaccccgttcccagagccctccacgccgcctggtgccagga
+ccccaggaaccctgtctgccctgcagcccgctcgctccctgtgagcgactcggtcctgag
+tgggtttgagcagcgggtccaggaggcccacctgactgaggaccagatcttctacttccc
+caagtacggtgagtgtccccagcaggtccccagctcagccacccccactctctggctgat
+gtccagcctgacccctgccttggcgccccaggcttctgcgaggctgcagaccagttccac
+gtcctggacggtgagtgcacagcgggggcaagcatggcggcgtggtgaggggggccactc
+gcaccggctgagtctcgtctctgctgcagaagtgaggaggtgaggccggcacacagctcc
+agtgctgagaagtcagtgccccgagagacgaccccaccagtggggtgcccgctgcctgtc
+ctccgtgaaaccagcctcagatcagggccctgccacccagggcaggggatcttctgccgg
+ctgccccagaggacagtgggtggagtggtacctacttattaaatgtctcagacccctctc
+tgactcttctgtccactctggaccggcgccagtaccaccaaggccctctctgcccccacc
+ccgcctctttaaaagcccggcgctccctgttggctggagtccacgcagggtcactgggcc
+gatttcggctcttgggatttgggaggggagatcctctctggcatatgccatcttgtgccc
+tgctggacctgggggcgtccacgtcactccaaggctgctcttgcctgggccatgcctgca
+gccc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summary.txt	Thu Aug 02 09:57:30 2018 -0400
@@ -0,0 +1,27 @@
+==================================================================
+                                                   o           all
+------------------------------------------------------------------
+                  Max number of transcripts per gene             1
+                                      Mean exon size         151.1
+           Mean gene locus size (first to last exon)        3294.0
+              Mean number of distinct exons per gene           8.0
+                 Mean number of transcripts per gene           1.0
+                     Mean transcript size (UTR, CDS)        1208.5
+                            Number of distinct exons            16
+                                     Number of genes             2
+Number of genes with alternative transcript variants      0 (0.0%)
+                          Number of multi-exon genes    2 (100.0%)
+                     Number of predicted transcripts             2
+                         Number of single-exon genes      0 (0.0%)
+------------------------------------------------------------------
+=====================================================================================================
+     o    % GC    % of genome    Average size (bp)    Median size (bp)    Number    Total length (Mb)
+-----------------------------------------------------------------------------------------------------
+  Exon     50%            20%                  151                 133        16                  0Mb
+  Gene     43%            56%                3,294               3,294         2                  0Mb
+Intron     39%            35%                  297                 250        14                  0Mb
+-----------------------------------------------------------------------------------------------------
+Exon_Length: Min=71 Max=410 N=15 Mean=153.2 SD=92.1160138087 Median=138.0 Sum=2298
+Intron_Length: Min=83 Max=732 N=13 Mean=319.076923077 SD=211.891649212 Median=271.0 Sum=4148
+Gene_Length: Min=579 Max=1719 N=2 Mean=1149.0 SD=570.0 Median=1149.0 Sum=2298
+Exon_Count: Min=6 Max=9 N=2 Mean=7.5 SD=1.5 Median=7.5 Sum=15
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Thu Aug 02 09:57:30 2018 -0400
@@ -0,0 +1,18 @@
+#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.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Aug 02 09:57:30 2018 -0400
@@ -0,0 +1,7 @@
+<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>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Thu Aug 02 09:57:30 2018 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+</tables>