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changeset 3:7c41dbaa9875 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
author devteam
date Mon, 21 Mar 2016 11:21:02 -0400
parents 642f30185af2
children 84d91cbf0c8d
files kraken.xml macros.xml test-data/kraken_test1.fa test-data/kraken_test1_output.tab test-data/test_database.loc test-data/test_db/database.idx test-data/test_db/database.kdb test-data/test_db/taxonomy/names.dmp test-data/test_db/taxonomy/nodes.dmp tool_data_table_conf.xml.test
diffstat 10 files changed, 193 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/kraken.xml	Wed Nov 11 12:50:49 2015 -0500
+++ b/kraken.xml	Mon Mar 21 11:21:02 2016 -0400
@@ -1,11 +1,14 @@
 <?xml version="1.0"?>
-<tool id="kraken" name="Kraken" version="1.1.2">
+<tool id="kraken" name="Kraken" version="1.2.0">
     <description>
         assign taxonomic labels to sequencing reads
     </description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
     <command>
         <![CDATA[
         @SET_DATABASE_PATH@ &&
@@ -47,7 +50,10 @@
         #if $split_reads:
             --classified-out "${classified_out}" --unclassified-out "${unclassified_out}"
         #end if
-        --output "${output}"
+
+        ## The --output option was changed to redirect as it does not work properly is some situations. For example, on test database the tool classifies 4 reads but does not write them into a file if --output is specified. It does however print correct output into STDOUT. This behavior can be re-created with test database provided in test-data/test_db/ folder. This is the reason for incrementing version number from 1.1.2 to 1.1.3
+
+        > "${output}"
         ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}"
         ]]>
     </command>
@@ -55,8 +61,8 @@
         <conditional name="single_paired">
             <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
                 <option value="collection">Collection</option>
-                <option value="yes">Yes</option>
-                <option selected="True" value="no">No</option>
+                <option value="yes">Paired</option>
+                <option selected="True" value="no">Single</option>
             </param>
             <when value="collection">
                 <param format="fasta,fastq" label="Collection of paired reads" name="input_pair" type="data_collection" collection_type="paired" help="FASTA or FASTQ datasets" />
@@ -101,6 +107,18 @@
         <data format="tabular" label="${tool.name} on ${on_string}: Classification" name="output" />
         <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
     </outputs>
+
+    <tests>
+        <test>
+            <param name="single_paired_selector" value="no"/>
+            <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
+            <param name="split_reads" value="false"/>
+            <param name="quick" value="no"/>
+            <param name="only-classified-output" value="false"/>
+            <param name="kraken_database" value="test_db"/>
+            <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
+        </test>
+    </tests>
     <help>
         <![CDATA[
 **What it does**
@@ -142,8 +160,5 @@
             e) the last 3 k-mers mapped to taxonomy ID #562
         ]]>
     </help>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
     <expand macro="citations" />
 </tool>
--- a/macros.xml	Wed Nov 11 12:50:49 2015 -0500
+++ b/macros.xml	Mon Mar 21 11:21:02 2016 -0400
@@ -2,7 +2,10 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.10.5">kraken</requirement>
+            <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement>
+        </requirements>
+        <requirements>
+            <requirement type="package" version="0.10.6-eaf8fb68">kraken</requirement>
         </requirements>
     </xml>
     <xml name="stdio">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken_test1.fa	Mon Mar 21 11:21:02 2016 -0400
@@ -0,0 +1,70 @@
+>gi|145231|gb|M33724.1|ECOALPHOA Escherichia coli K-12 truncated PhoA (phoA) gene, partial cds; and transposon Mu dI, partial sequence
+CAAAGCTCCGGGCCTCACCCAGGCGCTAAATACCAAAGATGGCGCAGTGATGGTGATGAGTTACGGGAAC
+TCCGAAGAGGATTCACAAGAACATACCGGCAGTCAGTTGCGTATTGCGGCGTATGGCCCGCATGCCGCCA
+ATGAAGCGGCGCACGAAAAACGCGAAAGCGT
+
+>gi|145232|gb|M33725.1|ECOALPHOB Escherichia coli K12 phoA pseudogene and transposon Mu dl-R, partial sequence
+CTGTCATAAAGTTGTCACGGCCGAGACTTATAGTCGCTTTGTTTTTATTTTTTAATGTATTTGTACATGG
+AGAAAATAAAGTGAAACAAAGCACTATTGCACTGGCACTCTTACCGTTACTGTTTACCCCTGTGACAAAA
+GCCCGGACACCAGTGAAGCGGCGCACGAAAAACGCGAAAGCGT
+
+>gi|145234|gb|M33727.1|ECOALPHOE Escherichia coli K12 upstream sequence of psiA5::Mu dI. is identical to psiA30 upstream sequence; putative (phoA) pseudogene and transposon Mu dl-R, partial sequence
+TTGTTTTTATTTTTTAATGTATTTGTACATGGAGAAAATAAAGTGAAACAAAGCACTATTGCACTGGTGA
+AGCGGCGCACGAAAAACGCGAAAGCGT
+
+>gi|146195|gb|J01619.1|ECOGLTA Eschericia coli gltA gene, sdhCDAB operon and sucABCD operons, complete sequence
+GAATTCGACCGCCATTGCGCAAGGCATCGCCATGACCAGGCAGGATACAAAAGAGAGTCGATAAATATTC
+ACGGTGTCCATACCTGATAAATATTTTATGAAAGGCGGCGATGATGCCGCAAAATAATACTTATTTATAA
+TCCAGCACGTAGGTTGCGTTAGCGGTTACTTCACCTGCCGTGACATCGACTGCATTATCAATTTGTTCCA
+TCCAGGCGAAAAAGTTCAGCGTCTGTTCTGATGAGCTTGCATCCAGGTCAAGATCTGGCGCGGCTGAACC
+TAATACGATGTTACCGTCATTTTTGTCCATCAGTCGTACACCGACCCCAGTTGCTTCGCCTGCACTGGTG
+TTGCTCAACAAAGGCGTAGCACCAGTTGTCTTAGCCGTGCTATCGAAGGTTACGCCAAACTTTGGATACC
+GGCATTCCGCTACCGTTGTCAGAAGCAGGCAGATCACAGTTGATCAAGCGAATGTCGACGGCCACTTTAT
+TGCTATGATGCTCCCGGTTTATATGGGTTGTCGTGACTTGTCCAAGATCTATGTTTTTATCAATATCTTC
+TGGATGAATTTCACAAGGTGCTTCAATAACCTCCCCCTTAAAGTGAATTTCGCCAGAACCTTCATCAGCA
+GCATAAACAGGTGCAGTGAACAGCAGAGATACGGCCAGTGCGGCCAATGTTTTTTGTCCTTTAAACATAA
+CAGAGTCCTTTAAGGATATAGAATAGGGGTATAGCTACGCCAGAATATCGTATTTGATTATTGCTAGTTT
+TTAGTTTTGCTTAAAAAATATTGTTAGTTTTATTAAATTGGAAAACTAAATTATTGGTATCATGAATTGT
+TGTATGATGATAAATATAGGGGGGATATGATAGACGTCATTTTCATAGGGTTATAAAATGCGACTACCAT
+GAAGTTTTTAATTCAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATA
+GGTCTGTTAATGGATTTTATTTTTACAAGTTTTTTGTGTTTAGGCATATAAAAATCAAGCCCGCCATATG
+AACGGCGGGTTAAAATATTTACAACTTAGCAATCGAACCATTAACGCTTGATATCGCTTTTAAAGTCGCG
+TTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAG
+TGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAATACCCATCG
+CTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTT
+CAGCGCGATGTTTTCCAGCTCCATAGCCACTTCCAGCAGGTCATCCTTCGTGCCCAGCTCTTTCAGCACT
+TCATGGCAGGTTTCACGCATTACGGTGGCGCGCGGGTCGTAATTTTTGTACACGCGGTGACCGAAGCCCA
+TCAGGCGGAAAGAATCATTTTTGTCTTTCGCACGACGAAAAAATTCCGGAATGTGTTTAACGGAGCTGAT
+TTCTTCCAGCATTTTCAGCGCCGCTTCGTTAGCACCGCCGTGCGCAGGTCCCCACAGTGAAGCAATACCT
+GCTGCGATACAGGCAAACGGGTTCGCACCCGAAGAGCCAGCGGTACGCACGGTGGAGGTAGAGGCGTTCT
+GTTCATGGTCAGCGTGCAGGATCAGAATACGGTCCATAGCACGTTCCAGAATCGGATTAACTTCATACGG
+TTCGCACGGCGTGGAGAACATCATATTCAGGAAGTTACCGGCGTAGGAGAGATCGTTGCGCGGGTAAACA
+AATGGCTGACCAATGGAATACTTGTAACACATCGCGGCCATGGTCGGCATTTTCGACAGCAGGCGGAACG
+CGGCAATTTCACGGTGACGAGGATTGTTAACATCCAGCGAGTCGTGATAGAACGCCGCCAGCGCGCCGGT
+AATACCACACATGACTGCCATTGGATGCGAGTCGCGACGGAAAGCATGGAACAGACGGGTAATCTGCTCG
+TGGATCATGGTATGACGGGTCACCGTAGTTTTAAATTCGTCATACTGTTCCTGAGTCGGTTTTTCACCAT
+TCAGCAGGATGTAACAAACTTCCAGGTAGTTAGAATCGGTCGCCAGCTGATCGATCGGGAAACCGCGGTG
+CAGCAAAATACCTTCATCACCATCAATAAAAGTAATTTTAGATTCGCAGGATGCGGTTGAAGTGAAGCCT
+GGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTT
+TCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGG
+TCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTAC
+CCGTTTTTTATTTGGCTCGCCGCTCTGTGAAAGAGGGGAAAACCTGGGTACAGAGCTCTGGGCGCTTGCA
+GGTAAAGGATCCATTGATGACGAATAAATGGCGAATCAAGTACTTAGCAATCCGAATTATTAAACTTGTC
+TACCACTAATAACTGTCCCGAATGAATTGGTCAATACTCCACACTGTTACATAAGTTAATCTTAGGTGAA
+ATACCGACTTCATAACTTTTACGCATTATATGCTTTTCCTGGTAATGTTTGTAACAACTTTGTTGAATGA
+TTGTCAAATTAGATGATTAAAAATTAAATAAATGTTGTTATCGTGACCTGGATCACTGTTCAGGATAAAA
+CCCGACAAACTATATGTAGGTTAATTGTAATGATTTTGTGAACAGCCTATACTGCCGCCAGTCTCCGGAA
+CACCCTGCAATCCCGAGCCACCCAGCGTTGTAACGTGTCGTTTTCGCATCTGGAAGCAGTGTTTTGCATG
+ACGCGCAGTTATAGAAAGGACGCTGTCTGACCCGCAAGCAGACCGGAGGAAGGAAATCCCGACGTCTCCA
+GGTAACAGAAAGTTAACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAGAACAGCATGTGGGCGTTATTC
+ATGATAAGAAATGTGAAAAAACAAAGACCTGTTAATCTGGACCTACAGACCATCCGGTTCCCCATCACGG
+CGATAGCGTCCATTCTCCATCGCGTTTCCGGTGTGATCACCTTTGTTGCAGTGGGCATCCTGCTGTGGCT
+TCTGGGTACCAGCCTCTCTTCCCCTGAAGGTTTCGAGCAAGCTTCCGCGATTATGGGCAGCTTCTTCGTC
+AAATTTATCATGTGGGGCATCCTTACCGCTCTGGCGTATCACGTCGTCGTAGGTATTCGCCACATGATGA
+TGGATTTTGGCTATCTGGAAGAAACATTCGAAGCGGGTAAACGCTCCGCCAAAATCTCCTTTGTTATTAC
+TGTCGTGCTTTCACTTCTCGCAGGAGTCCTCGTATGGTAAGCAACGCCTCCGCATTAGGACGCAATGGCG
+TACATGATTTCATCCTCGTTCGCGCTACCGCTATCGTCCTGACGCTCTACATCATTTATATGGTCGGTTT
+TTTCGCTACCAGTGGCGAGCTGACATATGAAGTCTGGATCGGTTTCTTCGCCTCTGCGTTCACCAAAGTG
+TTCACCCTGCTGGCGCTGTTTTCTATCTTGATCCATGCCTGGATCGGCATGTGGCAGGTGTTGACCGACT
+ACGTTAAACCGCTGGCTTTGCGCCTGATGCTGCAACTGGTGATTGTCGTTGCACTGGTGGTTTACGTGAT
+TTATGGATTCGTTGTGGTGTGGGGTGTGTGATGAAATTGCCAGTCAGAGAATTTGATGCAGTTGTGATTG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken_test1_output.tab	Mon Mar 21 11:21:02 2016 -0400
@@ -0,0 +1,4 @@
+C	gi|145231|gb|M33724.1|ECOALPHOA	83333	171	83333:162
+C	gi|145232|gb|M33725.1|ECOALPHOB	83333	183	83333:174
+C	gi|145234|gb|M33727.1|ECOALPHOE	83333	97	83333:88
+C	gi|146195|gb|J01619.1|ECOGLTA	83333	3850	83333:3841
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_database.loc	Mon Mar 21 11:21:02 2016 -0400
@@ -0,0 +1,1 @@
+test_db	test_db	${__HERE__}
\ No newline at end of file
Binary file test-data/test_db/database.idx has changed
Binary file test-data/test_db/database.kdb has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_db/taxonomy/names.dmp	Mon Mar 21 11:21:02 2016 -0400
@@ -0,0 +1,74 @@
+83333	|	Escherichia coli K-12	|		|	scientific name	|
+83333	|	Escherichia coli K12	|		|	equivalent name	|
+562	|	"Bacillus coli" Migula 1895	|		|	authority	|
+562	|	"Bacterium coli commune" Escherich 1885	|		|	authority	|
+562	|	"Bacterium coli" (Migula 1895) Lehmann and Neumann 1896	|		|	authority	|
+562	|	ATCC 11775	|		|	type material	|
+562	|	Bacillus coli	|		|	synonym	|
+562	|	Bacterium coli	|		|	synonym	|
+562	|	Bacterium coli commune	|		|	synonym	|
+562	|	CCUG 24	|		|	type material	|
+562	|	CCUG 29300	|		|	type material	|
+562	|	CIP 54.8	|		|	type material	|
+562	|	DSM 30083	|		|	type material	|
+562	|	Enterococcus coli	|		|	synonym	|
+562	|	Escherchia coli	|		|	misspelling	|
+562	|	Escherichia coli	|		|	scientific name	|
+562	|	Escherichia coli (Migula 1895) Castellani and Chalmers 1919	|		|	authority	|
+562	|	Escherichia sp. MAR	|		|	includes	|
+562	|	Escherichia/Shigella coli	|		|	equivalent name	|
+562	|	Eschericia coli	|		|	misspelling	|
+562	|	JCM 1649	|		|	type material	|
+562	|	LMG 2092	|		|	type material	|
+562	|	NBRC 102203	|		|	type material	|
+562	|	NCCB 54008	|		|	type material	|
+562	|	NCTC 9001	|		|	type material	|
+562	|	bacterium 10a	|		|	includes	|
+562	|	bacterium E3	|		|	includes	|
+561	|	Escherchia	|		|	misspelling	|
+561	|	Escherichia	|		|	scientific name	|
+561	|	Escherichia Castellani and Chalmers 1919	|		|	authority	|
+543	|	Enterobacteraceae	|		|	synonym	|
+543	|	Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev.	|		|	synonym	|
+543	|	Enterobacteriaceae	|		|	scientific name	|
+543	|	Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev.	|		|	synonym	|
+543	|	Enterobacteriaceae Rahn 1937	|		|	synonym	|
+543	|	gamma-3 proteobacteria	|	gamma-3 proteobacteria <#1>	|	in-part	|
+91347	|	'Enterobacteriales'	|		|	synonym	|
+91347	|	Enterobacteriaceae and related endosymbionts	|		|	synonym	|
+91347	|	Enterobacteriaceae group	|		|	synonym	|
+91347	|	Enterobacteriales	|		|	scientific name	|
+91347	|	enterobacteria	|	enterobacteria<blast91347>	|	blast name	|
+91347	|	gamma-3 proteobacteria	|	gamma-3 proteobacteria <#5>	|	in-part	|
+1236	|	Gammaproteobacteria	|		|	scientific name	|
+1236	|	Gammaproteobacteria Garrity et al. 2005	|		|	synonym	|
+1236	|	Proteobacteria gamma subdivision	|		|	synonym	|
+1236	|	Purple bacteria, gamma subdivision	|		|	synonym	|
+1236	|	g-proteobacteria	|	gamma proteos<blast1236>	|	blast name	|
+1236	|	gamma proteobacteria	|		|	synonym	|
+1236	|	gamma subdivision	|		|	synonym	|
+1236	|	gamma subgroup	|		|	synonym	|
+1224	|	Proteobacteria	|		|	scientific name	|
+1224	|	Proteobacteria Garrity et al. 2005	|		|	authority	|
+1224	|	Proteobacteria [class] Stackebrandt et al. 1988	|		|	authority	|
+1224	|	not Proteobacteria Cavalier-Smith 2002	|		|	authority	|
+1224	|	proteobacteria	|	proteobacteria<blast1224>	|	blast name	|
+1224	|	purple bacteria	|		|	common name	|
+1224	|	purple bacteria and relatives	|		|	common name	|
+1224	|	purple non-sulfur bacteria	|		|	common name	|
+1224	|	purple photosynthetic bacteria	|		|	common name	|
+1224	|	purple photosynthetic bacteria and relatives	|		|	common name	|
+2	|	Bacteria	|	Bacteria <prokaryote>	|	scientific name	|
+2	|	Monera	|	Monera <Bacteria>	|	in-part	|
+2	|	Procaryotae	|	Procaryotae <Bacteria>	|	in-part	|
+2	|	Prokaryota	|	Prokaryota <Bacteria>	|	in-part	|
+2	|	Prokaryotae	|	Prokaryotae <Bacteria>	|	in-part	|
+2	|	bacteria	|	bacteria <blast2>	|	blast name	|
+2	|	eubacteria	|		|	genbank common name	|
+2	|	not Bacteria Haeckel 1894	|		|	synonym	|
+2	|	prokaryote	|	prokaryote <Bacteria>	|	in-part	|
+2	|	prokaryotes	|	prokaryotes <Bacteria>	|	in-part	|
+1	|	all	|		|	synonym	|
+1	|	root	|		|	scientific name	|
+131567	|	biota	|		|	synonym	|
+131567	|	cellular organisms	|		|	scientific name	|
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_db/taxonomy/nodes.dmp	Mon Mar 21 11:21:02 2016 -0400
@@ -0,0 +1,10 @@
+83333	|	562	|	no rank	|		|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+562	|	561	|	species	|	EC	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+561	|	543	|	genus	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+543	|	91347	|	family	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+91347	|	1236	|	order	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+1236	|	1224	|	class	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+1224	|	2	|	phylum	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+2	|	131567	|	superkingdom	|		|	0	|	0	|	11	|	0	|	0	|	0	|	0	|	0	|		|
+131567	|	1	|	no rank	|		|	8	|	1	|	1	|	1	|	0	|	1	|	1	|	0	|		|
+1	|	1	|	no rank	|		|	8	|	0	|	1	|	0	|	0	|	0	|	0	|	0	|		|
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Mon Mar 21 11:21:02 2016 -0400
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of Kraken database in the required format -->
+    <table name="kraken_databases" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/test_database.loc" />
+    </table>
+</tables>