# HG changeset patch
# User iuc
# Date 1636742363 0
# Node ID d505990b8c893e9484863557c361be36c999ee1c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt commit 04aaa266f5b2e557f42c7feca4e081c7e9c1dae6"
diff -r 000000000000 -r d505990b8c89 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Nov 12 18:39:23 2021 +0000
@@ -0,0 +1,29 @@
+
+ 0.5.3
+ 0
+ 20.09
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+ malt
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+ https://doi.org/10.1101/050559
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diff -r 000000000000 -r d505990b8c89 malt_run.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/malt_run.xml Fri Nov 12 18:39:23 2021 +0000
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+
+
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+ macros.xml
+
+
+ '$alignments_output'
+ #end if
+ #if $additional_outputs_cond.output_aligned:
+ ## malt-run always compresses these outputs.
+ && gunzip -c 'aligned_output.${aligned_ext}' > '$aligned_output'
+ #end if
+ #if $additional_outputs_cond.output_unaligned:
+ ## malt-run always compresses these outputs.
+ && gunzip -c 'unaligned_output.fna.gz' > '$unaligned_output'
+ #end if
+#end if
+]]>
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+ additional_outputs_cond['additional_outputs'] == 'yes' and additional_outputs_cond['output_alignments_cond']['output_alignments']
+
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+ additional_outputs_cond['additional_outputs'] == 'yes' and additional_outputs_cond['output_aligned']
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+ additional_outputs_cond['additional_outputs'] == 'yes' and additional_outputs_cond['output_unaligned']
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+**What it does**
+
+Align one or more files of input sequences (DNA or proteins) against an index representing a collection of reference DNA
+or protein sequences. Depending on the type of input and reference sequences, the program can be be run in BLASTN, BLASTP
+or BLASTX mode.
+
+**Options**
+
+ **Input file** - specify all input files which must be in FastA or FastQ format and may be gzipped.
+ **Referencegenome ** - select the index built by the **MALT index builder** tool.
+ **Alignment mode** - run the program in BlastN mode, BlastP mode or BlastX mode. that is, to align DNA and DNA, protein and protein, or DNA reads against protein references, respectively. BlastN mode can only be used if the employed index contains DNA sequences, whereas the BlastP and BlastX modes are only applicable to an index based on protein reference sequences.
+ **Alignmentment type - specify the type of alignments to be performed. By default, this is set to Local and the program performs local alignment just like BLAST programs do. Alternatively, this can be set to SemiGlobal and the program will perform semi global alignment in which reads are aligned end-to-end.
+ **Include unaligned queries in RMA output file** - ensure that all unaligned queries are placed into the output RMA file. By default, only queries that have an alignment are included.
+
+
+ https://doi.org/10.1101/050559
+
+
+
diff -r 000000000000 -r d505990b8c89 test-data/alignments_output1.sam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignments_output1.sam Fri Nov 12 18:39:23 2021 +0000
@@ -0,0 +1,5 @@
+@HD VN:1.5 SO:unsorted GO:query
+@PG ID:1 PN:MALT CL:--mode BlastN --matchScore 2 --mismatchScore -3 --setLambda 0.625 --setK 0.41 --alignmentType Local --inFile input_fastq_gz.fastq.gz --index
+@RG ID:1 PL:unknown SM:unknown
+@CO BlastN-like alignments
+@CO Reporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length
diff -r 000000000000 -r d505990b8c89 test-data/alignments_output2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignments_output2.txt Fri Nov 12 18:39:23 2021 +0000
@@ -0,0 +1,50 @@
+BLASTN output produced by MALT
+
+
+Query= YP_009137150.1
+
+***** No hits found ******
+
+Query= YP_009137151.1
+
+***** No hits found ******
+
+Query= YP_009137152.1
+
+***** No hits found ******
+
+Query= YP_009137153.1
+
+***** No hits found ******
+
+Query= YP_009137154.1
+
+***** No hits found ******
+
+Query= YP_009137155.1
+
+***** No hits found ******
+
+Query= YP_009137156.1
+
+***** No hits found ******
+
+Query= YP_009137157.1
+
+***** No hits found ******
+
+Query= YP_009137158.1
+
+***** No hits found ******
+
+Query= YP_009137159.1
+
+***** No hits found ******
+
+Query= YP_009137160.1
+
+***** No hits found ******
+
+Query= YP_009137161.1
+
+***** No hits found ******
diff -r 000000000000 -r d505990b8c89 test-data/input.fastq.gz
Binary file test-data/input.fastq.gz has changed
diff -r 000000000000 -r d505990b8c89 test-data/malt_indices.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/malt_indices.loc Fri Nov 12 18:39:23 2021 +0000
@@ -0,0 +1,18 @@
+# This is a sample file distributed with Galaxy that enables tools
+# to use a directory of MALT indexed data files. The malt_index.loc
+# file has this format (longer white space characters are TAB characters):
+#
+#
+#
+# So, for example, if you have the phiX indexe stored in
+# /depot/data2/galaxy/phiX/base/,
+# then the malt_index.loc entry would look like this:
+#
+# phiX phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
+#
+# and your /depot/data2/galaxy/phiX/base/ directory
+# would contain phiX.fa.* files:
+#
+#-rw-r--r-- 1 galaxy universe 830134 2005-09-13 10:12 phiX.fa
+#...etc...
+phiX phiX Coliphage phiX ${__HERE__}/phiX
diff -r 000000000000 -r d505990b8c89 test-data/phiX/index0.idx
Binary file test-data/phiX/index0.idx has changed
diff -r 000000000000 -r d505990b8c89 test-data/phiX/ref.db
Binary file test-data/phiX/ref.db has changed
diff -r 000000000000 -r d505990b8c89 test-data/phiX/ref.idx
Binary file test-data/phiX/ref.idx has changed
diff -r 000000000000 -r d505990b8c89 test-data/phiX/ref.inf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX/ref.inf Fri Nov 12 18:39:23 2021 +0000
@@ -0,0 +1,2 @@
+sequences 1
+letters 5386
diff -r 000000000000 -r d505990b8c89 test-data/phiX/table0.db
Binary file test-data/phiX/table0.db has changed
diff -r 000000000000 -r d505990b8c89 test-data/phiX/table0.idx
Binary file test-data/phiX/table0.idx has changed
diff -r 000000000000 -r d505990b8c89 test-data/unaligned_output2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unaligned_output2.fasta Fri Nov 12 18:39:23 2021 +0000
@@ -0,0 +1,26 @@
+>YP_009137150.1
+NNNNNGNNNNGNNNNNNNGANANNNNGANANNNNGANNTANNNNNNANNNGTANNNANAANNNNNNNNNNNNANNNNNANNAGNNNANNANNNNNNGGGNANNANNAANAAACNNNNNNNNNGNNNNNNNNNANNNNTTTNNNANNNNNNNNNNANNNANANNGNNCNNNNNNNNNNNANNTAANNANNGNNANNNANNNNNNNNNAAANANNGNCNNNNANANANANANANNNGGNANNNNAAAAANGNNAAAGNGNNAN
+>YP_009137151.1
+NNNNNGTNNNANNGNNNNNNNTNGTNNAANNANGNNNNNNNNANNNNNNNTNNGNNNNNNNNNNTNNAGNTNTNNNNAGNNNAATNNANNNANNNGNNTNANANGNCGGGNNGNNNANAGGGGNNCANCTNNNANNNNCNNNNCNNNNCNNCNNTNNNNNNTCNNCNTNNANNNNGNTANGNNNTNNNNNNNNTNNNANAANNAGTANNNNNTGNNNTANNNNNNGGNTNNANNNTNNNNGTNNNNNNNANNNNNNNANNNANNNGGGGAGATNGTNNNAATNNANNGANNNNNNGGANNNAGNGNGNGGGNANAANNNNNANNNNAAGGGNANANNNGNNAAAANGNTNNAGNNNAANNNNNNNNNNNNNNNNNNAGNGNNNNNNNNNANNNNGNGGGGNNNNNGNAANNNAANANNNNNNNNAAAANNNNANANAAGNANNANNNNANNANNNNNTNANTNTNANNNGNAGATNANGNGGNGANGGNGNNNGTNTNGAANNAANGAAANNNNNNGNNNGNAANNNANNNAANNNNNANNGNGANNAANNNANNNNNGNNGNGNNANANAGAANNNANNNNNAANAAAANNNNNAANNNNNAANNNNNAANNNNNAANNNNAANNNNNNNNANNNAGGAGGNNANANGAGNNNNTNNGNNAAANNGNNNCANNTNNANGGNNNGANNNANGNTNNNNNAGNNNNNANANNNNNTNTGNCNNNNNNNTGNNGANNNNNNNTGNNANNNNAAANANNNNTNNNNNANNCNNNNNNNTNNANNNNNNNNTNNGNNNNNNGTNNGANNNNGNNNNNNNNNNNGANANAGNANAGNGN
+>YP_009137152.1
+NGNNCNNGNNNNGANGANGGNNATNNNNNNNNANNNGNNNNNNCNNTNANNNNNNNNANNNNNNANNNGNNNNNNCNGNNTNNNNNNANNANNNNNNNNAAGNNNNNNNNNNNANTNNTTTNNANNNNNNNANGNNNNANNNANNNAGCNNNNNNNTNNCNGNNNNNNANTTNTNNNNNNNNNNANNNNNNNATNNNNNANNNANNNNNNNTNGNNNNTNNNNN
+>YP_009137153.1
+NNNANNNNNNNNNNNNNNNNTNNNGGNNNNNNGAGNNANNATNNNCNANNNGNGAGNNTNNAAGNANNNNNNNGCNNGNNNNANTTNNNNNGNNGNATNNNNTNNNNNNAANNNANNNNNANNNNNNNNNANNNTANNNANNNNNCNTNNNNNNNNNNNNNTNNCTNNNNNNNNNGNNNNNNNGNANGNANNNNANNNNNNNNNNNNAANNNCNNNANNNGNGCNNNNANNGNNNNNTTNTNNNGAAANNNNNGNNNNNGGNNNNNAANNNGNNNNNNGANANNANNNNNNNNNNNNNNNNNNNNNNNNGTCNNNNAANNNNNTNNNNNNNNNN
+>YP_009137154.1
+NNGNGNNNNNNANTNNANNGNTNANNNNNNGANNNTTNNNNNAGTANNANNGNNNGNNNNNANNNNTNNNAGNNNGANGNNNTNNTNNNNNNNNNNGNNNNTNTNNNNNNNNNANNNNACTNTNNNNGTAANNNNNGANNNNTCNNNNNNNNNNNNNCNNANAANNNNNNNANNNNNNNNNNNTNNNNGNNCNANNNNNNNNNNNNNNNNNNNNNNNNTNNN
+>YP_009137155.1
+NGNNNTTNANNNNNNNANNTNANNNAANNNNNNNNGTNANNTNGNANNNNNNNGGNNNNNTNNGNNNNNNCNANNCANNNNGNANTNNNNNNNNANNNANNNNNNNNNNNGNNNNNATAGNNTNNNTNNTNNNTATNNGTANNAANGCNNANNNNNNTTNNANNNNTAGNNNANTTNNNNNNNNNNNNNNTNNNANNTNGT
+>YP_009137156.1
+NAANGGNGNNNNNANGNNNNNNGANNANNNNNNANNNNTNNNGNNNNNANNNNNNNNNNNNTNNNNNNNNNNNAANNNNTGNNNNNNNNAANNNTGNAGNGNNTCNNTNNNNNNCNNTGATNNAANNNNNNNNGANNNNNNNTNNNNNGNNGNNNNANNGNNNNTNANNNANNNNNNNNNNTNNNNNNNNNTNNANAANGGNNANNNNNANTANNNTNGNGNGANTNNANNTNGANNANTNNNNNNNNNAGNNGNNNNTTNNNCNNNNNANNNTNNNAGNNNNNNNCNGNNTNTANNNNTNNNNNNNCNNNNNNNNNTNNNCNNTNNNNTNNNNNNANNNNNNNCNNNNNGNNNNNNNNGNNNTNNNNNNNNNNNNNNNNNTNNANNNGNTNNNNNNNNNNANNANNNANNNNTNNGNNNNNTNNNNTNNNNNNNNNNNNNTNNNTNTNNNNNTANANNNTNNNNNNNNNAGNNNCNNNNNNNNNNANNNNTNNNNNNNANTANNNNNNNGNNGTNNTNNANNNNNNNNNTNGNTNNNNANNNNNNNNNGGNNNNNNNNNNNGNNATNNTNANGNNGNNTANNNNNNNNAAGANATNAANTNNNNNGNNANNNNNNGNNNGGNNNNNNNNNNNNNAGNNNNNNNNNNCNNANNNNNTTAANNANNGNNNNANNGNNNNNNNNNGNNNNNANNNTNNNNNNNNGCNNNTGNNNGGNNNNANNTNNNTNNGNTNTNNNANANNNNNNNATAGNANNNNNNNNNNNNNNNNNGNNNNNNTNNNNNNNNNNNTNNANANNANNGNNNNNANTNTNNNGNNNNNNANCNTNGNNNNNNANNANNNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNN
+>YP_009137157.1
+NAANNANANANNTNGGNAANCANNNGNNNNNNTNGTNNNNNNNNGNNGNTNGNGNNNNNNNNNAATNNNNAANNNANNNATTNNNNNNNNNNNNNANGNNNNNNNNNNNNANNGNNAGNANNNNNTNNCTNNTTNNNNANGNNNCNANGGNNGNTNNNNNNNNNTCNGNNNNNNNTNNGNATNNNGANNNNNTNNNNNATNAGAANNAGNGNNNNANANNNTNNANNNNNNNNNNNNNGNNNNNNNNNGNNGNCNNNCNNNNTGNNNNNNNNNNNNCNNNNACNANNNNANNCNNNNTANNNNNNGNNNNNNNGNAGAANNNNNANGNNNNTNAGNAANNNNNNNNNNNGNNNNGNNNNTNNANNNNAGGNNNNTNANNNTNNGNGNGGTGNGNANNNNGANNNNNNNANNTANNNNNNGNNNGNNNNNNGTNNNNNNTNAGNATNNNANNNNNNNANAGANNNNNNAANNAAGGGAGNNANANNNNANNNNNNNNNNNNNNTNNANNNNNNNNNANGNNNNNNNNNNNNNNNNCNNNNNNNNNNGNNTNNNNNNGANANNNANNNNNNNNANNAGANNTGNNNNNGNNNNNNANNNNTNNNTNNTNNAANNNANNNNAANNNNNNNTNANNNANANNNGGNNNNTNTNNNNNGNTNNGANNNGNGNNNNNGNNNANN
+>YP_009137158.1
+NANNTNANNGTAAANNNNANAGNNNNNNNANGNNNNANNNNACNNNNNNNNNNNNTATNNNNNNNTNNGNNNNNNNGNNNNANNANNNNNNNCGNNNTNNGNANNNNTANNNNNNNNANNNNNNNNNNNNNNNTNNNNNNNNCNNNNNNNCNNNNATNNNNNNNNANNGNNANNANNNNNNNCNNNNNCNNNNNTNNCNAGNNNNNNNNNNNNNNNANNNNANNNNNNNNANNCATNNNNANNNNGNNNNTNCNANNNAGNNGNCNNNNNNNNANNNNNNNGNNNNNTNNNNNNNC
+>YP_009137159.1
+NNANGNNNNNNNNNANTNNANNNNNNTNNCNNANNNNNCNNAAGNANANNANNNNGNNNNNNNNGNNNNNAAGANAAANAATANAANNNNNNGNNTNNNANNACNNAANNNNTGNNANNNNNNNGNNNNTGNNNNNNNANNGNNAANNAANNNNNANNNNNNNANNANNANNNGANNANANNAANNNNNNCANNANNANTNTTNTANNANNNTTNANNNTNNNGANANNNNNCNNGNNNNGNNNNNTANNNNNNGNNNNNNAGNGNNANANNANNNNNNTTNNAANGANANNNANNGNGNNNNGGNNNNNANNGNNGNNTNTNNAAAAANNANNNNNGAAATNAACNGANNANGANNNNNNNANNANANNAAGNNNNANNNANANNNNTATTNNNNNNNAANGNNNTANNCNNGNNANNNAANAGNGNAGNNNANGNAGNNNNNANNAAANNNNNANANNNNNNNNACNACNANNNNNGGNNAANCNNNNNTANNNNNANCGGTGAANNGNNNNNNGNANAANGANNNANNANNANNNANNNANGNNNNNANNNANNGNNTNNNTNNNTGANNNNNNNNTNNNNGNNNNGNANAAAANNNNNANNNNNNNNAAGNNNNANCAANGNNNNACNNNNNNANGNNNNANNNNNNTNNGNANNNNNNTANNGGANNNANNNNNNNNNNCNGGGNNNGNNNNNNNNNNNNNNNNCANNNNNNNNNNNNNNTGNNNGNNGNGGNNNNNNNNNNNNNNN
+>YP_009137160.1
+NANTNNNATCTNNTNNAANANGATNANGAANGNNNGANNNNGNNNCNNNTNNNNNANNNNGGNNANNNNNNNNNTTNNNNNNGNNTNNNANANTANCNTNNNANNGNGNTTANNNNNGNANNNNNTNNNNNNCNNNNTNTNATNNANNGNNNNNTNNNNTNNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNTNGNNNNNTNNNNGNNNANNNNNNNTCNNNNANNATANANNNNNNCNNNGNNNNNNNNGNNANNGNNANNCNNNNNNGNNNNNAANNNNGNAGGANNNNANNNATNNGNNNANNAGGNNNCNNNNTNNNANNNANNCNNNTNNNNNNNNNTNNGNNTTNGNNNNNNNTTNNTNGNNNNNNNNNNNNANNNNNNNGNNNNNNNNNNGNNNTNNNGNNNNNNNGNGANNNNNNTNNNNNNNNNANGNNNANNNNNTNNNCNNNNGNCNANNANAANANGNNNNNNNNNNNNNNNCTNACNANNNNNNNNNNTNNCNNNNNNGNNAANTNNNNCNNNNGNNNNANNANNNNNNNNCNNNNTNNNANAANTNNNGNNNNNNNNNNNANANNNANNNGNNNNNGNTNNNNNNNNNACNNNNNAANNNANNNNNNNNNATGNNNTNNAAGNNNNNANNNTNNNANNNNNNNNCNTNAACNNNNNNAGGNGNTNNNNNNNNNNNNNNNNNNNNNNNNGNCNNTNGNNNNNNANNNNANANNGCNNNGNNNNTNNANNNNNNNNGNNNGNNNANNTNTNNGAGNNNNNTNNANNNNNNANNNNNNACNTNNNNNANNNANNNNNAGANNNNNANANGNCNNTNANGANNNTNNNNNAANNNNNTNANNNNNGANNNNTN
+>YP_009137161.1
+NGNNANNGNNNAANGANNANGANAANNNNCNNNATNNNNANCNNGNNNNANNNNNNNNCNNANATNNANANATNNNNGGNANNNNNNTNNNNATNANTNTNNNAAANNAANGANTNNNNNANNAANNNAAANNANNNATNNAGNNCANNNNNTNNNNANNNNNNANNNNNNNNACNNNNAANNCTNGNNNGTNNNNNNGNNNNANTNNNNNGNNNANNTNANNNGTNNCTAAAANNNNTNAANNNNNNANNNNNCNTTNNANNNNNNNNNNNGNNCNNNNNNNGNNNGANAATGNNGNACNNNNTGGNNNNNNNNNGANTGNNNANANNAANANANANNNCTNANNNNNNNNTNNNNNNNNTNNNANNANNNNNNNNNGNNNGGNNGNNGNANTNNANNNNNANNNNNGNNNGNNNNNNNANNNNANNNANNNNNGNNNNANNNNNTNNGNANNNAGNNNNNTNNNN
+>YP_009137162.1
+NGNANNGANNCCCNNNNNTTNGGNNNNNTANNNNNNNNNNNNNGNNNNNNNNNNNTNANGNNNNNANNNNNNNTNNNNNNNANNNATNTNNNNNNN
diff -r 000000000000 -r d505990b8c89 test-data/viral.1.protein.fasta.gz
Binary file test-data/viral.1.protein.fasta.gz has changed
diff -r 000000000000 -r d505990b8c89 tool-data/malt_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/malt_indices.loc.sample Fri Nov 12 18:39:23 2021 +0000
@@ -0,0 +1,19 @@
+# This is a sample file distributed with Galaxy that enables tools
+# to use a directory of MALT indexed data files. The malt_index.loc
+# file has this format (longer white space characters are TAB characters):
+#
+#
+#
+# So, for example, if you have the phiX indexe stored in
+# /depot/data2/galaxy/phiX/base/,
+# then the malt_index.loc entry would look like this:
+#
+# phiX phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
+#
+# and your /depot/data2/galaxy/phiX/base/ directory
+# would contain phiX.fa.* files:
+#
+#-rw-r--r-- 1 galaxy universe 830134 2005-09-13 10:12 phiX.fa
+#...etc...
+
+#phiX phiX Coliphage phiX /phiX
diff -r 000000000000 -r d505990b8c89 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Nov 12 18:39:23 2021 +0000
@@ -0,0 +1,7 @@
+
+
+