| Next changeset 1:87a1202c03e8 (2022-05-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/malt commit 04aaa266f5b2e557f42c7feca4e081c7e9c1dae6" |
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added:
macros.xml malt_run.xml test-data/alignments_output1.sam test-data/alignments_output2.txt test-data/input.fastq.gz test-data/malt_indices.loc test-data/phiX/index0.idx test-data/phiX/ref.db test-data/phiX/ref.idx test-data/phiX/ref.inf test-data/phiX/table0.db test-data/phiX/table0.idx test-data/unaligned_output2.fasta test-data/viral.1.protein.fasta.gz tool-data/malt_indices.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| 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 |
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| @@ -0,0 +1,29 @@ +<macros> + <token name="@TOOL_VERSION@">0.5.3</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.09</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.53">malt</requirement> + </requirements> + </xml> + <macro name="sub_matrix"> + <param name="sub_matrix" type="select" label="Select the protein substitution matrix to use"> + <option value="BLOSUM62" selected="True">BLOSUM62</option> + <option value="BLOSUM45">BLOSUM45</option> + <option value="BLOSUM50">BLOSUM50</option> + <option value="BLOSUM80">BLOSUM80</option> + <option value="BLOSUM90">BLOSUM90</option> + </param> + </macro> + <macro name="forward_reverse_only"> + <param name="forward_only" type="boolean" truevalue="--forwardOnly" falsevalue="" checked="false" label="Align query forward strand only?"/> + <param name="reverse_only" type="boolean" truevalue="--reverseOnly" falsevalue="" checked="false" label="Align query reverse strand only?"/> + </macro> + <xml name="citations"> + <citations> + <citation type="doi">https://doi.org/10.1101/050559</citation> + </citations> + </xml> +</macros> + |
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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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| b'@@ -0,0 +1,274 @@\n+<tool id="malt_run" name="MALT analyzer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description></description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+#import re\n+\n+## This will point to a directory.\n+#set ref = str($reference.fields.path)\n+\n+#set input_identifier = re.sub(\'[^\\s\\w\\-]\', \'_\', str($input.element_identifier))\n+## malt-run uses the file extension to determine the input format.\n+#if $input.is_of_type(\'fasta\', \'fasta.gz\'):\n+ #set input_identifier = $input_identifier + \'.fasta\'\n+#else:\n+ #set input_identifier = $input_identifier + \'.fastq\'\n+#end if\n+#if $input.ext.endswith(\'.gz\'):\n+ #set input_identifier = $input_identifier + \'.gz\'\n+#end if\n+ln -s \'${input}\' \'${input_identifier}\' &&\n+\n+malt-run \n+--mode \'$mode_cond.mode\'\n+\n+#if str($mode_cond.mode) == \'BlastN\':\n+ --matchScore \'$mode_cond.matchScore\'\n+ --mismatchScore \'$mode_cond.mismatchScore\'\n+ --setLambda \'$mode_cond.setLambda\'\n+ --setK \'$mode_cond.setK\'\n+ $mode_cond.forward_only\n+ $mode_cond.reverse_only\n+#else if str($mode_cond.mode) == \'BlastP\':\n+ --subMatrix \'$mode_cond.sub_matrix\'\n+#else if str($mode_cond.mode) == \'BlastX\':\n+ --subMatrix \'$mode_cond.sub_matrix\'\n+ $mode_cond.forward_only\n+ $mode_cond.reverse_only\n+#end if\n+\n+--alignmentType \'$alignmentType\'\n+--inFile \'$input_identifier\'\n+--index \'$ref\'\n+## malt-run requires correct output file extensions.\n+--output \'./output.rma6\'\n+--numThreads \\${GALAXY_SLOTS:-12}\n+\n+--memoryMode \'$advanced_options_performance.memoryMode\'\n+--maxTables \'$advanced_options_performance.maxTables\'\n+$advanced_options_performance.replicateQueryCache\n+\n+--minBitScore \'$advanced_options_filter.minBitScore\'\n+--maxExpected \'$advanced_options_filter.maxExpected\'\n+--minPercentIdentity \'$advanced_options_filter.minPercentIdentity\'\n+--maxAlignmentsPerQuery \'$advanced_options_filter.maxAlignmentsPerQuery\'\n+--maxAlignmentsPerRef \'$advanced_options_filter.maxAlignmentsPerRef\'\n+\n+--topPercent \'$advanced_options_lca.topPercent\'\n+--minSupportPercent \'$advanced_options_lca.minSupportPercent\'\n+--minSupport \'$advanced_options_lca.minSupport\'\n+--minPercentIdentityLCA \'$advanced_options_lca.minPercentIdentityLCA\'\n+$advanced_options_lca.useMinPercentIdentityFilterLCA\n+$advanced_options_lca.weightedLCA\n+$advanced_options_lca.magnitudes\n+\n+--maxSeedsPerFrame \'$advanced_options_heuristics.maxSeedsPerFrame\'\n+--maxSeedsPerRef \'$advanced_options_heuristics.maxSeedsPerRef\'\n+--seedShift \'$advanced_options_heuristics.seedShift\'\n+\n+--gapOpen \'$advanced_options_alignment.gapOpen\'\n+--gapExtend \'$advanced_options_alignment.gapExtend\'\n+--band \'$advanced_options_alignment.band\'\n+\n+#if str($additional_outputs_cond.additional_outputs) == \'yes\':\n+ $additional_outputs_cond.includeUnaligned\n+ #if $additional_outputs_cond.output_alignments_cond.output_alignments:\n+ ## malt-run requires correct output file extensions.\n+ #set alignments_ext = $additional_outputs_cond.output_alignments_cond.format + \'.gz\'\n+ ## This param value must be a path, not a file name so we\'ll use the ./ approach.\n+ --alignments \'./alignments_output.${alignments_ext}\'\n+ --format \'$additional_outputs_cond.output_alignments_cond.format\'\n+ #end if\n+ #if $additional_outputs_cond.output_aligned:\n+ ## malt-run requires correct output file extensions.\n+ #set aligned_ext = \'fna.gz\'\n+ ## This param value must be a path, not a file name so we\'ll use the ./ approach.\n+ --outAligned \'./aligned_output.${aligned_ext}\'\n+ #end if\n+ #if $additional_outputs_cond.output_unaligned:\n+ ## malt-run requires correct output file extensions.\n+ ## This param value must be a path, not a file name so we\'ll use the ./ approach.\n+ --outUnaligned \'./unaligned_output.fna.gz\'\n+ #end if\n+#end if\n+\n+&& mv \'output.rma6\' \'$rma6_output\'\n+\n'..b' <when input="additional_outputs_cond.output_alignments_cond.format" value="Tab" format="tabular"/>\n+ <when input="additional_outputs_cond.output_alignments_cond.format" value="Text" format="txt"/>\n+ </change_format>\n+ </data>\n+ <data name="aligned_output" format="fasta" label="${tool.name} on ${on_string} (aligned)">\n+ <filter>additional_outputs_cond[\'additional_outputs\'] == \'yes\' and additional_outputs_cond[\'output_aligned\']</filter>\n+ </data>\n+ <data name="unaligned_output" format="fasta" label="${tool.name} on ${on_string} (unaligned)">\n+ <filter>additional_outputs_cond[\'additional_outputs\'] == \'yes\' and additional_outputs_cond[\'output_unaligned\']</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="2">\n+ <param name="input" value="input.fastq.gz" ftype="fastqsanger.gz" dbkey="phiX"/>\n+ <param name="additional_outputs" value="yes"/>\n+ <param name="includeUnaligned" value="--includeUnaligned"/>\n+ <param name="output_alignments" value="true"/>\n+ <output name="rma6_output" ftype="rma6">\n+ <assert_contents>\n+ <has_size value="76465"/>\n+ </assert_contents>\n+ <metadata name="dbkey" value="phiX"/>\n+ </output>\n+ <output name="alignments_output" file="alignments_output1.sam" ftype="sam" compare="contains"/>\n+ </test>\n+ <test expect_num_outputs="3">\n+ <param name="input" value="viral.1.protein.fasta.gz" ftype="fasta.gz" dbkey="phiX"/>\n+ <param name="alignmentType" value="SemiGlobal"/>\n+ <param name="additional_outputs" value="yes"/>\n+ <param name="includeUnaligned" value="--includeUnaligned"/>\n+ <param name="output_alignments" value="true"/>\n+ <param name="format" value="Text"/>\n+ <param name="output_unaligned" value="true"/>\n+ <output name="rma6_output" ftype="rma6">\n+ <assert_contents>\n+ <has_size value="29338"/>\n+ </assert_contents>\n+ <metadata name="dbkey" value="phiX"/>\n+ </output>\n+ <output name="alignments_output" file="alignments_output2.txt" ftype="txt" compare="contains"/>\n+ <output name="unaligned_output" file="unaligned_output2.fasta" ftype="fasta" compare="contains"/>\n+ </test>\n+ </tests>\n+ <help>\n+**What it does**\n+\n+Align one or more files of input sequences (DNA or proteins) against an index representing a collection of reference DNA\n+or protein sequences. Depending on the type of input and reference sequences, the program can be be run in BLASTN, BLASTP\n+or BLASTX mode.\n+\n+**Options**\n+\n+ **Input file** - specify all input files which must be in FastA or FastQ format and may be gzipped.\n+ **Referencegenome ** - select the index built by the **MALT index builder** tool.\n+ **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.\n+ **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. \n+ **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.\n+ </help>\n+ <citations>\n+ <citation type="doi">https://doi.org/10.1101/050559</citation>\n+ </citations>\n+</tool>\n+\n' |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 ****** |
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| diff -r 000000000000 -r d505990b8c89 test-data/input.fastq.gz |
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| Binary file test-data/input.fastq.gz has changed |
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| 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 |
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| @@ -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): +# +# <unique_build_id> <dbkey> <display_name> <file_path> +# +# 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 |
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| diff -r 000000000000 -r d505990b8c89 test-data/phiX/index0.idx |
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| Binary file test-data/phiX/index0.idx has changed |
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| diff -r 000000000000 -r d505990b8c89 test-data/phiX/ref.db |
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| Binary file test-data/phiX/ref.db has changed |
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| diff -r 000000000000 -r d505990b8c89 test-data/phiX/ref.idx |
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| Binary file test-data/phiX/ref.idx has changed |
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| 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 |
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| @@ -0,0 +1,2 @@ +sequences 1 +letters 5386 |
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| diff -r 000000000000 -r d505990b8c89 test-data/phiX/table0.db |
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| Binary file test-data/phiX/table0.db has changed |
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| diff -r 000000000000 -r d505990b8c89 test-data/phiX/table0.idx |
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| Binary file test-data/phiX/table0.idx has changed |
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| 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 |
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| @@ -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 |
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| diff -r 000000000000 -r d505990b8c89 test-data/viral.1.protein.fasta.gz |
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| Binary file test-data/viral.1.protein.fasta.gz has changed |
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| 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 |
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| @@ -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): +# +# <unique_build_id> <dbkey> <display_name> <file_path> +# +# 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 |
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| 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 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Location of Malt indices for FASTA files --> + <table name="malt_indices" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/malt_indices.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r d505990b8c89 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Nov 12 18:39:23 2021 +0000 |
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| @@ -0,0 +1,6 @@ +<tables> + <table name="malt_indices" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/malt_indices.loc" /> + </table> +</tables> |