| Previous changeset 3:8afa8799d50f (2020-10-02) Next changeset 5:56d7dc39eec8 (2021-01-01) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina commit f670d67c5943709ec6bd406becd60954621e4585" |
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modified:
sina.xml |
| b |
| diff -r 8afa8799d50f -r 482052b30b78 sina.xml --- a/sina.xml Fri Oct 02 08:01:21 2020 +0000 +++ b/sina.xml Fri Oct 02 08:18:09 2020 +0000 |
| [ |
| b'@@ -1,100 +1,97 @@\n-<tool id="sina" name="SINA" version="@TOOL_VERSION@+@WRAPPER_VERSION@" profile="18.01">\n+<tool id="sina" name="SINA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">\n <description>reference based multiple sequence alignment</description>\n <macros>\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+ <token name="@TOOL_VERSION@">1.7.1</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n </macros>\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- #if $db.select == \'custom\'\n- #if $db.custom.ext == \'fasta\'\n- sina -i \'$db.custom\' --prealigned -o \'reference.arb\' &&\n- #else\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- #end if\n+## initialize\n+#if $db.select == \'custom\'\n+ ## parse custom reference from fasta to arb file format\n+ #if $db.custom.ext == \'fasta\'\n+ sina -i \'$db.custom\' --prealigned -o \'reference.arb\' &&\n+ #else\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+#end if\n \n- ## run\n- sina\n- --in=\'$in\'\n- --db=\'reference.arb\'\n- -p \\${GALAXY_SLOTS:-4}\n- --num-pts=\\${GALAXY_SLOTS:-4}\n- #if $os.type == \'arb\'\n- --outtype=\'arb\'\n- --out=\'output.arb\'\n- #elif $os.type == \'fasta\'\n- --outtype=\'fasta\'\n- --out=\'output.fasta\'\n- --min-idty=$os.minidty\n- #elif $os.type == \'fasta_meta\'\n- --outtype=\'fasta\'\n- --out=\'output.fasta\'\n- --min-idty=$os.minidty\n- --meta-fmt=\'csv\'\n- #end if\n- #if $log == \'yes\'\n- --log-file=\'$logfile\'\n- #elif $log == \'yes_meta\'\n- --log-file=\'$logfile\'\n- --show-diff\n- #end if\n- ## Advanced alignment parameters\n- --overhang=$ap.overhang\n- --insertion=$ap.insertion\n- #if $ap.turn == \'yes\'\n- -t\n- #elif $ap.turn == \'all\'\n- -t all\n- #end if\n- ## Expert Alignment Parameters\n- --fs-min=$eap.fsmin\n- --fs-max=$eap.fsmax\n- --fs-msc=$eap.fsmsc\n- --fs-weight=$eap.fsweight\n- --fs-req=$eap.fsreq\n- --fs-req-full=$eap.fsreqfull\n- --fs-full-len=$eap.fsfulllen\n- --gene-start=$eap.genestart\n- --gene-end=$eap.geneend\n- --fs-cover-gene=$eap.fscovergene\n- --match-score=$eap.matchscore\n- --mismatch-score=$eap.mismatchscore\n- --pen-gap=$eap.pengap\n- --pen-gapext=$eap.pengapext\n- --fs-kmer-len=$eap.fskmerlen\n- --fs-kmer-mm=$eap.fskmermm\n- $eap.fskmernofast\n- $eap.fskmernorel\n- ## Advanced search and classification parameters\n- #if $asacp.activate == \'yes\'\n- --search\n- --search-kmer-candidates=$asacp.searchkmercandidates\n- --lca-quorum=$asacp.lcaquorum\n- --search-kmer-len=$asacp.searchkmerlen\n- '..b' <has_text text="FJ203641.1"/>\n <has_n_lines n="18"/>\n </assert_contents>\n </output>\n- <output name="output_fasta">\n+ <output name="out_fasta">\n <assert_contents>\n <has_line line=">FJ203641.1"/>\n <has_line line=">WH051F03"/>\n@@ -264,18 +250,18 @@\n </assert_contents>\n </output>\n </test>\n- <!-- #4 in: *.fasta; db: *.arb; out: *.arb; standard parameters -->\n+ <!-- #4 in: *.fasta; db: *.arb; out: *.arb; default parameters -->\n <test>\n <param name="in" value="sequence.fasta"/>\n <conditional name="db">\n <param name="custom" value="reference.arb"/>\n </conditional>\n- <section name="os">\n- <param name="type" value="arb"/>\n+ <section name="oo">\n+ <param name="out" value="arb"/>\n </section>\n- <output name="output_arb">\n+ <output name="out_arb">\n <assert_contents>\n- <has_size value="19999"/>\n+ <has_size value="19736"/>\n </assert_contents>\n </output>\n </test>\n@@ -285,8 +271,8 @@\n <conditional name="db">\n <param name="custom" value="reference.arb"/>\n </conditional>\n- <section name="os">\n- <param name="type" value="fasta"/>\n+ <section name="oo">\n+ <param name="out" value="fasta"/>\n <param name="minidty" value="0.0"/>\n </section>\n <section name="ap">\n@@ -323,7 +309,7 @@\n <param name="searchkmernorel" value="--search-kmer-norel"/>\n <param name="searchmaxresult" value="10"/>\n </section>\n- <output name="output_fasta">\n+ <output name="out_fasta">\n <assert_contents>\n <has_line line=">FJ203641.1"/>\n <has_line line=">WH051F03"/>\n@@ -331,19 +317,19 @@\n </assert_contents>\n </output>\n </test>\n- <!-- #6 in: *.fasta; db: <arb_databases>.arb; out: *.fasta; standard parameters -->\n+ <!-- #6 in: *.fasta; db: <arb_databases>.arb; out: *.fasta; default parameters -->\n <test>\n <param name="in" value="sequence.fasta"/>\n <conditional name="db">\n <param name="select" value="local"/>\n <param name="arb_databases" value="testarb"/>\n </conditional>\n- <section name="os">\n- <param name="type" value="arb"/>\n+ <section name="oo">\n+ <param name="out" value="arb"/>\n </section>\n- <output name="output_arb">\n+ <output name="out_arb">\n <assert_contents>\n- <has_size value="19999"/>\n+ <has_size value="19736"/>\n </assert_contents>\n </output>\n </test>\n@@ -365,13 +351,13 @@\n \n **Output**\n \n-Results are provided in FASTA or ARB file format, whereas additional metadata is provided as CSV.\n+Results are provided in FASTA or ARB file format, whereas additional metadata is provided as tabular text file.\n \n .. class:: infomark\n \n **References**\n \n-More information can be found on the `project website <https://sina.readthedocs.io/en/latest>`_, and on `github <https://github.com/epruesse/SINA>`_. An `online version <https://www.arb-silva.de/aligner>`_ of SINA is provided by the SILVA project.\n+More information can be found on the `project website <https://sina.readthedocs.io/en/latest>`_ and on `GitHub <https://github.com/epruesse/SINA>`_. An `online version <https://www.arb-silva.de/aligner>`_ of SINA is provided by the SILVA project.\n ]]></help>\n <citations>\n <citation type="doi">10.1093/bioinformatics/bts252</citation>\n' |