# HG changeset patch
# User bgruening
# Date 1575412805 18000
# Node ID 62c9df8382c204088f52ab53b33a8edc18909ffd
# Parent  64be1ac2110916566c6755d1a1dc7f8eafdda4fb
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"

diff -r 64be1ac21109 -r 62c9df8382c2 diamond.xml
--- a/diamond.xml	Thu Sep 27 06:30:30 2018 -0400
+++ b/diamond.xml	Tue Dec 03 17:40:05 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="bg_diamond" name="Diamond" version="@VERSION@.0">
+<tool id="bg_diamond" name="Diamond" version="@VERSION@.0" profile="19.01">
     <description>alignment tool for short sequences against a protein database</description>
     <macros>
         <import>macros.xml</import>
@@ -64,7 +64,7 @@
         --subject-cover '$subject_cover'
         --block-size '$block_size'
         #if str($unal) == '1':
-            --unal 1 --un '$unalqueries' 
+            --unal 1 --un '$unalqueries'
         #end if
         $no_self_hits
         #if $tax_cond.tax_select == 'file':
@@ -103,7 +103,7 @@
                     <option value="26">Pachysolen tannophilus Nuclear Code</option>
                 </param>
                 <param argument="--min-orf" name="min_orf" type="integer" value="1" label="ignore translated sequences without an open reading frame of at least this length" help="By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature" />
-    
+
                 <param name="query_strand" argument="--strand" type="select" label="query strands to search" help="">
                     <option value="both" selected="True">Both</option>
                     <option value="plus">Plus</option>
@@ -165,7 +165,7 @@
         <param argument="--masking" type="boolean" truevalue="1" falsevalue="0" checked="true" label="enable masking of low complexity regions?" help="Masked residues appear in the output as X"/>
         <conditional name="tax_cond">
             <param name="tax_select" type="select" label="Restrict search taxonomically?" help="Any taxonomic rank can be used, and only reference sequences matching one of the specified taxon ids will be searched against">
-                <option value="no">No</option>
+                <option value="no" selected="True">No</option>
                 <option value="list">list of taxids entered manually</option>
                 <option value="file">list of taxids from single column tabular file</option>
             </param>
@@ -179,7 +179,7 @@
         </conditional>
         <conditional name="filter_score">
             <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)">
-                <option value="evalue">Maximum e-value to report alignments</option>
+                <option value="evalue" selected="True">Maximum e-value to report alignments</option>
                 <option value="min-score">Minimum bit score to report alignments</option>
             </param>
             <when value="evalue">
diff -r 64be1ac21109 -r 62c9df8382c2 diamond_makedb.xml
--- a/diamond_makedb.xml	Thu Sep 27 06:30:30 2018 -0400
+++ b/diamond_makedb.xml	Tue Dec 03 17:40:05 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="bg_diamond_makedb" name="Diamond makedb" version="@VERSION@">
+<tool id="bg_diamond_makedb" name="Diamond makedb" version="@VERSION@" profile="19.01">
     <description>Build database from a FASTA file</description>
     <macros>
         <import>macros.xml</import>
@@ -73,9 +73,9 @@
 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
 
 
-- taxonmap: Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. The file can be downloaded from NCBI: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz
+- taxonmap: Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. The file can be downloaded from NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz
 
-- taxonnodes: Path to the nodes.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
+- taxonnodes: Path to the nodes.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
 ]]>
     </help>
 
diff -r 64be1ac21109 -r 62c9df8382c2 diamond_view.xml
--- a/diamond_view.xml	Thu Sep 27 06:30:30 2018 -0400
+++ b/diamond_view.xml	Tue Dec 03 17:40:05 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="bg_diamond_view" name="Diamond" version="@VERSION@">
+<tool id="bg_diamond_view" name="Diamond" version="@VERSION@" profile="19.01">
     <description>generate formatted output from DAA files</description>
     <macros>
         <import>macros.xml</import>
@@ -7,7 +7,7 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-    ## need to link because diamont tries to open dataset_xxx.dat.daa 	
+    ## need to link because diamont tries to open dataset_xxx.dat.daa
     ln -s '$daa' input.daa &&
     diamond
         view
@@ -57,7 +57,7 @@
                 <param name="max_target_seqs" value="1" />
             </conditional>
             <param name="forwardonly" value="--forwardonly" />
-            <output name="blast_tabular" file="diamond_results.sam"/>
+            <output name="blast_tabular" file="diamond_results.sam" lines_diff="2"/>
         </test>
     </tests>
 
diff -r 64be1ac21109 -r 62c9df8382c2 macros.xml
--- a/macros.xml	Thu Sep 27 06:30:30 2018 -0400
+++ b/macros.xml	Tue Dec 03 17:40:05 2019 -0500
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">0.9.21</token>
+    <token name="@VERSION@">0.9.29</token>
 
     <xml name="requirements">
         <requirements>
@@ -9,12 +9,9 @@
 
     <xml name="stdio">
         <stdio>
-            <!-- disabled error detection by exit code to be able to detect oom errors by 
-                 regex, can be reenabled when https://github.com/galaxyproject/galaxy/pull/6338 is merged
             <exit_code range=":-1" level="fatal"  description="Error occurred. Please check Tool Standard Error" />
-            <exit_code range="1:" level="fatal"  description="Error occurred. Please check Tool Standard Error" />-->
+            <exit_code range="1:" level="fatal"  description="Error occurred. Please check Tool Standard Error" />
             <regex match="Failed to allocate sufficient memory." source="stderr" level="fatal_oom" />
-            <regex match=".+" source="stderr" level="fatal" description=""/>
         </stdio>
     </xml>
 
@@ -65,6 +62,11 @@
                     <option value="salltitles">All Subject Title(s)</option>
                     <option value="qcovhsp">Query Coverage Per HSP</option>
                     <option value="qtitle">Query title</option>
+                    <option value="full_qseq">Query sequence</option>
+                    <option value="full_sseq">Subject sequence</option>
+                    <option value="qqual">Query quality values for the aligned part of the query</option>
+                    <option value="full_qqual">Query quality values</option>
+                    <option value="qstrand">Query strand</option>
                 </param>
             </when>
             <when value="100">
diff -r 64be1ac21109 -r 62c9df8382c2 repository_dependencies.xml
--- a/repository_dependencies.xml	Thu Sep 27 06:30:30 2018 -0400
+++ b/repository_dependencies.xml	Tue Dec 03 17:40:05 2019 -0500
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <repositories description="This requires the Diamond data manager.">
-    <repository changeset_revision="ce62d0912b10" name="data_manager_diamond_database_builder" owner="bgruening" toolshed="https://toolshed.g2.bx.psu.edu" />
-</repositories>
+    <repository changeset_revision="5a0d0bee4f8d" name="data_manager_diamond_database_builder" owner="bgruening" toolshed="https://toolshed.g2.bx.psu.edu"/>
+</repositories>
\ No newline at end of file
diff -r 64be1ac21109 -r 62c9df8382c2 test-data/db-wtax.dmnd
Binary file test-data/db-wtax.dmnd has changed
diff -r 64be1ac21109 -r 62c9df8382c2 test-data/db.dmnd
Binary file test-data/db.dmnd has changed
diff -r 64be1ac21109 -r 62c9df8382c2 test-data/diamond_results.daa
Binary file test-data/diamond_results.daa has changed
diff -r 64be1ac21109 -r 62c9df8382c2 test-data/diamond_results.pairwise
--- a/test-data/diamond_results.pairwise	Thu Sep 27 06:30:30 2018 -0400
+++ b/test-data/diamond_results.pairwise	Tue Dec 03 17:40:05 2019 -0500
@@ -8,7 +8,7 @@
 >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
 Length=284
 
- Score = 541.2 bits (1393),  Expect = 2.0e-158
+ Score = 547.4 bits (1409),  Expect = 2.7e-160
  Identities = 283/284 (99%), Positives = 283/284 (99%), Gaps = 1/284 (0%)
  Frame = 1
 
@@ -20,9 +20,9 @@
             AIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL FTMVALAGVHLTFLHETGSNNPLGL
 Sbjct   61  AIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGL 120
 
-Query  358  TSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE 537
-            TSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE
-Sbjct  121  TSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE 180
+Query  358  TSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE 537
+            TSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE
+Sbjct  121  TSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPE 180
 
 Query  538  WYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMD 717
             WYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMD
diff -r 64be1ac21109 -r 62c9df8382c2 test-data/diamond_results.sam
--- a/test-data/diamond_results.sam	Thu Sep 27 06:30:30 2018 -0400
+++ b/test-data/diamond_results.sam	Tue Dec 03 17:40:05 2019 -0500
@@ -1,6 +1,6 @@
 @HD	VN:1.5	SO:query
-@PG	PN:DIAMOND
+@PG	PN:DIAMOND	VN:0.9.29	CL:diamond view --daa input.daa --outfmt 101 --out /tmp/tmpgnYFop/files/3/3/7/dataset_3370e74a-4639-49d2-b5de-fe40b7c3b66a.dat --top 0 --forwardonly --compress 0
 @mm	BlastP
 @CO	BlastP-like alignments
 @CO	Reporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length, ZF: frame, ZS: query start DNA coordinate
-sequence	0	gi|5524211|gb|AAD44166.1|	1	255	94M1D189M	*	0	0	LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY	*	AS:i:541	NM:i:1	ZL:i:284	ZR:i:1393	ZE:f:2.0e-158	ZI:i:99	ZF:i:1	ZS:i:1	MD:Z:94^P189
+sequence	0	gi|5524211|gb|AAD44166.1|	1	255	94M1D189M	*	0	0	LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY	*	AS:i:547	NM:i:1	ZL:i:284	ZR:i:1409	ZE:f:2.7e-160	ZI:i:99	ZF:i:1	ZS:i:1	MD:Z:94^P189
diff -r 64be1ac21109 -r 62c9df8382c2 test-data/diamond_results.tabular
--- a/test-data/diamond_results.tabular	Thu Sep 27 06:30:30 2018 -0400
+++ b/test-data/diamond_results.tabular	Tue Dec 03 17:40:05 2019 -0500
@@ -1,2 +1,2 @@
-sequence	gi|5524211|gb|AAD44166.1|	99.6	284	0	1	1	283	1	284	2.0e-158	541.2
-sequence	gi|5524212|gb|AAD44167.1|	74.6	284	71	1	1	283	1	284	1.3e-106	369.0
+sequence	gi|5524211|gb|AAD44166.1|	99.6	284	0	1	1	283	1	284	2.7e-160	547.4
+sequence	gi|5524212|gb|AAD44167.1|	79.2	284	58	1	1	283	1	284	1.1e-116	402.5
diff -r 64be1ac21109 -r 62c9df8382c2 test-data/diamond_results.wtax.tabular
--- a/test-data/diamond_results.wtax.tabular	Thu Sep 27 06:30:30 2018 -0400
+++ b/test-data/diamond_results.wtax.tabular	Tue Dec 03 17:40:05 2019 -0500
@@ -1,1 +1,1 @@
-sequence	gi|5524211|gb|AAD44166.1|	99.6	284	0	1	1	283	1	284	2.0e-158	541.2
+sequence	gi|5524211|gb|AAD44166.1|	99.6	284	0	1	1	283	1	284	2.7e-160	547.4
diff -r 64be1ac21109 -r 62c9df8382c2 test-data/diamond_results.xml
--- a/test-data/diamond_results.xml	Thu Sep 27 06:30:30 2018 -0400
+++ b/test-data/diamond_results.xml	Tue Dec 03 17:40:05 2019 -0500
@@ -2,9 +2,9 @@
 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
 <BlastOutput>
   <BlastOutput_program>blastp</BlastOutput_program>
-  <BlastOutput_version>diamond 0.9.21</BlastOutput_version>
+  <BlastOutput_version>diamond 0.9.29</BlastOutput_version>
   <BlastOutput_reference>Benjamin Buchfink, Xie Chao, and Daniel Huson (2015), &quot;Fast and sensitive protein alignment using DIAMOND&quot;, Nature Methods 12:59-60.</BlastOutput_reference>
-  <BlastOutput_db>.dmnd</BlastOutput_db>
+  <BlastOutput_db></BlastOutput_db>
   <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
   <BlastOutput_query-def>sequence</BlastOutput_query-def>
   <BlastOutput_query-len>283</BlastOutput_query-len>
@@ -33,9 +33,9 @@
   <Hit_hsps>
     <Hsp>
       <Hsp_num>1</Hsp_num>
-      <Hsp_bit-score>541.2</Hsp_bit-score>
-      <Hsp_score>1393</Hsp_score>
-      <Hsp_evalue>2.0e-158</Hsp_evalue>
+      <Hsp_bit-score>547.4</Hsp_bit-score>
+      <Hsp_score>1409</Hsp_score>
+      <Hsp_evalue>2.7e-160</Hsp_evalue>
       <Hsp_query-from>1</Hsp_query-from>
       <Hsp_query-to>284</Hsp_query-to>
       <Hsp_hit-from>1</Hsp_hit-from>
@@ -46,9 +46,9 @@
       <Hsp_positive>283</Hsp_positive>
       <Hsp_gaps>1</Hsp_gaps>
       <Hsp_align-len>284</Hsp_align-len>
-         <Hsp_qseq>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL-FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_qseq>
-         <Hsp_hseq>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_hseq>
-      <Hsp_midline>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_midline>
+         <Hsp_qseq>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL-FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_qseq>
+         <Hsp_hseq>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_hseq>
+      <Hsp_midline>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_midline>
     </Hsp>
   </Hit_hsps>
 </Hit>