| Previous changeset 2:49b937f12aa4 (2019-12-25) Next changeset 4:482052b30b78 (2020-10-02) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina commit 8f89414ecee8120447febc2902ff1ddbbd71e638" |
|
modified:
sina.xml |
|
added:
README.rst |
|
removed:
README.md macros.xml test-data/output_fasta_arb.arb test-data/output_fasta_fasta.arb |
| b |
| diff -r 49b937f12aa4 -r 8afa8799d50f README.md --- a/README.md Wed Dec 25 12:09:28 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,8 +0,0 @@ -**Add reference libraries** - -[Reference databases](https://www.arb-silva.de/download/arb-files/) provided by the [SILVA project](https://www.arb-silva.de/) can be used within this wrapper by adding the corresponding files to the tool-data directory and editing` tool-data/sina_references.loc.sample` as follows: - - LSU_Parc ${__HERE__}/SILVA_132_LSUParc_12_12_17_opt.arb - LSU_Ref ${__HERE__}/SILVA_132_LSURef_07_12_17_opt.arb - SSU_Ref ${__HERE__}/SILVA_132_SSURef_12_12_17_opt.arb - Ref_NR_99 ${__HERE__}/SILVA_132_SSURef_NR99_13_12_17_opt.arb \ No newline at end of file |
| b |
| diff -r 49b937f12aa4 -r 8afa8799d50f README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Oct 02 08:01:21 2020 +0000 |
| [ |
| @@ -0,0 +1,11 @@ +**Add reference libraries** + +[Reference databases](https://www.arb-silva.de/download/arb-files/) provided by the [SILVA project](https://www.arb-silva.de/) can be used within this wrapper by adding the corresponding files to the tool-data directory and editing `tool-data/sina_references.loc.sample` as follows: + + `LSU_Parc ${__HERE__}/SILVA_132_LSUParc_12_12_17_opt.arb` + + `LSU_Ref ${__HERE__}/SILVA_132_LSURef_07_12_17_opt.arb` + + `SSU_Ref ${__HERE__}/SILVA_132_SSURef_12_12_17_opt.arb` + + `Ref_NR_99 ${__HERE__}/SILVA_132_SSURef_NR99_13_12_17_opt.arb` \ No newline at end of file |
| b |
| diff -r 49b937f12aa4 -r 8afa8799d50f macros.xml --- a/macros.xml Wed Dec 25 12:09:28 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ -<macros> - <token name="@TOOL_VERSION@">1.5.0</token> - <token name="@WRAPPER_VERSION@">galaxy1</token> - <xml name="requirements"> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">sina</requirement> - <yield/> - </requirements> - </xml> -</macros> |
| b |
| diff -r 49b937f12aa4 -r 8afa8799d50f sina.xml --- a/sina.xml Wed Dec 25 12:09:28 2019 -0500 +++ b/sina.xml Fri Oct 02 08:01:21 2020 +0000 |
| [ |
| b'@@ -1,51 +1,54 @@\n <tool id="sina" name="SINA" version="@TOOL_VERSION@+@WRAPPER_VERSION@" profile="18.01">\n <description>reference based multiple sequence alignment</description>\n <macros>\n- <import>macros.xml</import>\n+ <token name="@TOOL_VERSION@">1.6.1</token>\n+ <token name="@WRAPPER_VERSION@">galaxy0</token>\n+ <xml name="minidty">\n+ <param name="minidty" type="float" value="0.7" min="0.0" max="1.0" label="Exclude sequences sharing less than this value fractional identity with any of the alignment reference sequences from the output?" help="(--min-idty)"/>\n+ </xml>\n </macros>\n- <expand macro="requirements"/>\n- <stdio></stdio>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">sina</requirement>\n+ </requirements>\n+ <version_command>sina --version</version_command>\n <command detect_errors="exit_code"><![CDATA[\n ## initialize\n ## parse custom reference from fasta to arb file format\n-\n #if $db.select == \'custom\'\n #if $db.custom.ext == \'fasta\'\n- sina -i \'$db.custom\' --prealigned -o reference.arb &&\n+ sina -i \'$db.custom\' --prealigned -o \'reference.arb\' &&\n #else\n- ln -s \'$db.custom\' reference.arb &&\n+ ln -s \'$db.custom\' \'reference.arb\' &&\n #end if\n #elif $db.select == \'local\'\n- ln -s \'$db.arb_databases.fields.path\' reference.arb &&\n+ ln -s \'$db.arb_databases.fields.path\' \'reference.arb\' &&\n #end if\n \n ## run\n sina\n --in=\'$in\'\n- --db=reference.arb\n+ --db=\'reference.arb\'\n -p \\${GALAXY_SLOTS:-4}\n --num-pts=\\${GALAXY_SLOTS:-4}\n-\n #if $os.type == \'arb\'\n --outtype=\'arb\'\n- --out=output.arb\n+ --out=\'output.arb\'\n #elif $os.type == \'fasta\'\n --outtype=\'fasta\'\n- --out=output.fasta\n+ --out=\'output.fasta\'\n --min-idty=$os.minidty\n #elif $os.type == \'fasta_meta\'\n --outtype=\'fasta\'\n- --out=output.fasta\n+ --out=\'output.fasta\'\n --min-idty=$os.minidty\n --meta-fmt=\'csv\'\n #end if\n #if $log == \'yes\'\n- --log-file=$logfile\n+ --log-file=\'$logfile\'\n #elif $log == \'yes_meta\'\n- --log-file=$logfile\n+ --log-file=\'$logfile\'\n --show-diff\n #end if\n-\n ## Advanced alignment parameters\n --overhang=$ap.overhang\n --insertion=$ap.insertion\n@@ -54,7 +57,6 @@\n #elif $ap.turn == \'all\'\n -t all\n #end if\n-\n ## Expert Alignment Parameters\n --fs-min=$eap.fsmin\n --fs-max=$eap.fsmax\n@@ -74,7 +76,6 @@\n --fs-kmer-mm=$eap.fskmermm\n $eap.fskmernofast\n $eap.fskmernorel\n-\n ## Advanced search and classification parameters\n #if $asacp.activate == \'yes\'\n --search\n@@ -86,7 +87,6 @@\n $asacp.searchnofast\n $asacp.searchkmernorel\n #end if\n-\n ## convert meta file to tabular\n #if $os.type == \'fasta_meta\'\n && cat output.csv | sed \'s/,/\\t/g\' > output.tsv\n@@ -94,17 +94,17 @@\n ]]></command>\n <!-- Sections and default parameters are based on https://www.arb-silva.de/aligner -->\n <inputs>\n- <param argument="--in" type="data" format="fasta" multiple="false" label="Sequence file" help="FASTA file format"/>\n+ <param argument="--in" type="data" format="fasta" label="Select sequence file" help="FASTA file format"/>\n <conditional name="db">\n- <param name="select" type="select" label="Reference library type" help="">\n+ '..b'e column numbers for the range in which the full gene is expected be specified via --gene-start and --gene-end. (--fs-cover-gene)"/>\n+ <param name="matchscore" type="integer" value="2" min="0" label="Set score given for a match" help="(--match-score)"/>\n+ <param name="mismatchscore" type="integer" value="-1" max="0" label="Set score given for a mismatch" help="(--mismatch-score)"/>\n+ <param name="pengap" type="integer" value="5" min="0" label="Set penalty subtracted from the score for opening a gap" help="(--pen-gap)"/>\n+ <param name="pengapext" type="integer" value="2" min="0" label="Set penalty subtracted from the score for extending a gap" help="(--pen-gapext)"/>\n+ <param name="fskmerlen" type="integer" value="10" min="0" label="Set size of k for the reference search" help="For SSU rRNA sequences, the default of 10 is a good value. For different sequence types, different values may perform better. For 5S, for example, 6 has shown to be more effective. (--fs-kmer-len)"/>\n+ <param name="fskmermm" type="integer" value="0" min="0" label="Set k-mer matches in the reference database to contain this number of mismatches" help=" (--fs-kmer-mm)"/>\n+ <param name="fskmernofast" type="boolean" truevalue="--fs-kmer-no-fast" falsevalue="" label="Use all k-mers occurring in the query sequence in the search?" help="By default, only k-mers starting with an A are used for extra performance. (--fs-kmer-no-fast)"/>\n+ <param name="fskmernorel" type="boolean" truevalue="--fs-kmer-norel" falsevalue="" label="Use absolute match scores in the kmer search?" help="Absolute (number of shared k-mers) rather than relative (number or shared k-mers divided by length of reference sequence) (--fs-kmer-norel)"/>\n </section>\n </inputs>\n <outputs>\n@@ -234,7 +234,11 @@\n <section name="os">\n <param name="type" value="arb"/>\n </section>\n- <output name="output_arb" file="output_fasta_fasta.arb" compare="sim_size" delta="100"/>\n+ <output name="output_arb">\n+ <assert_contents>\n+ <has_size value="21369"/>\n+ </assert_contents>\n+ </output>\n </test>\n <!-- #3 in: *.fasta; db: *.arb; out: *.fasta; standard parameters -->\n <test>\n@@ -269,7 +273,11 @@\n <section name="os">\n <param name="type" value="arb"/>\n </section>\n- <output name="output_arb" file="output_fasta_arb.arb" compare="sim_size" delta="1000"/>\n+ <output name="output_arb">\n+ <assert_contents>\n+ <has_size value="19999"/>\n+ </assert_contents>\n+ </output>\n </test>\n <!-- #5 in: *.fasta; db: *.arb; out: *.fasta; custom parameters -->\n <test>\n@@ -333,10 +341,13 @@\n <section name="os">\n <param name="type" value="arb"/>\n </section>\n- <output name="output_arb" file="output_fasta_arb.arb" compare="sim_size" delta="1000"/>\n+ <output name="output_arb">\n+ <assert_contents>\n+ <has_size value="19999"/>\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n-\n <help><![CDATA[\n .. class:: infomark\n \n@@ -350,7 +361,7 @@\n \n **Input**\n \n-SINA requires sequences in FASTA file format, whereas libraries can be also provided as ARB files. Furthermore, reference databases can be added as data tables. See README.md for more information.\n+SINA requires sequences in FASTA file format, whereas libraries can be also provided as ARB files. Furthermore, reference databases can be added as data tables. See README.rst for more information.\n \n **Output**\n \n@@ -365,4 +376,4 @@\n <citations>\n <citation type="doi">10.1093/bioinformatics/bts252</citation>\n </citations>\n-</tool>\n+</tool>\n\\ No newline at end of file\n' |
| b |
| diff -r 49b937f12aa4 -r 8afa8799d50f test-data/output_fasta_arb.arb |
| b |
| Binary file test-data/output_fasta_arb.arb has changed |
| b |
| diff -r 49b937f12aa4 -r 8afa8799d50f test-data/output_fasta_fasta.arb |
| b |
| Binary file test-data/output_fasta_fasta.arb has changed |