| Previous changeset 0:cd00b4fe6552 (2014-12-22) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob commit 1527e05bcd748a2b3cef22e0e356697066a55635 |
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modified:
rnabob.xml |
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removed:
tool_dependencies.xml |
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| diff -r cd00b4fe6552 -r 5a4b00c84f50 rnabob.xml --- a/rnabob.xml Mon Dec 22 09:08:31 2014 -0500 +++ b/rnabob.xml Sat Nov 11 15:08:06 2017 -0500 |
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| b'@@ -1,30 +1,31 @@\n <tool id="rbc_rnabob" name="RNABOB" version="2.2.1.0">\n <description>Fast Pattern searching for RNA secondary structures</description>\n+\n <requirements>\n <requirement type="package" version="2.2.1">rnabob</requirement>\n </requirements>\n- <version_command>echo "2.2.1"</version_command>\n- <command>\n-<![CDATA[\n- rnabob \n- \t-q\n- \t$fancy\n- \t$compStrands\n- \t$skipOverlapping\n- \t$descriptorFile\n- \t$sequenceFile > $stdout\n-]]>\n- </command>\n <stdio>\n <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />\n <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />\n </stdio>\n+ <version_command>echo "2.2.1"</version_command>\n+ <command>\n+<![CDATA[\n+ rnabob\n+ -q\n+ $fancy\n+ $compStrands\n+ $skipOverlapping\n+ $descriptorFile\n+ $sequenceFile > $stdout\n+]]>\n+ </command>\n <inputs>\n <param name="descriptorFile" type="data" format="txt" multiple="false" label="Motif Descriptor File" help="This file contains the description of the motif for which to search"/>\n-\t <param name="sequenceFile" type="data" format="fasta" multiple="false" label="Sequence File" help="This file specifies the sequence in which the motif will be searched"/>\n-\t <param name="compStrands" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Also search on complementary strands" help="-c : Search both strands of the supplied sequence"/>\n-\t <param name="skipOverlapping" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Skip overlapping matches" help="-s : This is a workaround to avoid a problem in the DNABANK, overlapping matches will be ignored"/>\n-\t <param name="fancy" type="boolean" checked="false" truevalue="-F" falsevalue="" label="Show Alignments" help="Display full alignments to pattern"/>\n+ <param name="sequenceFile" type="data" format="fasta" multiple="false" label="Sequence File" help="This file specifies the sequence in which the motif will be searched"/>\n+ <param name="compStrands" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Also search on complementary strands" help="-c : Search both strands of the supplied sequence"/>\n+ <param name="skipOverlapping" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Skip overlapping matches" help="-s : This is a workaround to avoid a problem in the DNABANK, overlapping matches will be ignored"/>\n+ <param name="fancy" type="boolean" checked="false" truevalue="-F" falsevalue="" label="Show Alignments" help="Display full alignments to pattern"/>\n </inputs>\n <outputs>\n <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />\n@@ -48,6 +49,7 @@\n </test>\n </tests>\n <help>\n+<![CDATA[\n **What RNABOB does**\n \n RNABOB allows searching a sequence database for RNA structural motifs.\n@@ -59,158 +61,159 @@\n \n **Sequence database format**\n \n-RNABOB is currently restricted to reading sequence files in FASTA format. \n+RNABOB is currently restricted to reading sequence files in FASTA format.\n The command line version of RNABOB can also read sequence files in GCG, EMBL, GenBank and other formats.\n \n -----\n \n **Descriptor file syntax**\n \n-The descriptor file syntax is fairly powerful, and allows a great deal of freedom for specifying \n+The descriptor file syntax is fairly powerful, and allows a great deal of freedom for specifying\n RNA motifs. The syntax is therefore a bit complicated.\n \n The descriptor file has two parts: a **topology** description and an **explicit** description.\n \n-The first non-blank, non-comment line of the file is the topology description. It defines the \n-order of occurrence of a series of single-stranded, double-stranded and related elements. Each \n-element must be given a unique name (a number, typically) and must be prefixed wi'..b'piler.\n \n **Options**\n \n The behavior of RNABOB can be modified by use of the following options:\n \n-*Complement*: Selecting this option will cause RNABOB to search for the pattern also on the \n+*Complement*: Selecting this option will cause RNABOB to search for the pattern also on the\n complementary strands.\n \n-*Skip*: This is a workaround to avoid a problem in the DNABANK. There are some sequences in the \n-database which have long stretches of ambiguous sequence (N\'s). Descriptors with no primary \n-sequence constraints will match these garbage sequences at many, many positions, and generate huge \n-outputs. This option toggles a search strategy that skips forward a pattern-length rather than a \n-single base when a match is found, thus printing out only a single match when overlapping matches \n-are found. \n+*Skip*: This is a workaround to avoid a problem in the DNABANK. There are some sequences in the\n+database which have long stretches of ambiguous sequence (N\'s). Descriptors with no primary\n+sequence constraints will match these garbage sequences at many, many positions, and generate huge\n+outputs. This option toggles a search strategy that skips forward a pattern-length rather than a\n+single base when a match is found, thus printing out only a single match when overlapping matches\n+are found.\n \n **Examples**\n \n-The following example descriptors included in the source distribution \n+The following example descriptors included in the source distribution\n (http://selab.janelia.org/software/rnabob/rnabob.tar.gz):\n \n-\t- trna.des - a general descriptor of a tRNA structure\n-\t- r17.des - descriptor of the consensus binding site for the r17 phage coat protein\n-\t- pseudoknot.des - description of a simple pseudoknotted structure\n+ - trna.des - a general descriptor of a tRNA structure\n+ - r17.des - descriptor of the consensus binding site for the r17 phage coat protein\n+ - pseudoknot.des - description of a simple pseudoknotted structure\n \n-An example cosmid ``F22B7.fa`` from the *C. elegans* genome sequencing project is also provided \n+An example cosmid ``F22B7.fa`` from the *C. elegans* genome sequencing project is also provided\n for running these descriptors against.\n \n ::\n \n-\t\\\n-\t\t# trna.des\n-\t\t#\n-\t\t# Generalized descriptor of a tRNA cloverleaf. Doesn\'t\n-\t\t# find them all though. \n-\t\t#\n+ \\\n+ # trna.des\n+ #\n+ # Generalized descriptor of a tRNA cloverleaf. Doesn\'t\n+ # find them all though.\n+ #\n \n-\t\th1 s1 h2 s2 h2\' s3 h3 s4 h3\' s5 h4 s6 h4\' h1\' s8\n+ h1 s1 h2 s2 h2\' s3 h3 s4 h3\' s5 h4 s6 h4\' h1\' s8\n \n-\t\th1 0:2 NNNNNNN:NNNNNNN\n-\t\th2 0:1 *NNN:NNN*\n-\t\th3 0:1 NNNNN:NNNNN\n-\t\th4 0:1 NNNNN:NNNNN\n-\t\ts1 0 TN\n-\t\ts2 0 NNNN**********\n-\t\ts3 0 N\n-\t\ts4 0 NNNNNN*\n-\t\ts5 0 NN********************\n-\t\ts6 0 TTC****\n-\t\ts8 0 NCCA\n+ h1 0:2 NNNNNNN:NNNNNNN\n+ h2 0:1 *NNN:NNN*\n+ h3 0:1 NNNNN:NNNNN\n+ h4 0:1 NNNNN:NNNNN\n+ s1 0 TN\n+ s2 0 NNNN**********\n+ s3 0 N\n+ s4 0 NNNNNN*\n+ s5 0 NN********************\n+ s6 0 TTC****\n+ s8 0 NCCA\n \n-Running RNABOB with ``trna.des`` against ``F22B7.fa`` searches the top strand of the cosmid for \n-the above motif. ``trna.des`` hits twice, once on each strand. (F22B7 has several other tRNA genes \n+Running RNABOB with ``trna.des`` against ``F22B7.fa`` searches the top strand of the cosmid for\n+the above motif. ``trna.des`` hits twice, once on each strand. (F22B7 has several other tRNA genes\n in it which the pattern fails to detect - this is *not* a pattern to use for tRNA genefinding!).\n- </help> \n+]]>\n+ </help>\n <citations>\n-\t<citation type="doi">10.1093/bioinformatics/6.4.325</citation>\n-\t<citation type="bibtex">@UNPUBLISHED{rnabob,\n+ <citation type="doi">10.1093/bioinformatics/6.4.325</citation>\n+ <citation type="bibtex">@UNPUBLISHED{rnabob,\n author = {Eddy S.R},\n title = {RNABOB: a program to search for RNA secondary structure motifs in sequence databases},\n note = {}}</citation>\n' |
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| diff -r cd00b4fe6552 -r 5a4b00c84f50 tool_dependencies.xml --- a/tool_dependencies.xml Mon Dec 22 09:08:31 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,21 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="rnabob" version="2.2.1"> - <install version="1.0"> - <actions> - <action type="download_by_url" target_filename="rnabob-2.2.1.tar.gz">http://selab.janelia.org/software/rnabob/rnabob.tar.gz</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>rnabob</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -Compiling rnabob requires a C compiler (typically gcc) - </readme> - </package> -</tool_dependency> |